Overview of the different libraries investigated in this study.

If no additional reference for a library is given, the reference for the library is : A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing Landgraf, Pablo; Rusu, Mirabela; Sheridan, Robert; Sewer, Alain; Iovino, Nicola; Aravin, Alexei; Pfeffer, S bastien; Rice, Amanda; Kamphorst, Alice O.; Landthaler, Markus; Lin, Carolina; Socci, Nicholas D.; Hermida, Leandro; Fulci, Valerio; Chiaretti, Sabina; Fo , Robin; Schliwka, Julia; Fuchs, Uta; Novosel, Astrid; M ller, Roman-Ulrich; Schermer, Bernhard; Bissels, Ute; Inman, Jason; Phan, Quang; Chien, Minchen; Weir, David B.; Choksi, Ruchi; De Vita, Gabriella; Frezzetti, Daniela; Trompeter, Hans-Ingo; Hornung, Veit; Teng, Grace; Hartmann, Gunther; Palkovits, Miklos; Di Lauro, Roberto; Wernet, Peter; Macino, Giuseppe; Rogler, Charles E.; Nagle, James W.; Ju, Jingyue; Papavasiliou, F. Nina; Benzing, Thomas; Lichter, Peter; Tam, Wayne; Brownstein, Michael J.; Bosio, Andreas; Borkhardt, Arndt; Russo, James J.; Sander, Chris; Zavolan, Mihaela; Tuschl, Thomas doi:10.1016/j.cell.2007.04.040 (volume 129 issue 7 pp.1401 - 1414) Tissue type code

Sequence type Library name Mouse Neuronal tissues/cell lines Brain Cerebellum Cortex Midbrain Brain-WT Brain-FMR-KO SpinalCord Hippocamp-HT22 Neurobl-N2A Neurobl-N2A-TPA Neurobl-N2A-RA Neurobl-N1E-norm Neurobl-N1E-noFBS NG-norm NG-RA NG-dcAMP

Description

Tissue type

Species

9.1.1.0 nervous system, central nervous system, brain 9.1.1.0 nervous system, central nervous system, brain 9.1.1.0 nervous system, central nervous system, brain whole brain, 4 days old, males, littermates of FMRP KO whole brain, 4 days old, males, littermates of WT HT-22 N2A, Control, 48h N2A, differentiation (20 nM TPA (phorbol ester)), 48h N2A, differentiation (20 M RA), 48h N1E-115, Control (standard media, 10% FBS), 60h N1E-115, differentiation (no FBS in media), 60h NG108-15, Control (standard media, 10% FBS), 60h NG108-15, differentiation (20 M RA, 1% FBS), 60h NG108-15, differentiation (1mM dibutyryl cAMP, 1% FBS), 60h 9.1.1.0 9.1.1.0 9.1.2.0 9.1.1.0 9.2.1.0 9.2.1.0 9.2.1.0 9.2.1.0 9.2.1.0 9.2.1.0 9.2.1.0 9.2.1.0 nervous system, central nervous system, brain

mmu mmu mmu mmu mmu

Spinal cord Hippocampal cell line Neuroblastoma

Neuroblastoma x

nervous nervous nervous nervous nervous nervous nervous nervous nervous nervous nervous

system, system, system, system, system, system, system, system, system, system, system,

central nervous system, brain central nervous system, spinal cord central nervous system, brain sympathetic ganglion, neuroblastoma sympathetic ganglion, neuroblastoma sympathetic ganglion, neuroblastoma sympathetic ganglion, neuroblastoma sympathetic ganglion, neuroblastoma sympathetic ganglion, neuroblastoma sympathetic ganglion, neuroblastoma sympathetic ganglion, neuroblastoma

cell cell cell cell cell cell cell cell

mmu mmu mmu mmu mmu mmu mmu mmuxrno mmuxrno mmuxrno

Sensory organs (other) Eye Skin Skin Adipocytes

Eye

9.3.1.0 nervous system, sense organ, eye

mmu

Skin Adipo-diff Adipo-undiff

2.3.0.0 connective tissue, skin 2.1.0.0 connective tissue, adipose tissue 2.1.0.0 connective tissue, adipose tissue

mmu mmu mmu

Parenchymatous organs Kidney Kidney embryonic kidney Embryonic-kidney Collecting Duct (Kidney)

7.0.0.0 kidney 7.0.0.0 kidney

mmu mmu

mmu 7.2.2.1 Kidney-collecting-duct kidney, nephron, renal tubule, collecting duct mmu 7.1.0.0 Podocytes-K8-undiff 7.1.0.0 Podocytes-K8-diff kidney, epithelial cell mmu 7.2.1.1 Glomeruli Liver Lung kidney, nephron, renal corpuscle, glomerulus 8.0.0.0 liver 11.1.0.0 respiratory system, lung kidney, epithelial cell mmu

Podocytes

Glomeruli

Liver Lung Digestive tract Small intestine Colon Heart Heart Hematopoetic organs T-lymphocytes

mmu mmu

Small-intestine Colon

5.1.2.0 gastrointestinal tract, intestine, small intestine 5.1.1.1 gastrointestinal tract, intestine, large intestine, colon

mmu mmu

Heart

1.1.0.0 cardiovascular system, heart

mmu

T-cell-CD8-ctrl T-cell-CD8-polyIC

CD8+ cells from mouse spleen CD8+ cells from mouse spleen after polyI:C induction

6.1.2.3 6.1.2.3

mmu hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD8 mmu hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD8

Spleen Thymus B-cells (CD19+)

T-cell-CD8-conA Spleen Thymus B-cell-K1-Tg-naive B-cell-K2-Tg-anergic B-cell-K4-WT B-cell-spleen-unstim B-cell-spleen-IL4LPS8h B-cell-spleen-IL4LPS24h B-cell-spleen-IL4LPS48h B-cell-spleen-IL4LPS72h

CD8+ cells from mouse spleen after concanavalin A induction

naive IgHel transgenic CD19+ B lymphocytes anergic IgHel X Hel transgenic CD19+ B lymphocytes wild type CD19+ B lymphocytes Splenic B-cells unstimulated Splenic B-cells 8h after stimulated with IL-4 (5 ng/ml) and LPS (25 g/ml) Splenic B-cells 24h after stimulated with IL-4 (5 ng/ml) and LPS (25 g/ml) Splenic B-cells 48h after stimulated with IL-4 (5 ng/ml) and LPS (25 g/ml) Splenic B-cells 72h after stimulated with IL-4 (5 ng/ml) and LPS (25 g/ml)

Dendritic cells

DC-unstim

DC from myeloid precursor cells from bone marrow

DC-GCSF B-lymphoma B-lymphoma-S11 B-lymphoma-S11E B-lymphoma-A20_OP B-lymphoma-A20_NP Endocrine organs Pancreatic beta cell Beta-pancreas-MIN Pancreatic alpha cell Alpha-pancreas-TC1 Reproductive organs Testis

DC from myeloid precursor cells from bone marrow, stimulated with endotoxin for 24h B-lymphoma latently infected with mouse herpesvirus MuHV68 B-lymphoma latently infected with mouse herpesvirus MuHV68. Subclone of S11. Reticulum cell sarcoma, old protocol Reticulum cell sarcoma, alternative protocol

mmu hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD8 6.2.1.0 hematopoietic system, lymphoid tissue, spleen mmu 6.2.2.0 hematopoietic system, lymphoid tissue, thymus mmu mmu 6.1.1.4 hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte mmu 6.1.1.4 hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte mmu 6.1.1.4 hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte mmu 6.1.1.4 hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte mmu 6.1.1.4 hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte mmu 6.1.1.4 hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte mmu 6.1.1.4 hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte mmu 6.1.1.4 hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte mmu 6.3.8.0 hematopoietic system, myeloid lineage, dendritic cell mmu 6.3.8.0 hematopoietic system, myeloid lineage, dendritic cell mmu 6.1.1.4 hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte mmu 6.1.1.4 hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte 6.1.1.4 hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte mmu 6.1.1.4 hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte mmu 6.1.2.3

