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Series GSE205285 Query DataSets for GSE205285
Status Public on May 03, 2024
Title Mouse single positive thymocyte bulk RNA-seq from Kmt2d knockout and control littermates.
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Third-party reanalysis
Summary To evaluate the hypothesis that dysregulated thymocyte development contributes to immune deficiencies in individuals with KS1. We generated bulk murine CD4+ or CD8+ single positive thymocyte RNA-seq data from cells which lack the histone methyltransferase, Kmt2d SET domain (exons 50/51), with a conditional Cre-recombinase driven by Lck-CreMar (T cell specific) or Vav1-iCre (hematopoietic). Expression profiling by high throughput sequencing.
 
Overall design 1) RNA-sequencing from 3 biological replicates of paired single positive (SP) thymocytes from Cre-recombinase (Lck-CreMar-driven: CD4+ and CD8+ SP thymocytes; or Vav1-iCre-driven: CD8+ SP thymocytes) Kmt2d knockout single positive thymocytes and corresponding Cre-negative control littermate. 2) Re-analysis of 7 Lck-Cre; Dot1l control and knockout CD8+ thymocyte RNA-Seq samples (GSE138910; GSM4121514-GSM4121516, GSM4121521-GSM4121524) and Kmt2d control and knockout peripheral naive CD4+ T cells RNA-seq (GSE69162; GSM1694174-GSM1694177) and ChIP-Seq (GSE69162; GSM1694154, GSM1694155) samples.
Web link https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1341745/full
 
Contributor(s) Potter SJ
Citation(s) 38765012
Submission date Jun 01, 2022
Last update date May 29, 2024
Contact name Sarah J Potter
Organization name Cincinnati Children's Hospital Medical Center
Department Allergy and Immunology
Lab Barski Lab
Street address 240 Albert Sabin Way, S6.540, MLC 7028
City Cincinnati
State/province Ohio
ZIP/Postal code 45229
Country USA
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (18)
GSM6209734 RNA_LckKmt2d_WT_CD4SP_Biol rep1
GSM6209735 RNA_LckKmt2d_WT_CD4SP_Biol rep2
GSM6209736 RNA_LckKmt2d_WT_CD4SP_Biol rep3
Relations
Reanalysis of GSM4121514
Reanalysis of GSM4121515
Reanalysis of GSM4121516
Reanalysis of GSM4121521
Reanalysis of GSM4121522
Reanalysis of GSM4121523
Reanalysis of GSM4121524
Reanalysis of GSM1694174
Reanalysis of GSM1694175
Reanalysis of GSM1694176
Reanalysis of GSM1694177
Reanalysis of GSM1694155
Reanalysis of GSM1694154
BioProject PRJNA844331

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE205285_RAW.tar 11.4 Mb (http)(custom) TAR (of TSV)
GSE205285_README.txt 1.5 Kb (ftp)(http) TXT
GSE205285_projects-E2bqDGwX6XyRK9ef7-CrJZ3jeABtm7pzy9G-srr2037221.bigWig 109.3 Mb (ftp)(http) BIGWIG
GSE205285_projects-E2bqDGwX6XyRK9ef7-szLTnNLjf6qJ6crqi-srr2037222.bigWig 114.4 Mb (ftp)(http) BIGWIG
GSE205285_projects-TQngs8NzyZ7wA84BQ-GkyrqCYtHWgMRStcF-srr10285428.genes.tsv.gz 608.5 Kb (ftp)(http) TSV
GSE205285_projects-TQngs8NzyZ7wA84BQ-MnmuGngeJQhiGGtmv-srr10285421.genes.tsv.gz 611.4 Kb (ftp)(http) TSV
GSE205285_projects-TQngs8NzyZ7wA84BQ-QqSSTHLfHdBNut6p6-srr10285420.genes.tsv.gz 602.6 Kb (ftp)(http) TSV
GSE205285_projects-TQngs8NzyZ7wA84BQ-a7czDhRzA4qS8Firc-srr10285427.genes.tsv.gz 604.2 Kb (ftp)(http) TSV
GSE205285_projects-TQngs8NzyZ7wA84BQ-bZ8ockCmTiPkNhc7h-srr10285429.genes.tsv.gz 610.5 Kb (ftp)(http) TSV
GSE205285_projects-TQngs8NzyZ7wA84BQ-c3mEXAqQBkmgrH2po-srr10285430.genes.tsv.gz 610.8 Kb (ftp)(http) TSV
GSE205285_projects-TQngs8NzyZ7wA84BQ-yhuWbs34e6DwrMaF5-srr10285422.genes.tsv.gz 606.6 Kb (ftp)(http) TSV
GSE205285_projects-o7E36vSb6X5oX5ExF-FCjsGxGczuFe9oxmM-SRR2037263.genes.tsv.gz 627.0 Kb (ftp)(http) TSV
GSE205285_projects-o7E36vSb6X5oX5ExF-P2ZoZA6euJKoTpKAH-SRR2037260.genes.tsv.gz 623.5 Kb (ftp)(http) TSV
GSE205285_projects-o7E36vSb6X5oX5ExF-Q8Cg3A6XREL8sF4SJ-SRR2037261.genes.tsv.gz 623.6 Kb (ftp)(http) TSV
GSE205285_projects-o7E36vSb6X5oX5ExF-axKFMz28bQpiJ3cuz-SRR2037262.genes.tsv.gz 625.0 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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