Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome of double-positive thymocyte precursors transduced with a retrovirus encoding Lin28a

ABSTRACT: We performed paired-end RNA-seq to compare the transcriptome of DP thymocytes that ectopically express Lin28 in vivo versus untransduced (GFP-ve) DP thymocytes.

ORGANISM(S): Mus musculus

PROVIDER: GSE34854 | GEO | 2012/02/17

SECONDARY ACCESSION(S): PRJNA150133

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome of double-positive thymocyte precursors transduced with a retrovirus encoding Lin28a

Project description:We performed paired-end RNA-seq to compare the transcriptome of DP thymocytes that ectopically express Lin28 in vivo versus untransduced (GFP-ve) DP thymocytes. Transduced (GFP+) and untransduced (GFP-) CD4+ CD8+ CD3- thymocytes were sorted and pooled from three recipients of hematopoietic stem and progenitor cells transduced with Lin28-RV six weeks post-reconstitution. Total RNA was extracted and paired-end library construction and sequencing was performed on oligo-dT purified RNA.

2012-02-17 | E-GEOD-34854 | biostudies-arrayexpress

miRNA profiling of double-positive thymocytes transduced with a retrovirus encoding Lin28a compared to untransduced controls

Project description:We used the NanoString mouse nCounter miRNA expression platform to compare the miRNA expression in double-positive (DP) thymocytes that developed in the presence (GFP+) or absence (GFP-ve) of ectopic mLin28 expression. Transduced (GFP+) and untransduced (GFP-ve) CD4+ CD8+ CD3- thymocytes were FACS sorted and pooled from three recipients of hematopoietic stem and progenitor cells transduced with Lin28-RV six weeks post-reconstitution (bone marrow chimeric mice). Total RNA was extracted and used for sample preparation and hybridization per manufacturer's recommendations.

2012-02-17 | E-GEOD-35081 | biostudies-arrayexpress

miRNA profiling of double-positive thymocytes transduced with a retrovirus encoding Lin28a compared to untransduced controls

2012-02-17 | GSE35081 | GEO

Genes regulated by HEB and E2A during DP stage of thymocyte development

Project description:To investigate gene targets of the E-proteins HEB and E2A during the CD4+CD8+ double positive (DP) stage of T cell development. We examined E-protein function by simultaneous removal of both HEB (Tcf12) and E2A (Tcfe2a) genes at the DP stage. This was done by crossing mice containing HEB floxed and E2A floxed alleles to a CD4Cre background (Tcf12f/fTcfe2af/fCD4Cre mice). Microarray analysis was used to compare gene expression in HEB and E2A double deficient DP thymocytes (Cre+) to Cre- control DP thymocytes. Keywords: genetic modification

2007-12-04 | GSE9749 | GEO

HDAC3 restrains cytokine signaling during thymocyte development for the generation of CD4 T cells (RNA-Seq)

Project description:CD4 and CD8 T cells are vital components of the immune system. According to the kinetic signaling model, commitment to the CD4 or CD8 lineage is determined by whether persistent TCR signaling or cytokine signaling predominates, respectively. We found histone deacetylase 3 (HDAC3) is critical for the development of CD4 T cells, as its deletion leads to the generation of only CD8SP thymocytes. In the absence of HDAC3, MHC Class II-restricted OT-II thymocytes are redirected to the CD8 cytotoxic lineage. Analysis of histone acetylation and RNA-seq reveals HDAC3-deficient DP thymocytes are biased towards the CD8 lineage prior to positive selection. In addition, HDAC3-deficient DP thymocytes have increased IL-21R expression and STAT5 activation. As a result, HDAC3 is required to restrain cytokine signaling in DP thymocytes and is required for the generation of CD4 T cells.

2019-01-20 | GSE109530 | GEO

HDAC3 restrains cytokine signaling during thymocyte development for the generation of CD4 T cells (ChIP-Seq)

2019-01-20 | GSE109529 | GEO

Global dynamics of stage-specific transcription factor binding during thymocyte development

Project description:ATAC-seq in DN, DP, CD4 SP and CD8 SP thymocytes isolated from 9 weeks-old wild type C57BL/6J mouse

2018-04-04 | GSE107076 | GEO

Gene expression analysis of thymocyte subsets

Project description:Mouse thymocytes can be classified into four major subsets based on expression of CD4 and CD8 co-receptors. CD4-CD8- (double negative, DN) cells become CD4+CD8+ (double positive, DP) cells following productive T cell receptor (TCR) beta chain rearrangement. A small proportion of DP cells are selected through interaction of clonal TCRalpha/beta and MHC self peptide complex expressed on thymic stromal cells. DP cell expressing MHC class I-restricted TCR become CD4-CD8+ cells, which will finally differentiate into cytotoxic T cells, while MHC class II restricted selection generates CD4+CD8- helper lineage T cells. We used microarrays to identify genes important for thymocyte differentiation and lineage determination by profiling gene expression in different thymocyte subsets. Mouse thymocytes were divided into four subsets based on CD4, CD8a, and TCRb expression and purified by flw cytometry. FACS purified DN (CD4-CD8a-TCRb-), DP (CD4+CD8a+), CD4SP (CD4+CD8a-TCRbhi) and CD8SP (CD4-CD8a+TCRbhi) populations were lysed in Trizol, and provided to the Genomics Core Facility of the Memorial Sloan-Kettering Cancer Center (MSKCC) for quality control, quantification, reverse transcription, labeling and hybridization to MOE430A 2.0 microarray chips (Affymetrix). Arrays were scanned per the manufacturer’s specifications for the Affymetrix MOE430v2 chip.

2011-08-09 | E-GEOD-31082 | biostudies-arrayexpress

The transcription factor Gli3 promotes differentiation from double positive to CD4 single positive thymocyte by repression of Shh

Project description:We used Affymetrix microarrays to understand the genome wide differences in Wildtype and Gli3 mutant (Gli3+/- and Gli3-/-) (n=2) embryonic day 18.5 DP CD69-, DP CD69+ and SP4 thymocytes.

2018-01-19 | GSE87499 | GEO

Gene expression analysis of thymocyte subsets

2011-08-10 | GSE31082 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data