MIN6 pancreatic beta cell line TC1 pancreatic alpha cell line

4.2.2.0 4.2.1.0

mmu endocrine gland, pancreatic islet, pancreatic beta cell endocrine gland, pancreatic islet, pancreatic alpha cell

mmu

Placenta Embryonic cells/tumours Embryos

Testis Spermatogonia-C18 Ovary Placenta

immortalized spermatogoneal cell line mouse placenta, total RNA, standard size fraction ( 19-24 nt )

10.2.1.0 10.2.1.0 10.1.1.0 10.1.3.0

reproductive reproductive reproductive reproductive

system, system, system, system,

male reproductive system, testis male reproductive system, testis female reproductive system, ovary female reproductive system, placenta

mmu mmu mmu mmu

Embryo-E11 Embryo-E12 ESC-WT-frac-21 ESC-fem Teratocarcinoma-F9 Teratocarcinoma-P19 19-24nt size fraction male stem cells (Bruce-4 ES) ES cell female F9 (can be induced to differentiate into parietal endoderm) P19 (can be induced to differentiate into neural and glial like cells or cardiac and skeletal muscle-like elements) 3T12 lytically infected with mouse herpesvirus MuHV68 (6h.p.i.) 3T12_20g RNA input 3T12_200g RNA input

3.0.0.0 embryo 3.0.0.0 embryo embryo, embryonic stem cell 3.1.0.0 embryo, embryonic stem cell 3.4.1.0 embryo, germ cell tumor, teratocarcinoma 3.4.1.0 3.2.0.0 embryo, germ cell tumor, teratocarcinoma 3.1.0.0

mmu mmu mmu

Germ cell tumor

mmu mmu mmu

Embryonic fibroblast Fibrobl-3T12-MuHV Fibrobl-3T12-20 Fibrobl-3T12-200 Fibrobl-MEF-mock Fibrobl-MEF-HSV1-6h Fibrobl-MEF-HSV1-12h Fibrobl-MEF-HSV2-12h Rat Neuronal tissues/cell lines Brain Cortex-adult Cortex-embryo Hippocamp-adult Striatum-adult adult_hippocampus adult_striatum adult_cortex embryonic_cortex, E18 MEF lytically infected with HSV1 (6hpi) MEF lytically infected with HSV1 (12hpi) MEF lytically infected with HSV2 (12hpi)

mmu

embryo, embryonic fibroblast 3.2.0.0 embryo, embryonic fibroblast 3.2.0.0 embryo, embryonic fibroblast embryo, embryonic fibroblast embryo, embryonic fibroblast embryo, embryonic fibroblast embryo, embryonic fibroblast

3.2.0.0 3.2.0.0 3.2.0.0 3.2.0.0

mmu mmu mmu

mmu

mmu

mmu

9.1.1.0 9.1.1.0 9.1.1.0 9.1.1.0

rno nervous system, central nervous system, brain rno nervous system, central nervous system, brain rno nervous system, central nervous system, brain rno nervous system, central nervous system, brain

embryonic_striatum, E18 Glioma Pheochromocytoma Neuroblastoma Striatum-embryo Glioma-C6 Pheochrom-PC12 Pheochrom-PC12-NGF Neurobl-B35 Neurobl-B35-RA Neurobl-B35-noFBS Neurobl-B35-dcAMP C6 PC12, Control, 48h PC12, differentiation (nerve growth factor 50 ng/ml), 48h B35, Control (media with 5%FBS), 72h B35, differentiation (10 uM RA, 5% FBS), 72h B35, differentiation (no FBS in media), 72h B35, differentiation (1mM dibutyryl cAMP, 5% FBS), 72h

9.1.1.0 9.1.2.1 4.1.1.0 4.1.1.0 9.2.1.0 9.2.1.0 9.2.1.0 9.2.1.0 4.4.1.0

rno nervous system, central nervous system, brain nervous system, central nervous system, spinal cord, glioma endocrine gland, adrenal gland, pheochromocytoma endocrine gland, adrenal gland, pheochromocytoma nervous system, sympathetic ganglion, neuroblastoma cell nervous system, sympathetic ganglion, neuroblastoma cell nervous system, sympathetic ganglion, neuroblastoma cell nervous system, sympathetic ganglion, neuroblastoma cell rno rno rno rno rno rno rno rno endocrine gland, thyroid gland, FRTL-5 cell rno endocrine gland, thyroid gland, FRTL-5 cell rno endocrine gland, thyroid gland, FRTL-5 cell rno endocrine gland, thyroid gland, FRTL-5 cell

Endocrine organs

Thyroid-FRTL5 Thyroid-FRTL5-Ras Thyroid-FRTL5-Ras-tamox-48h Thyroid-FRTL5-Ras-tamox-7d FRTL-5 with inducible ras FRTL-5 48 hrs after induction FRTL-5 7d after induction

4.4.1.0 4.4.1.0 4.4.1.0

Human Neuronal tissues/cell lines Brain_normal adult Cerebellum-adult Frontal-cortex-adult Midbrain-adult Hippocamp-adult Medullobl-DAOY Gliobl-SNB19 Gliobl-U87 cerebellar cortex from the hemispheres of a 20 year old healthy male, 6 hours postmortem sample from Brodman area 9 (superior frontal gyrus) of a 20 year old healthy male, 6 hours postmortem whole midbrain from caudal edge of mammillary bodies to the caudal edge of the inferior collicle of a 78 year old man, 2 hours postmortem 9.1.1.0 9.1.1.0 9.1.1.0 9.1.1.0 nervous system, central nervous system, brain nervous system, central nervous system, brain nervous system, central nervous system, brain nervous nervous nervous nervous system, system, system, system, brain brain, medulloblastoma brain, glioblastoma cell brain, glioblastoma cell hsa hsa hsa hsa hsa hsa hsa

Medulloblastoma Glioblastoma

nervous system, central 9.1.1.3 nervous system, central 9.1.1.2 nervous system, central 9.1.1.2 nervous system, central 9.1.1.1

Pilocytic astrocytoma

Astrocytoma-FC020688

pilocytic astrocytoma (Patient sample) 9.1.1.1

nervous system, central nervous system, brain, astrocytoma cell

hsa

Astrocytoma-WL210995

pilocytic astrocytoma (Patient sample) 3.5.1.1

nervous system, central nervous system, brain, astrocytoma cell

hsa

Astroblastoma Neuroblastoma

Astroblastoma-DD040800 Neurobl-BE2 Neurobl-SHSY5Y Neurobl-SHSY5Y-RA Neurobl-SHSY5Y-IFNg-24h

astroblastoma (Patient sample) BE(2)-M17 SH-SY5Y, Control SH-SY5Y, differentiation (10 M RA) SH-SY5Y, apoptosis induction (IFN gamma), 24h

9.2.1.0 9.2.1.0 9.2.1.0 9.2.1.0

embryo, neuroblast, astroblast, astroblastoma nervous system, sympathetic ganglion, neuroblastoma nervous system, sympathetic ganglion, neuroblastoma nervous system, sympathetic ganglion, neuroblastoma nervous system, sympathetic ganglion, neuroblastoma

cell cell cell cell

hsa hsa hsa hsa hsa

Skin Foreskin fibroblasts Fibrobl-CMV Primary fibroblasts lytically infected with Cytomegalovirus 2.3.2.0 connective tissue, skin, fibroblast hsa

Parenchymatous organs 7.1.0.0 Kidney Podocytes-Moins-undiff Podocytes_undiff 7.1.0.0 Podocytes-Moins-diff Podocytes_diff 7.0.0.0 renal_carcinoma-DH1 renal carcinoma derived cell line undifferentiated 2.2.0.0 renal_carcinoma-DH1-diff-3d renal carcinoma derived cell line. Osteoblasts differentiated for 3d 2.2.0.0 renal_carcinoma-DH1-diff-6d Liver Hepatocellular carcinoma Liver renal carcinoma derived cell line. Osteoblasts differentiated for 6d liver from a 43 year old female, 6 hours post mortem Huh7.5 cell line infected with Hepatitis C Virus. This strain has a single nucleotide substitution of RIG-I rendering an amino acid change in codon 55 (T55I) leading to permissiveness for HCV RNA replication Huh7.5 cell line not infected. This strain has a single nucleotide substitution of RIG-I rendering an amino acid change in codon 55 (T55I) leading to permissiveness for HCV RNA replication Hepatoma cell line, HBV infected Hepatoma cell line 8.0.0.0 8.1.0.0 liver, hepatocellular carcinoma cell 8.1.0.0 8.1.0.0 8.1.0.0 liver, hepatocellular carcinoma cell liver, hepatocellular carcinoma cell hsa liver, hepatocellular carcinoma cell hsa hsa hsa connective tissue, bone liver hsa hsa connective tissue, bone hsa kidney hsa kidney, epithelial cell hsa kidney, epithelial cell hsa

Hepatocell-carcinoma-Huh7-HCV Hepatocell-carcinoma-Huh7-mock Hepatoma-PLC Hepatoma-HepG2

Lung adeno carcinoma

Hepatoma-HepG2-HBV Lung-adenoc-A549-mock Lung-adenoc-A549-IFNa Lung-adenoc-A549-IFNb Lung-adenoc-A549-IFNg

Hepatoma cell line, HBV infected A549 (model for typII epithelial cells) A549-IF alpha treated A549-IF beta treated A549-IF gamma treated

8.1.0.0 11.1.1.0 11.1.1.0 11.1.1.0 11.1.1.0

hsa liver, hepatocellular carcinoma cell respiratory system, lung, adenocarcinoma respiratory system, lung, adenocarcinoma respiratory system, lung, adenocarcinoma respiratory system, lung, adenocarcinoma cell cell cell cell hsa hsa hsa hsa

Heart Heart Heart Hematopoetic organs

1.1.0.0

hsa cardiovascular system, heart

Spleen pluripotent hematopoetic stem cell T-lymphocytes

Spleen

spleen from a 65 year old female, 5 hours post mortem

6.2.1.0 6.4.0.0

hematopoietic system, lymphoid tissue, spleen

hsa hsa

HSC-CD34 T-cell-CD4

CD34+ - sorted cells T helper cells, peripheral blood (pool from 4 healthy donors)

T-cell-CD4-2 T-cell-CD4-A301 T-cell-CD4-ACH2 T-cell-CD4-ACH2-stim T-cell-CD4-naive T-cell-CD4-effector T-cell-CD4-memory

T helper cells CD4+ T-cell line CD4+ T-cell line, HIV integrated, not replicating CD4+ T-cell line, HIV replicating after 10h induction with PMA/Ionomycin CD4+ CD45 RA+(CD45RO-) nave cells CD4+, CD45RO+, CD27-, CCR7-. Effector cells CD4+CD45RO+(CD45RA-) memory cells

T-cell-CD8-2 T-cell-CD8 T-cell-CD8-naive B-cell-CD19 B-cell-CD19-pool

cytotoxic T-cells cytotoxic T-cells, peripheral blood(pool from 4 healthy donors) CD8+, CD45RA+, CD27+, CCR7+ B cells from peripheral blood B cells from peripheral blood (pool from 4 healthy donors)

hematopoietic system, pluripotent hematopoietic stem cell 6.1.2.2 hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD4 hsa hsa 6.1.2.2 hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD4 hsa 6.1.2.2 hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD4 hsa 6.1.2.2 hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD4 hsa 6.1.2.2 hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD4 hsa 6.1.2.2 hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD4 hsa 6.1.2.2 hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD4 hsa 6.1.2.2 hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD4 hsa 6.1.2.3 hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD8 hsa 6.1.2.3 hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD8 hsa 6.1.2.3 hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD8 6.1.1.4 hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte hsa 6.1.1.4 6.1.1.4 hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte hsa

NK cells Monocytes Granulocytes Dendritic cells

B-cell-CD19-2 NK-CD56 Monocytes-CD14 Granulocytes-CD15

B cells from peripheral blood NK cells from peripheral blood (pool from 4 healthy donors) Monocyte cells from peripheral blood (pool from 4 healthy donors) Granulocyte cells from peripheral blood (pool from 4 healthy donors)

hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte 6.1.3.0 hematopoietic system, lymphoid lineage, natural killer cell 6.3.7.0 hematopoietic system, myeloid lineage, monocyte 6.3.6.0 hematopoietic system, myeloid lineage, granulocyte 6.3.8.0

hsa hsa hsa hsa

DC-unstim

myeloid dendritic cells not stimulated 6.3.8.0

hematopoietic system, myeloid lineage, dendritic cell

hsa

B-ALL

DC-stim B-ALL-REH

myeloid dendritic cells stimulated with endotoxin precursor ALL

hematopoietic system, myeloid lineage, dendritic cell hsa 6.1.1.2 hematopoietic system, lymphoid lineage, B lineage, pre-B-lymphoblasthsa 6.1.1.2

