Human Data

Marra embryonic stem cells
 No GEO data found.

Library ID GEO no. Desc.
d0 -- Sequence data from undifferentiated human embryonic stem cells (hESC library) raw 5' grouping
d15 -- Sequence data from differentiating human embryonic stem cells (EB library) raw 5' grouping
ALL -- All data from this library combined raw collapsed 5' grouping


Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells.
Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL, Zhao Y, McDonald H, Zeng T, Hirst M, Eaves CJ, Marra MA.
PMID 18285502


Tuschl multi-tissue
Description: "[S]equenced over 250 small RNA libraries from 26 different organ systems and cell types of human and rodents that were enriched in neuronal as well as normal and malignant hematopoietic cells and tissues."
No GEO sets found.

Library ID GEO no. Desc.
LAN -- 26 different organ systems and cell types of human raw 5' grouping


A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing PMID: 17604727
Data obtained from smiRNAdb


Rajewsky HeLa cells
GSE10829
Title: High-throughput sequencing of small RNAs from HeLa cells
Public on Apr 07, 2008

Library ID GEO no. Desc.
cHELA GSM274171 Solexa sequencing of small RNAs from HeLa cells raw 5' grouping


Discovering microRNAs from deep sequencing data using miRDeep. PMID 18392026


Siomi AGO IP in Jurkat cells
No GEO sets found.

Library IDGEO no.Desc.
JURKAThAGO2 -- Ago2 association in Jurkat cell raw 5' grouping
JURKAThAGO3 -- Ago3 association in Jurkat cell raw 5' grouping
ALL -- All data from this library combined raw collapsed 5' grouping


Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing PMID 18524951


Meister AGO IP in HEK293 cells
GSE13370
Title: High-throughput pyrosequencing of endogenous small RNAs associated to human Argonaute 1 & 2
Public on Nov 21, 2008

Library IDGEO no.Desc.
HEK293hAgo1 GSM337570 endogenous small RNA associated to human Argonaute 1 raw 5' grouping
HEK293hAgo2 GSM337571 endogenous small RNA associated to human Argonaute 2 raw 5' grouping
ALL -- All data from this library combined raw collapsed 5' grouping


A human snoRNA with microRNA-like functions. PMID 19026782


Combined human data sets

Library IDGEO no.Desc.
ALL AGO -- All AGO IP libraries combined (Siomi and Meister datasets listed above) raw collapsed 5' grouping
ALL HUMAN -- All human libraries listed above combined -- raw collapsed 5' grouping
No IP -- All human libraries listed above combined without IP data raw collapsed 5' grouping


Mouse Data


Sharp ES cells
GSE9306
Title: Short RNA profiling of ES cells with and without Dicer
Public on Oct 31, 2007

Library ID GEO no. Desc.
J1_ES_untr GSM237107 Untreated raw 5' grouping
J1_ES_demeth GSM237108 5 days after demethylation of J1 ES cells with 5-aza-deoxycytidine raw 5' grouping
ES_Dicer-DEL GSM237109 Several months after dicer deletion raw 5' grouping
ES_Dicer GSM237110 Before dicer deletion. raw 5' grouping
ALL GSE9306 All data from this library combined raw collapsed 5' grouping

Calabrese JM, Seila AC, Yeo GW, Sharp PA.
RNA sequence analysis defines Dicer's role in mouse embryonic stem cells.
Proc Natl Acad Sci U S A 2007 Nov 13;104(46):18097-102. PMID: 17989215


Hannon mouse oocytes
GSE10364
Title: Small RNA profile in fully grown mammalian oocytes
Public on Mar 28, 2008

Library ID GEO no. Desc.
TAM GSM261959 Total RNA isolated and size-fractionated by PAGE into 19-30nt raw 5' grouping


Tam OH, Aravin AA, Stein P, Girard A et al.
Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes.
Nature 2008 May 22;453(7194):534-8. PMID 18404147


Young mouse ES cells
GSE11724
Title: Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells
Public on Jul 30, 2008

Library ID GEO no. Desc.
mESv6_5 GSM307156 murine embryonic stem cellsraw5' grouping
mEF GSM307157 mouse embryonic fibroblasts raw5' grouping
NPC GSM307158 murine neural precursor cells raw5' grouping
ZHBT-c4_0h GSM307159 ZHBT-c4 cells (from Austin Smith) untreated raw5' grouping
ZHBT-c4_12h GSM307160 ZHBT-c4 cells with 12 hours of doxycyclin treatment raw5' grouping
ZHBT-c4_24h GSM307161 ZHBT-c4 cells with 24 hours of doxycyclin treatment raw5' grouping
ALL GSE9306 All data from this library combined raw collapsed 5' grouping


