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Series GSE248159 Query DataSets for GSE248159
Status Public on Nov 18, 2023
Title PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape [RNA-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary T cells trigger non-specific signaling pathways to elicit specialized effector functions to eliminate pathogens and cancers. Chromatin accessibility at T effector loci prior to antigen encounter poises cells to couple antigen recognition to the activation of lineage-specific responses. Here, by tracing the chromatin accessibility profiles unique to T effector functions during development, we find that the majority of T effector loci become accessible prior to antigen receptor expression. Epigenomic feature analysis, biochemical studies, and inducible perturbations identified two mechanistic linchpins: the physical association of the mSWI/SNF remodeling complex to the pleiotropic transcription factor (TF) RUNX1, and the cooperativity between RUNX1 and lineage-defining TFs PU.1 and BCL11B that respectively facilitate the establishment and maintenance of chromatin accessibility at T effector loci in early thymocyte progenitors. These findings reflect a design principle that allows distinct cell types to use the same signaling pathways to execute disparate roles which collectively orchestrate the immune response.
 
Overall design RNA-seq profiling was performed on at various stages of development in wild-type untreated, wild-type FK506-treated, Smarca4 cKO, Bcl11b cKO, and Runx1 cKO murine thymocytes.
 
Contributor(s) Gamble N, Bradu A, Caldwell JA, McKeever J, Bolonduro O, Kim Y, Parks B, Klemm S, Greenleaf WJ, Crabtree GR, Koh AS
Citation(s) 38632339
BioProject PRJNA971212
Submission date Nov 17, 2023
Last update date May 31, 2024
Contact name Alexandra Bradu
E-mail(s) abradu@uchicago.edu
Organization name University Of Chicago
Department Pathology
Lab Koh Lab
Street address 924 East 57th Street
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (20)
GSM7906591 Runx1 WT DN1 thymocytes Rep1
GSM7906592 Runx1 cKO DN1 thymocytes Rep1
GSM7906593 Runx1 WT DN1 thymocytes Rep2
This SubSeries is part of SuperSeries:
GSE234331 PU.1 and BCL11B sequentially cooperate with RUNX1 to anchor mSWI/SNF to poise the T cell effector landscape

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

Supplementary file Size Download File type/resource
GSE248159_RNA_Master_Matrix.txt.gz 6.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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