B-ALL1-d0

ALL_Down Syndrom 6.1.1.1

hematopoietic system, lymphoid lineage, B lineage, pre-B-lymphoblasthsa

B-ALL2-d0

pro-B-ALL, initial, MLL/AF4 translocation 6.1.1.1

hematopoietic system, lymphoid lineage, B lineage, pre-pre-B-lymphob hsa

B-ALL2-d29

pro-B-ALL,first remission 4.3 Mio blasts 6.1.1.1

hematopoietic system, lymphoid lineage, B lineage, pre-pre-B-lymphob hsa

B-ALL3-d0

pro-B-All relapse, initial, TEL/AML1 fusion 6.1.1.1

hematopoietic system, lymphoid lineage, B lineage, pre-pre-B-lymphob hsa

B-ALL3-d29

pro-B-All relapse, d29 12.5 Mio blasts 6.1.1.3

hematopoietic system, lymphoid lineage, B lineage, pre-pre-B-lymphob hsa

B-ALL4-d0

cALL_at diagnosis, Down syndrome 6.1.1.3

hematopoietic system, lymphoid lineage, B lineage, pre-B-lymphoblasthsa

B-ALL4-d29

cALL_d29 1st remission 0.4 million blasts, Down syndrome

hematopoietic system, lymphoid lineage, B lineage, pre-B-lymphoblasthsa

6.1.1.3 B-ALL5-d0 cALL_at diagnosis 10 million blasts, , TEL/AML1 fusion 6.1.1.3 B-ALL5-d29 cALL_d29 1st remission 0.4 million blasts 6.1.1.2 B-ALL6-d0 pre-B-ALL at diagnosis 6.1.1.2 B-ALL6-d29 pre-B-ALL, 1st remission 6.1.1.2 B-ALL7-d0 pre-B-ALL relapse at diagnosis 6.1.1.2 B-ALL7-d29 pre-B-ALL relapse 10 million blasts 6.1.1.2 B-ALL8-d0 pre-B-ALL at diagnosis 60% blasts, 5 million 6.1.1.2 B-ALL8-d29 pre-B-ALLd29 2.5 million blasts, <5% blasts, beginning regeneration 6.1.1.2 B-ALL8-d43 B-ALL9-d0 T-ALL-Jurkat T-ALL1-d0 T-ALL2-d0 pre-B-ALL d43 1.4 million blasts, <5% blasts ALL from patient peripheral blood, B cells jurkat cell line ALL from patient peripheral blood, T cells ALL from patient peripheral blood, T cells 6.1.1.2 hematopoietic system, lymphoid lineage, B lineage, pre-B-lymphoblasthsa hematopoietic system, lymphoid lineage, B lineage, pre-B-lymphoblasthsa 6.1.2.1 hematopoietic system, lymphoid lineage, T lineage, T-lymphoblast hsa 6.1.2.1 6.1.2.1 6.1.2.1 T-ALL3-d0 T-ALL, 90% blasts initial (1 Mio blasts) 6.1.2.1 T-ALL3-d29 T-ALL,d29 8 Mio blasts, <5% blasts 6.1.2.1 T-ALL4-d0 T-ALL, 90% blasts 6.1.2.1 T-ALL4-d29 T-ALL d29, 2 million blasts 6.1.2.1 T-ALL5-d0 T-ALL, initial 70% blasts 10 million 6.1.2.1 B-CLL T-ALL5-d29 B-CLL-EHEB B-CLL-Mec2 B-CLL1 B-CLL4 B-CLL5 B-CLL5_2 B-CLL6 B-CLL7 B-CLL8 B-CLL11 B-CLL12 B-CLL13 AML-THP1 AML-Kas1 AML-HL60 T-ALL d29 1st remission 0.5 million B-CLL cell line established from 69 year old woman, EBV+ B-CLL cell line established from 62 year old man, EBV+ sample from B-CLL patient1 progressive, igvh mutated sample from B-CLL patient4 stable, igvh unmutated sample from B-CLL patient5 progressive, igvh unmutated,ZAP70+, no del13q14,del17p13, trisomy 12,del11q23 sample from B-CLL patient5 progressive, igvh unmutated,ZAP70+, no del13q14,del17p13, trisomy 12,del11q23 sample from B-CLL patient6 stable, igvh mutated sample from B-CLL patient7 igvh unmutated, ZAP70+, no del13q14,del17p13, trisomy 12,del11q23 sample from B-CLL patient8 stable, igvh mutated sample from B-CLL patient11, stable, igvh mutated, del13q14 pos no del17p13, trisomy 12,del11q23 sample from B-CLL patient12 stable, igvh na sample from B-CLL patient13 igvh mutated AML FAB M5 cell line, monocytic Kasumi-1, with ETO-AML1 fusion protein (t(8;21), AML FAB M2 cell line, myeloblastic with differentiation HL-60 cell line, AML FAB M3, promyelocytic leukemia hematopoietic system, lymphoid lineage, T lineage, T-lymphoblast 6.1.1.4 hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte 6.1.1.4 hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte 6.1.1.4 6.1.1.4 6.1.1.4 6.1.1.4 6.1.1.4 6.1.1.4 6.1.1.4 6.1.1.4 6.1.1.4 6.1.1.4 hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte hsa hsa hsa hsa hsa hsa hsa hsa hsa hsa hsa hsa hsa hsa hsa hsa hematopoietic system, lymphoid lineage, T lineage, T-lymphoblast hsa hematopoietic system, lymphoid lineage, T lineage, T-lymphoblast hsa hematopoietic system, lymphoid lineage, T lineage, T-lymphoblast hsa hematopoietic system, lymphoid lineage, T lineage, T-lymphoblast hsa hematopoietic system, lymphoid lineage, T lineage, T-lymphoblast hsa hematopoietic system, lymphoid lineage, T lineage, T-lymphoblast hematopoietic system, lymphoid lineage, T lineage, T-lymphoblast hsa hsa hematopoietic system, lymphoid lineage, B lineage, pre-B-lymphoblasthsa hematopoietic system, lymphoid lineage, B lineage, pre-B-lymphoblasthsa hematopoietic system, lymphoid lineage, B lineage, pre-B-lymphoblasthsa hematopoietic system, lymphoid lineage, B lineage, pre-B-lymphoblasthsa hematopoietic system, lymphoid lineage, B lineage, pre-B-lymphoblasthsa hematopoietic system, lymphoid lineage, B lineage, pre-B-lymphoblasthsa hematopoietic system, lymphoid lineage, B lineage, pre-B-lymphoblasthsa hematopoietic system, lymphoid lineage, B lineage, pre-B-lymphoblasthsa

T-ALL

AML

hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte 6.3.4.0 hematopoietic system, myeloid lineage, monocyte FAB M5 6.3.1.0 hematopoietic system, myeloid lineage, myeloblast FAB M2 6.3.2.0 hematopoietic system, myeloid lineage, pro-myelocyte FAB M3

6.3.5.0 AML1-d0 AML M6 40%Blasts patient sample 6.3.5.0 AML1-d29 AML M6 2.8 Mio Blasts patient sample AML 80% blasts initial (10Mio), AML M4, AF10/calm Rearrangement (t(10;11)(p12-14;q1421)) AML d29 no remission (10Mio), AML M4, AF10/calm Rearrangement (t(10;11)(p12-14;q1421)) 6.3.3.0 hematopoietic system, myeloid lineage, myelomonocyte FAB M4 6.3.3.0 hematopoietic system, myeloid lineage, myelomonocyte FAB M4 6.3.3.0 AML3-d0 AML, 90% blasts initial, AML-M4 6.3.3.0 AML3-d29 Hodgkin-L428 Hodgkin-KMH2 Hodgkin-L591 Hodgkin-L1236 BL-BCBL1-new BL-BCBL1-old Burkitt-BL41-95-EBV Burkitt-BL41-mock Burkitt-Raji AML, d29 10 Mio blasts, AML-M4 Hodgkin Lymphoma cell line Hodgkin Lymphoma cell line Hodgkin Lymphoma cell line, EBV + Hodgkin Lymphoma cell line Latently infected with KSHV/HHV8. Cloned with alternate protocol Latently infected with KSHV/HHV8. Cloned with classic protocol Latently infected with EBV 6.1.1.9 6.1.1.9 6.1.1.9 6.1.1.9 6.1.1.4 6.1.1.4 6.1.1.6 6.1.1.6 Burkitt lymphoma cell line established from a 12 year old boy, EBV+ hematopoietic system, myeloid lineage, myelomonocyte FAB M4 hsa hematopoietic system, myeloid lineage, myelomonocyte FAB M4 hsa hsa hsa hematopoietic system, myeloid lineage, erythrocyte FAB M6 hsa hematopoietic system, myeloid lineage, erythrocyte FAB M6 hsa

AML2-d0

AML2-d29

Hodgkin Lymphoma

hematopoietic system, lymphoid lineage, B lineage, Hodgkin Lymphomhsa hematopoietic system, lymphoid lineage, B lineage, Hodgkin Lymphomhsa hematopoietic system, lymphoid lineage, B lineage, Hodgkin Lymphomhsa hematopoietic system, lymphoid lineage, B lineage, Hodgkin Lymphomhsa hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte hsa hsa

