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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
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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.
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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.
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Web link |
https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1341745/full
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Contributor(s) |
Potter SJ |
Citation(s) |
38765012 |
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Submission date |
Jun 01, 2022 |
Last update date |
May 29, 2024 |
Contact name |
Sarah J Potter |
Organization name |
Cincinnati Children's Hospital Medical Center
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Department |
Allergy and Immunology
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Lab |
Barski Lab
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Street address |
240 Albert Sabin Way, S6.540, MLC 7028
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City |
Cincinnati |
State/province |
Ohio |
ZIP/Postal code |
45229 |
Country |
USA |
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Platforms (1) |
GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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Samples (18)
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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 |
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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |