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Series GSE21630

Query DataSets for GSE21630

Status

Public on Jun 07, 2010

Title

Regulation of microRNA Expression and Abundance during Lymphopoiesis

Organism

Experiment type

Non-coding RNA profiling by high throughput sequencing

Summary

Although the cellular concentration of miRNAs is critical to their function, how miRNA expression and abundance are regulated during ontogeny is unclear. We used deep-sequencing to characterize the microRNome from most developing lymphocytes, various hematopoietic cell lineages, and representative mouse tissues. Epigenetic and transcriptome profiles were also compiled from selected T and B cell stages by ChIP-Seq and mRNA-Seq respectively. We show that lymphocyte-specific miRNAs are either tightly regulated during development by polycomb group-mediated H3K27me3, or maintained in a semi-activated state prior to full expression. Because of extensive miRNA biogenesis, the cellular concentration of mature miRNAs does not typically reflect transcriptional changes. However, we here uncovered a subset of miRNAs for which abundance is directly regulated by miRNA gene expression. Our data provides the most comprehensive view of the microRNome in the immune system and reveal underlying epigenetic and transcriptional forces that shape miRNA homeostasis.

Overall design

small RNA expression profiles of 27 well defined cell types from the mouse immune system, hematopoietic progenitor cells, embryonic stem cells, as well as 12 tissues. Biological and technical replicates for 3 of the cell types were included.

Regulation of MicroRNA Expression and Abundance during Lymphopoiesis
Immunity, Volume 32, Issue 6, 25 June 2010, Pages 828-839
doi:10.1016/j.immuni.2010.05.009

Contributor(s)

Kuchen S, Resch W, Yamane A, Kuo N, Li Z, Chakraborty T, Wei L, Laurence A, Yasuda T, Peng S, Hu-Li J, Lu K, Dubois W, Kitamura Y, Charles N, Sun H, Muljo S, Schwartzberg PL, Paul WE, O'Shea J, Rajewsky K, Casellas R

Citation(s)

20605486, 21113164, 23706737

Submission date

May 03, 2010

Last update date

May 15, 2019

Contact name

Seolkyoung Jung

Organization name

NIH

Department

NIAMS

Lab

biodata mining and discovery section

Street address

10 Center Dr

City

bethesda

State/province

MD

ZIP/Postal code

20892

Country

USA

Platforms (1)

Illumina Genome Analyzer II (Mus musculus)

Samples (46)

More...

GSM539835	mouse pro B cells [09-002]
GSM539836	mouse pre B cells [09-002]
GSM539837	mouse immature B cells [09-002]

GSM539838	mouse mature B cells (spleen) replicate 1 [09-002]
GSM539839	mouse mature B cells (spleen) replicate 2 [09-002]
GSM539840	mouse B cells activated in vitro with LPS/IL4 replicate 1 [09-002]
GSM539841	mouse B cells activated in vitro with LPS/IL4 replicate 2 [09-002]
GSM539842	mouse B cells activated in vitro with LPS/IL4 replicate 3 [09-002]
GSM539843	mouse B cells activated in vitro with LPS/aIgD-Dextran [09-002]
GSM539844	mouse B1 B cells [09-002]
GSM539845	mouse marginal zone B cells (spleen) [09-002]
GSM539846	mouse germinal center B cells (lymph node) [09-002]
GSM539847	mouse plasma cells [09-002]
GSM539848	mouse hematopoetic progenitor cells [09-002]
GSM539849	mouse mast cells [09-002]
GSM539850	mouse basophil cells [09-002]
GSM539851	mouse neutrophil cells replicate 1 [09-002]
GSM539852	mouse neutrophil cells replicate 2 [09-002]
GSM539853	mouse dendritic cells [09-002]
GSM539854	mouse macrophages [09-002]
GSM539855	mouse natural killer cells [09-002]
GSM539856	mouse CD4+CD8+ T cells (thymus) [09-002]
GSM539857	mouse CD4+ T cells (spleen) [09-002]
GSM539858	mouse CD8+ T cells (spleen) [09-002]
GSM539859	mouse T cells activated in vitro with Concanavalin A [09-002]
GSM539860	mouse Th1 cells [09-002]
GSM539861	mouse Th2 cells [09-002]
GSM539862	mouse Th17 cells [09-002]
GSM539863	mouse TFHS cells [09-002]
GSM539864	mouse iTreg cells [09-002]
GSM539865	mouse nTreg cells [09-002]
GSM539866	mouse embryonic stem cells [09-002]
GSM539867	mouse embryonic fibroblast cells [09-002]
GSM539868	mouse heart tissue [09-002]
GSM539869	mouse brain tissue [09-002]
GSM539870	mouse lung tissue [09-002]
GSM539871	mouse liver tissue [09-002]
GSM539872	mouse kidney tissue [09-002]
GSM539873	mouse pancreatic tissue [09-002]
GSM539874	mouse skin tissue [09-002]
GSM539875	mouse muscle tissue [09-002]
GSM539876	mouse salivary gland tissue [09-002]
GSM539877	mouse testicular tissue [09-002]
GSM539878	mouse ovaries [09-002]
GSM539879	mouse BclXL B activated with LPS/IL4 [BalbC] [09-002]
GSM539880	mouse BclXL germinal center B cells [BalbC] [09-002]

Relations

SRA

BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE21630_RAW.tar	980.0 Kb	(http)(custom)	TAR (of TXT)
SRA Run Selector
Processed data included within Sample table
Processed data provided as supplementary file
Raw data are available in SRA

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