Body cavity based Lymphoma(B-cell)

Burkitt-Lymphoma

hematopoietic system, lymphoid lineage, B lineage, Burkitt Lymphomahsa

hematopoietic system, lymphoid lineage, B lineage, Burkitt Lymphomahsa 6.1.1.6 hematopoietic system, lymphoid lineage, B lineage, Burkitt Lymphomahsa

6.1.1.6 Burkitt-CA-46 EBV6.1.1.6 Burkitt-DG-75 Burkitt lymphoma cell line established from a 10 year old boy, EBV+ 6.1.1.6 Burkitt-patient1 Burkitt Lymphoma patient samples (bone marrow) 6.1.1.6 Burkitt-patient2 Burkitt Lymphoma patient samples (bone marrow) 6.1.1.6 Burkitt-patient3 DLBCL-SUDHL6 DLBCL-Ly1 DLBCL-LY3 DLBCL-DLBL1 DLBCL-DLBL2 DLBCL-DLBL3 DLBCL-DLBL4 Burkitt-Lymphom, t (8;14) c-myc-Rearrangement, 82-90% blasts DLBL cell line derived from 43 year old man, EBV- (Germinal Center) OCI-Ly1, DLBCL cell line, relapse sample t(14;18) (Germinal Center) OCI-Ly3, relapse sample, produces IL-6 (act B cell) diffuse large B cell lymphoma(act B cell) Patient samples diffuse large B cell lymphoma(act B cell) Patient samples diffuse large B cell lymphoma(Germinal center) Patient samples diffuse large B cell lymphoma(Germinal center) Patient samples marginal zone lymphoma patient sample follicular Lymphoma patient sample follicular Lymphoma patient sample mantel cell lymphoma cell line established from relapse of a 58 year old woman, EBV+ mantel cell lymphoma cell line established from 63 year old woman, EBV+ EBVmantel cell lymphoma patient sample mantel cell lymphoma patient sample 6.1.1.7 6.1.1.7 6.1.1.7 6.1.1.7 6.1.1.7 6.1.1.7 6.1.1.7 6.1.1.10 6.1.1.8 6.1.1.8 hematopoietic system, lymphoid lineage, B lineage, Burkitt Lymphomahsa hematopoietic system, lymphoid lineage, B lineage, large B-cell lympho hsa hematopoietic system, lymphoid lineage, B lineage, large B-cell lympho hsa hematopoietic system, lymphoid lineage, B lineage, large B-cell lympho hsa hematopoietic system, lymphoid lineage, B lineage, large B-cell lympho hsa hematopoietic system, lymphoid lineage, B lineage, large B-cell lympho hsa hematopoietic system, lymphoid lineage, B lineage, large B-cell lympho hsa hematopoietic system, lymphoid lineage, B lineage, large B-cell lympho hsa hematopoietic system, lymphoid lineage, B lineage, marginal zone lymhsa hematopoietic system, lymphoid lineage, B lineage, follicular lymphom hsa lineage, lineage, lineage, lineage, B B B B lineage, lineage, lineage, lineage, follicular lymphom hsa mantel cell lymphohsa mantel cell lymphohsa mantel cell lymphohsa hematopoietic system, lymphoid lineage, B lineage, Burkitt Lymphomahsa hematopoietic system, lymphoid lineage, B lineage, Burkitt Lymphomahsa hematopoietic system, lymphoid lineage, B lineage, Burkitt Lymphomahsa hematopoietic system, lymphoid lineage, B lineage, Burkitt Lymphomahsa

Burkitt-Lymphoma

DLBCL

marginal zone lymphomaMZ-Lymphoma-MZ2 Follic-Lymphoma-F1 Follic-Lymphoma-F2 MC-Lymphoma-Granta-519 MC-Lymphoma-JVM-2 MC-Lymphoma-Jeko-1 MC-Lymphoma-M1 MC-Lymphoma-M2 Plasmocytoma-U266

Follicular Lymphoma

Mantel cell lymphoma

hematopoietic system, lymphoid 6.1.1.5 hematopoietic system, lymphoid 6.1.1.5 hematopoietic system, lymphoid 6.1.1.5 hematopoietic system, lymphoid 6.1.1.5 6.1.1.5 6.1.1.11

hematopoietic system, lymphoid lineage, B lineage, mantel cell lymphohsa hematopoietic system, lymphoid lineage, B lineage, mantel cell lymphohsa hematopoietic system, lymphoid lineage, B lineage, plasmacytoma cellhsa

Plasmocytoma

Endocrine organs Brain pituitary gland Small cell Adrenocarcinoma Pituitary Adrenocarcinoma-SW-mock Adrenocarcinoma-SW-YFV Thyroid Thyroid Pancreatic islets Pancreatic-islets Embryonic cells/tumours Unrestricted somatic stem cell USSC unrestricted somatic stem cells from umbilical cord 3.1.0.0 USSC-d1 unrestricted somatic stem cells from umbilical cord induced 1 day to osteoblasts 3.1.0.0 USSC-d3 unrestricted somatic stem cells from umbilical cord induced 3 day to osteoblasts 2.2.0.0 Teratocarcinoma USSC-d7 Teratocarcinoma-NT2-norm Teratocarcinoma-NT2-RA Teratocarcinoma-PA1 Seminoma-2073 Seminoma-2073-NE1 Kidney-embryo-HEK293 Kidney-embryo-HEK293-exp Kidney-embryo-HEK293-6d Kidney-embryo-HEK293-Fas12 unrestricted somatic stem cells from umbilical cord induced 7 day to osteoblasts NT2/D1, Control NT2/D1, differentiation (10 M RA) for 6 weeks PA1 NCCIT cell line NCCIT cell line, nuclear extract HEK293 cell line HEK293 cell line, exponential growth HEK293 cell line, 6 days of growth with contact inhibition HEK293 cell line, treated with FAS12 3.4.1.0 3.4.1.0 3.4.1.0 3.4.2.0 3.4.2.0 3.3.0.0 3.3.0.0 3.3.0.0 3.3.0.0 connective tissue, bone embryo, germ cell tumor, teratocarcinoma embryo, germ cell tumor, teratocarcinoma embryo, germ cell tumor, teratocarcinoma embryo, germ cell tumor, seminoma embryo, germ cell tumor, seminoma embryo, embryonic kidney cell embryo, embryonic kidney cell embryo, embryonic kidney cell embryo, embryonic kidney cell hsa hsa hsa hsa hsa hsa hsa hsa hsa hsa embryo, embryonic stem cell hsa embryo, embryonic stem cell hsa pituitary gland from a 50 year old male, 2 hours post mortem SW13 cell line SW13 cell line infected with Yellow Fever Virus 4.3.0.0 4.1.0.0 4.1.0.0 4.4.0.0 4.2.0.0 endocrine gland, pituitary gland endocrine gland, adrenal gland endocrine gland, adrenal gland endocrine gland, thyroid gland endocrine gland, pancreatic islet hsa hsa hsa hsa hsa