Marson A, Levine SS, Cole MF, Frampton GM et al.
Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells.
Cell 2008 Aug 8;134(3):521-33. PMID: 18692474


Bartel murine neutrophils
GSE12074
Title: Analysis of small RNAs in murine neutrophils by Solexa/Illumina genome analyzer
Public on Jul 31, 2008

Library ID GEO no. Desc.
bartel_NP GSM304914 Analysis of small RNAs in murine neutrophils cultured in vitro by Solexa/Illumina genome analyzer. raw5' grouping


Baek D, Villen J, Shin C, Camargo FD et al.
The impact of microRNAs on protein output.
Nature 2008 Sep 4;455(7209):64-71. PMID: 18668037


Blelloch Mouse ES cells
GSE12521
Title: Endogenous shRNAs, siRNAs, and Other Microprocessor-independent, Dicer-dependent Small RNAs in Mouse ES Cells
Public on Sep 10, 2008

Library ID GEO no. Desc.
ESC_WT_ILL GSM314552 Embryonic Stem Cell (ESC) wild type (Illumina) raw5' grouping
ESC_DCR_ILL GSM314553 ESC dicer (Illumina) raw5' grouping
ESC_DGCR8_ILL GSM314557 ESC DGCR8 (Illumina) raw5' grouping
ESC_WT_454 GSM314558 ESC wild type (454) raw5' grouping
ESC_DGCR8_454 GSM314559 ESC DGCR8 (454) raw5' grouping
ALL_ILL GSE12521 All illumina data combined raw collapsed 5' grouping
ALL_454 GSE12521 All 454 data combined raw collapsed 5' grouping
ALL GSE12521 All data combined (both 454 and illumina) raw collapsed 5' grouping


Babiarz JE, Ruby JG, Wang Y, Bartel DP et al.
Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs.
Genes Dev 2008 Oct 15;22(20):2773-85. PMID: 18923076


Miscellaneous sets not found on GEO

Library ID reference Desc.
STK Stark Mouse ovary, c-kit mutant ovary and Comma-Dbgeo cells (mammary epithelial cell line) raw5' grouping
WAT Watanabe mouse oocyte raw5' grouping
BER Berezikov data rat brain raw5' grouping
LAN_MUS Landgraf mouse, various organ systems raw5' grouping


All mouse (and rat) data combined

Library ID reference Desc.
All rodent data combined raw collapsed 5' grouping
All mouse data combined (berezikov rat data excluded raw collapsed 5' grouping


Data from other vertebrates

Rajewsky domestic dog lymphocytes
GSE10825
Title:MPI_Chen_domestic_dog_Solexa_2007
Public on Apr 07, 2008

Library ID GEO no. Desc.
cDog GSM273725 Domestic dog lymphocytesraw5' grouping


Friedlander MR, Chen W, Adamidi C, Maaskola J et al.
Discovering microRNAs from deep sequencing data using miRDeep.
Nat Biotechnol 2008 Apr;26(4):407-15. PMID: 18392026

Tizard chicken embryos
GSE10686
Title: Deep sequencing of small RNA libraries from chicken embryos
Public on May 12, 2008

Library ID GEO no. Desc.
CE5 GSM270187 Chick embryo day 5raw5' grouping
CE7 GSM270188 Chick embryo day 7raw5' grouping
CE9 GSM270189 Chick embryo day 9raw5' grouping
ALL GSE10686 All data combined.rawcollapsed5' grouping


Glazov EA, Cottee PA, Barris WC, Moore RJ et al.
A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach.
Genome Res 2008 Jun;18(6):957-64. PMID: 18469162

Dalmay chicken somite embryos
GSE15513
Title: High-throughput sequencing of small RNAs in chicken somite embryos
Public on Apr 28, 2009

Library ID GEO no. Desc.
CSOM GSM388803 White leghorn chicken embryos HH14-HH21 (~2-4 days) raw5' grouping


All chicken data combined

Library ID reference Desc.
All chicken data combined raw collapsed 5' grouping


Multi-species Data



Library ID reference Desc.
All genes--Human and mouse data combined raw collapsed 5' grouping
All genes--All vertebrate data combined raw collapsed 5' grouping
HC genes--Human and mouse data combined raw collapsed 5' grouping
HC genes--All vertebrate data combined raw collapsed 5' grouping