hsa 3.1.0.0 embryo, embryonic stem cell

Seminoma Embryonic Kidney Embryonic Kidney

Reproductive organs Ovary Testis Uterus Placenta Cervix epitheloid carcinoma Ovary Testis Uterus Placenta Cervix-HeLa-adh Cervix-HeLa-susp Cervix-HeLa-IFNa Cervix-HeLa-IFNg Cervix-HeLa-CD4 Cervix-HeLa-HIV Cervix-HeLa-adh-2 Epididymis Prostate Gland tissues Epithelial fibrocystic Mammae Adeno-CA breast, epithelial like Primary Ductal Breast carcinoma Ductile carcinoma breast B-cell-k3-tg-activated 10.1.4.3 10.1.4.1 10.1.4.2 10.1.4.2 10.1.4.2 10.1.4.2 reproductive system, epithelium reproductive system, adenocarcinoma reproductive system, carcinoma reproductive system, carcinoma reproductive system, carcinoma reproductive system, carcinoma female reproductive system, breast, mammary hsa female reproductive system, breast, hsa female reproductive system, breast, ductal hsa female reproductive system, breast, ductal hsa female reproductive system, breast, ductal hsa female reproductive system, breast, ductal hsa Epididymis Prostata HeLa HeLa HeLa HeLa S3, adherently grown S3, grown in suspension S3-IF alpha treated S3-IF gamma treated ovary from a 42 year old female, 11 hours post mortem testis from a 73 year old male, 2 hours post mortem 10.1.1.0 10.2.1.0 10.1.2.0 10.1.3.0 10.1.2.1 reproductive system, female reproductive system, ovary reproductive system, male reproductive system, testis reproductive system, female reproductive system, uterus reproductive system, female reproductive system, placenta reproductive reproductive reproductive reproductive system, system, system, system, uterus, uterus, uterus, uterus, cervical cervical cervical cervical hsa hsa hsa hsa carchsa carchsa carchsa carchsa

reproductive system, female 10.1.2.1 reproductive system, female 10.1.2.1 reproductive system, female 10.1.2.1 reproductive system, female 10.1.2.1 10.1.2.1 10.1.2.1 10.2.2.0

HeLa stably expressing CD4 HeLa CD4 infected with HIV HeLa S3 replica epididymis from a 73 year old man, 2 hours post mortem

reproductive system, female reproductive system, uterus, cervical carchsa reproductive system, female reproductive system, uterus, cervical carchsa reproductive system, female reproductive system, uterus, cervical carchsa hsa hsa

reproductive system, male reproductive system, epididymis 10.2.3.0 reproductive system, male reproductive system, prostate gland

Breast-epith-fibrocystic-MCF10A Breast-adenocarcinoma-MCF7 Breast-duct-HCC38 Breast-duct-carcinoma-SKBR3 Breast-invasive-duct-BT474 Breast-invasive-duct-T47

Fibrocystic Disease. Non tumorigenic epithelial cell line. ER- ; PgRInvasive Ductal Carcinoma (IDC). Expresses WNT7B oncogene. ER+; PgR+ IDC. Her2/neu- ; P53+. ER- ; PgRIDC. Overexpresses Her2. ER- ; PgRIDC. ER+ ; PgR+ IDC. Expresses WNT7B oncogene. ER+ ; PgR+

Connective Tissue Osteosarcoma Osteosarcoma-U2Os-uninduced U2Os with EWS/WT1 fusion protein-not induced 2.2.1.0

connective tissue, bone, osteosarcoma cell

hsa

Osteosarcoma-U2Os-ind-24h Osteosarcoma-SAOS2 Ewing sarcoma Ewing-Sarcoma-A673 Desmoplastic small round cell tumor Desmo-tumor-JN-Dsrct

U2Os-EWS/WT1 fusion protein-induced

2.2.1.0 2.2.1.0

connective tissue, bone, osteosarcoma cell connective tissue, bone, osteosarcoma cell connective tissue, bone, Ewing sarcoma cell connective tissue, bone, desmoplastic small round cell tumor

hsa hsa hsa hsa

Ewing sarcoma cell line with EWS/FLI1 fusion protein (der(22)t(11;22)(q24;q12) and der(13)t(13;11;22) fusion chromosomes) Dsrct with EWS/WT1 fusion protein

2.2.2.0 2.2.3.0

Zebrafish SJD ZFL Am Afm 0hr 4hr 12hr 48hr liver epithelium adult fibroblast cell lines derived from the caudal fin Adult male Adult female Embryo Embryo Embryo Embryo 8.0.0.0 0.0.0.0 0.0.0.0 0.0.0.0 3.0.0.0 3.0.0.0 3.0.0.0 3.0.0.0 liver Unclassified Unclassified Unclassified embryo embryo embryo embryo Dre Dre Dre Dre Dre Dre Dre Dre

Fruitfly Embryo_0-2h Embryo_2-4h Embryo_4-6h Embryo_6-12h Embryo_12-24h Larva_L1 Larva_L1+L2 Larva_L3 Adult Testes Egg first 2 hours Egg hours 2-4 Egg hours 4-6 Egg hours 6-12 Eggs hours 12-24 Larva Stage L1 Larva Stage L1-L2 Larva Stage L1 Adult fly Testes Dme Dme Dme Dme Dme Dme Dme Dme Dme Dme

3.0.0.0 3.0.0.0 3.0.0.0 3.0.0.0 3.0.0.0 0.0.0.0 0.0.0.0 0.0.0.0 10.2.1.0

embryo embryo embryo embryo embryo Unclassified Unclassified Unclassified reproductive system, male reproductive system, testis

Worm Mixed mixed-staged C. elegans 0.0.0.0 Unclassified Cel

Ref

Collaborator (source RNA)

R. Darnell, darnelr@rockefeller.edu R. Darnell, darnelr@rockefeller.edu

T.Benzing, benzing@med1.ukl.unifreiburg.de T.Benzing, benzing@med1.ukl.unifreiburg.de T.Benzing, benzing@med1.ukl.unifreiburg.de T.Benzing, benzing@med1.ukl.unifreiburg.de T.Benzing, benzing@med1.ukl.unifreiburg.de

G. Macino, macino@bce.uniroma1.it G. Macino, macino@bce.uniroma1.it

G. Macino, macino@bce.uniroma1.it

A. Tarakhovsky, tarakho@rockefeller.edu A. Tarakhovsky, tarakho@rockefeller.edu A. Tarakhovsky, tarakho@rockefeller.edu F.N. Papavasiliou, papavasiliou@rockefeller.edu F.N. Papavasiliou, papavasiliou@rockefeller.edu F.N. Papavasiliou, papavasiliou@rockefeller.edu F.N. Papavasiliou, papavasiliou@rockefeller.edu F.N. Papavasiliou, papavasiliou@rockefeller.edu G. Hartmann, gunther.hartmann@ukb.unibonn.de G. Hartmann, gunther.hartmann@ukb.unibonn.de L. van Dyk, Linda.VanDyk@UCHSC.edu L. van Dyk, Linda.VanDyk@UCHSC.edu

Poy, M. N., Eliasson, L., Krutzfeldt, J., Kuwajima, S., Ma, X., Macdonald, P. E., Pfeffer, S., Tuschl, T., Rajewsky, N., Rorsman, P. and Stoffel, M. (2004) Nature, 432, 226-30.

Poy, M. N., Eliasson, L., Krutzfeldt, J., Kuwajima, S., Ma, X., Macdonald, P. E., Pfeffer, S., Tuschl, T., Rajewsky, N., Rorsman, P. and Stoffel, M. (2004) Nature, 432, 226-30.

M.Stoffel, stoffel@rockefeller.edu M.Stoffel, stoffel@rockefeller.edu

K. Rajewsky, rajewsky@cbr.med.harvard.edu

L. van Dyk, Linda.VanDyk@UCHSC.edu

D. A. Leib, Leib@vision.wustl.edu D. A. Leib, Leib@vision.wustl.edu D. A. Leib, Leib@vision.wustl.edu D. A. Leib, Leib@vision.wustl.edu

P. Greengard, greengd@rockefeller.edu P. Greengard, greengd@rockefeller.edu P. Greengard, greengd@rockefeller.edu P. Greengard, greengd@rockefeller.edu

P. Greengard, greengd@rockefeller.edu

R. di Lauro, rdilauro@unina.it R. di Lauro, rdilauro@unina.it R. di Lauro, rdilauro@unina.it R. di Lauro, rdilauro@unina.it

M. Brownstein, mike@venterinstitute.org M. Brownstein, mike@venterinstitute.org M. Brownstein, mike@venterinstitute.org M. Brownstein, mike@venterinstitute.org

A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de

F.A. Grsser, graesser@med-rz.uni-sb.de

T.Benzing, benzing@med1.ukl.unifreiburg.de T.Benzing, benzing@med1.ukl.unifreiburg.de P.Wernet, peter.wernet@uniduesseldorf.de P.Wernet, peter.wernet@uniduesseldorf.de P.Wernet, peter.wernet@uniduesseldorf.de M. Brownstein, mike@venterinstitute.org C. Rice, ricec@rockefeller.edu C. Rice, ricec@rockefeller.edu C. Rogler, crogler@aecom.yu.edu C. Rogler, crogler@aecom.yu.edu

C. Rogler, crogler@aecom.yu.edu

M. Brownstein, mike@venterinstitute.org

M. Brownstein, mike@venterinstitute.org A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de F.A. Grsser, graesser@med-rz.uni-sb.de F.A. Grsser, graesser@med-rz.uni-sb.de F.A. Grsser, graesser@med-rz.uni-sb.de G Macino, macino@bce.uniroma1.it G Macino, macino@bce.uniroma1.it G Macino, macino@bce.uniroma1.it A.Borkhardt, arndt.borkhardt@med.unimuenchen.de G Macino, macino@bce.uniroma1.it G Macino, macino@bce.uniroma1.it G Macino, macino@bce.uniroma1.it A.Borkhardt, arndt.borkhardt@med.unimuenchen.de

G. Hartmann, gunther.hartmann@ukb.unibonn.de G. Hartmann, gunther.hartmann@ukb.unibonn.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de

A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de G Macino, macino@bce.uniroma1.it G Macino, macino@bce.uniroma1.it G Macino, macino@bce.uniroma1.it A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de

G Macino, macino@bce.uniroma1.it G Macino, macino@bce.uniroma1.it G Macino, macino@bce.uniroma1.it G Macino, macino@bce.uniroma1.it G Macino, macino@bce.uniroma1.it G Macino, macino@bce.uniroma1.it G Macino, macino@bce.uniroma1.it G Macino, macino@bce.uniroma1.it G Macino, macino@bce.uniroma1.it G Macino, macino@bce.uniroma1.it

A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de W. Tam, wtam@med.cornell.edu W. Tam, wtam@med.cornell.edu W. Tam, wtam@med.cornell.edu W. Tam, wtam@med.cornell.edu F.A. Grsser, graesser@med-rz.uni-sb.de F.A. Grsser, graesser@med-rz.uni-sb.de F.A. Grsser, graesser@med-rz.uni-sb.de F.A. Grsser, graesser@med-rz.uni-sb.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de A.Borkhardt, arndt.borkhardt@med.unimuenchen.de W. Tam, wtam@med.cornell.edu W. Tam, wtam@med.cornell.edu W. Tam, wtam@med.cornell.edu W. Tam, wtam@med.cornell.edu W. Tam, wtam@med.cornell.edu W. Tam, wtam@med.cornell.edu W. Tam, wtam@med.cornell.edu W. Tam, wtam@med.cornell.edu W. Tam, wtam@med.cornell.edu W. Tam, wtam@med.cornell.edu

W. Tam, wtam@med.cornell.edu W. Tam, wtam@med.cornell.edu W. Tam, wtam@med.cornell.edu

Pfeffer, S., Sewer, A., Lagos-Quintana, M., Sheridan, R., Sander, C., Grasser, F. A., van Dyk, L. F., Ho, C. K., Shuman, S., Chien, M., et al. (2005). Identification of microRNAs of the herpesvirus family. advanced online publication. Pfeffer, S., Sewer, A., Lagos-Quintana, M., Sheridan, R., Sander, C., Grasser, F. A., van Dyk, L. F., Ho, C. K., Shuman, S., Chien, M., et al. (2005). Identification of microRNAs of the herpesvirus family. advanced online publication.

M. Brownstein, mike@venterinstitute.org C. Rice, ricec@rockefeller.edu C. Rice, ricec@rockefeller.edu M. Brownstein, mike@venterinstitute.org M. Brownstein, mike@venterinstitute.org

P.Wernet, peter.wernet@uniduesseldorf.de P.Wernet, peter.wernet@uniduesseldorf.de P.Wernet, peter.wernet@uniduesseldorf.de P.Wernet, peter.wernet@uniduesseldorf.de

M. Brownstein, mike@venterinstitute.org M. Brownstein, mike@venterinstitute.org M. Brownstein, mike@venterinstitute.org M. Brownstein, mike@venterinstitute.org

D. Ho, dho@rockefeller.edu D. Ho, dho@rockefeller.edu M. Brownstein, mike@venterinstitute.org M. Brownstein, mike@venterinstitute.org

N.Rosen, rosenn@mskcc.org N.Rosen, rosenn@mskcc.org

N.Rosen, rosenn@mskcc.org

M.Ladanyi, ladanyim@MSKCC.ORG M.Ladanyi, ladanyim@MSKCC.ORG

M.Ladanyi, ladanyim@MSKCC.ORG M.Ladanyi, ladanyim@MSKCC.ORG

The developmental miRNA profiles of zebrafish as determined by small RNA cloning. The developmental miRNA profiles of zebrafish as determined by small RNA cloning. The developmental miRNA profiles of zebrafish as determined by small RNA cloning. The developmental miRNA profiles of zebrafish as determined by small RNA cloning. The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T. Genes Dev. 2005 Jun 1;19(11):1288-93.

The small RNA profile during Drosophila melanogaster development. The small RNA profile during Drosophila melanogaster development. The small RNA profile during Drosophila melanogaster development. The small RNA profile during Drosophila melanogaster development. The small RNA profile during Drosophila melanogaster development. The small RNA profile during Drosophila melanogaster development. The small RNA profile during Drosophila melanogaster development. The small RNA profile during Drosophila melanogaster development. The small RNA profile during Drosophila melanogaster development. The small RNA profile during Drosophila melanogaster development. Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder B, Gaasterland T, Meyer J, Tuschl T. Dev Cell. 2003 Aug;5(2):337-50. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP. Cell. 2006 Dec 15;127(6):1193-207.

Tissue type code

1.0.0.0 1.1.0.0 2.0.0.0 2.1.0.0 2.2.0.0 2.2.1.0 2.2.2.0 2.2.3.0 2.3.0.0 2.3.1.0 2.3.1.1 2.3.2.0 3.0.0.0 3.1.0.0 3.2.0.0 3.3.0.0 3.4.0.0 3.4.1.0 3.4.2.0 3.5.0.0 3.5.1.0 3.5.1.1 4.0.0.0 4.1.0.0 4.1.1.0 4.2.0.0 4.2.1.0 4.2.2.0 4.3.0.0 4.4.0.0 4.4.1.0 5.0.0.0 5.1.0.0 5.1.1.0 5.1.1.1 5.1.1.2 5.1.2.0 6.0.0.0

6.1.0.0 6.1.1.0 6.1.1.1 6.1.1.2 6.1.1.3 6.1.1.4 6.1.1.5 6.1.1.6 6.1.1.7 6.1.1.8 6.1.1.9 6.1.1.10 6.1.1.11 6.1.2.0 6.1.2.1 6.1.2.2 6.1.2.3 6.1.3.0 6.2.0.0 6.2.1.0 6.2.2.0 6.3.0.0 6.3.1.0 6.3.2.0 6.3.3.0 6.3.4.0 6.3.5.0 6.3.6.0 6.3.7.0 6.3.8.0

6.4.0.0 7.0.0.0 7.1.0.0 7.2.0.0 7.2.1.0 7.2.1.1 7.2.2.0 7.2.2.1 8.0.0.0 8.1.0.0 9.0.0.0 9.1.0.0 9.1.1.0 9.1.1.1 9.1.1.2 9.1.1.3 9.1.2.0 9.1.2.1 9.2.0.0 9.2.1.0 9.3.0.0 9.3.1.0

10.0.0.0

10.1.0.0 10.1.1.0 10.1.2.0 10.1.2.1 10.1.3.0 10.1.4.0 10.1.4.1 10.1.4.2 10.1.4.3

10.2.0.0 10.2.1.0 10.2.2.0 10.2.3.0 11.0.0.0 11.1.0.0 11.1.1.0

cardiovascular system cardiovascular system, heart

Malignancy status code

connective tissue

connective tissue, adipose tissue connective tissue, bone connective tissue, bone, osteosarcoma cell connective tissue, bone, Ewing sarcoma cell connective tissue, bone, desmoplastic small round cell tumor connective tissue, skin connective tissue, skin, epidermis connective tissue, skin, epidermis, hair follicle connective tissue, skin, fibroblast

Protocol used 1 2 3 4

embryo

embryo, embryonic stem cell embryo, embryonic fibroblast embryo, embryonic kidney cell embryo, germ cell tumor embryo, germ cell tumor, teratocarcinoma embryo, germ cell tumor, seminoma

Size markers used

Primers used RT and first PCR step Second PCR step

embryo, neuroblast embryo, neuroblast, astroblast embryo, neuroblast, astroblast, astroblastoma

lower case, RNA, App= a

endocrine gland

endocrine gland, adrenal gland endocrine gland, adrenal gland, pheochromocytoma endocrine gland, pancreatic islet endocrine gland, pancreatic islet, pancreatic alpha cell endocrine gland, pancreatic islet, pancreatic beta cell endocrine gland, pituitary gland endocrine gland, thyroid gland endocrine gland, thyroid gland, FRTL-5 cell

gastrointestinal tract

gastrointestinal tract, intestine gastrointestinal tract, intestine, large intestine gastrointestinal tract, intestine, large intestine, colon gastrointestinal tract, intestine, large intestine, colorectal carcinoma gastrointestinal tract, intestine, small intestine

hematopoietic system

hematopoietic system, lymphoid lineage hematopoietic system, lymphoid lineage, B lineage hematopoietic system, lymphoid lineage, B lineage, pre-pre-B-lymphoblast hematopoietic system, lymphoid lineage, B lineage, pre-B-lymphoblast hematopoietic system, lymphoid lineage, B lineage, pre-B-lymphoblast [cALL] hematopoietic system, lymphoid lineage, B lineage, B-lymphocyte hematopoietic system, lymphoid lineage, B lineage, mantel cell lymphoma cell hematopoietic system, lymphoid lineage, B lineage, Burkitt Lymphoma cell hematopoietic system, lymphoid lineage, B lineage, large B-cell lymphoma cell hematopoietic system, lymphoid lineage, B lineage, follicular lymphoma cell hematopoietic system, lymphoid lineage, B lineage, Hodgkin Lymphoma cell hematopoietic system, lymphoid lineage, B lineage, marginal zone lymphoma cell hematopoietic system, lymphoid lineage, B lineage, plasmacytoma cell hematopoietic system, lymphoid lineage, T lineage hematopoietic system, lymphoid lineage, T lineage, T-lymphoblast hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD4 hematopoietic system, lymphoid lineage, T lineage, T-lymphocyte CD8 hematopoietic system, lymphoid lineage, natural killer cell hematopoietic system, lymphoid tissue hematopoietic system, lymphoid tissue, spleen hematopoietic system, lymphoid tissue, thymus hematopoietic system, myeloid lineage hematopoietic system, myeloid lineage, myeloblast FAB M2 hematopoietic system, myeloid lineage, pro-myelocyte FAB M3 hematopoietic system, myeloid lineage, myelomonocyte FAB M4 hematopoietic system, myeloid lineage, monocyte FAB M5 hematopoietic system, myeloid lineage, erythrocyte FAB M6 hematopoietic system, myeloid lineage, granulocyte hematopoietic system, myeloid lineage, monocyte hematopoietic system, myeloid lineage, dendritic cell

hematopoietic system, pluripotent hematopoietic stem cell

kidney

kidney, epithelial cell kidney, nephron kidney, nephron, renal corpuscle kidney, nephron, renal corpuscle, glomerulus kidney, nephron, renal tubule kidney, nephron, renal tubule, collecting duct

liver

liver, hepatocellular carcinoma cell

nervous system

nervous system, central nervous system nervous system, central nervous system, brain nervous system, central nervous system, brain, astrocytoma cell nervous system, central nervous system, brain, glioblastoma cell nervous system, central nervous system, brain, medulloblastoma nervous system, central nervous system, spinal cord nervous system, central nervous system, spinal cord, glioma nervous system, sympathetic ganglion nervous system, sympathetic ganglion, neuroblastoma cell nervous system, sense organ nervous system, sense organ, eye

reproductive system

reproductive system, female reproductive system reproductive system, female reproductive system, ovary reproductive system, female reproductive system, uterus reproductive system, female reproductive system, uterus, cervical carcinoma cell reproductive system, female reproductive system, placenta reproductive system, female reproductive system, breast reproductive system, female reproductive system, breast, adenocarcinoma reproductive system, female reproductive system, breast, ductal carcinoma reproductive system, female reproductive system, breast, mammary epithelium

reproductive system, male reproductive system reproductive system, male reproductive system, testis reproductive system, male reproductive system, epididymis reproductive system, male reproductive system, prostate gland

respiratory system

respiratory system, lung respiratory system, lung, adenocarcinoma cell

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normal tissue cancer tissue non-cancer-derived cells/cell line cancer-derived cells/cell line

input dephosphorylated yes no no no

5' adaptor seq ACGGAATTCCTCACTaaa ACGGAATTCCTCACTaaa ACGGAATTCCTCACTaaa agggaggcaccgaugcgg

3'adaptor seq puuuAACCGCGAATTCCAGL AppTTTAACCGCGAATTCCAGL AppuuuAACCGCGGCACCAGL AppuuuAACCGCGGCACCAGL

Ligase used for 3' adaptor l Rnl1 Rnl2 Rnl2 Rnl2

19-nt RNA size marker 24-nt RNA size marker 5'-primer CAGCCAACGGAATTCCTCA CAGCCAACAGGCACCGAA TTCCTCACTAAA

cguacgcggguuuaaacga cguacgcggaauaguuuaaacugu 3'-primer GACTAGCTGGAATTCGCGGTTAAA GACTAGCTTGGTGCCGAATTCGCGGTTAA A