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Series GSE89177 Query DataSets for GSE89177
Status Public on May 03, 2017
Title Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis [ATAC-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Introduction: SP140 is a bromodomain/plant homeo domain (PHD)-containing reader with immune-restricted expression, and single nucleotide polymorphisms (SNPs) within SP140 associate with Crohn’s disease (CD). However, the function of SP140 and the consequences of disease-associated SP140 SNPs have remained unknown.
Results: Individuals carrying CD-associated SNPs within SP140 had defective SP140 mRNA splicing, diminished SP140 protein, and severely suppressed innate immune signatures that stratified them from other CD patients.
Conclusion: SP140 is a critical orchestrator of macrophage identity, and a loss of SP140 due to genetic variation contributes to a molecularly defined subset of CD characterized by suppressed innate immunity.
 
Overall design ATAC-seq in human macrophages stimulated with IFNg for 24h, and LPS stimulation for 4 hours: siRNA mediated knockdown of SP140 versus controls.
 
Contributor(s) Mehta S, Pantano L, Sui SH, Jeffrey KL
Citation Stuti Mehta, D. Alexander Cronkite, Megha Basavappa, Tahnee L. Saunders, Fatemeh Adiliaghdam, Hajera Amatullah, Sara A. Morrison, Jose D. Pagan, Robert M. Anthony, Pierre Tonnerre, Georg M. Lauer, James C. Lee, Sreehaas Digumarthi, Lorena Pantano, Shannan J. Ho Sui, Fei Ji, Ruslan Sadreyev, Chan Zhou, Alan C. Mullen, Vinod Kumar, Yang Li, Cisca Wijmenga, Ramnik J. Xavier, Terry K. Means, Kate L. Jeffrey (2017). Maintenance of macrophage transcriptional programs and intestinal homeostasis by epigenetic reader SP140. Science Immunology. March 3 Vol. 2, Issue 9, doi: 10.1126/sciimmunol.aag3160
Submission date Oct 25, 2016
Last update date May 15, 2019
Contact name Kate L Jeffrey
E-mail(s) KJeffrey@mgh.harvard.edu
Phone 6176435887
Organization name Massachusetts General Hospital, Harvard Medical School
Department Medicine
Lab Jeffrey
Street address 50 Blossom St, Thier 340
City Boston
State/province Massachusetts
ZIP/Postal code 02114
Country USA
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (4)
GSM2359978 Control_0hr
GSM2359979 Control_4hr
GSM2359980 SP140_siRNA_0hr
This SubSeries is part of SuperSeries:
GSE89876 Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis
Relations
BioProject PRJNA350528
SRA SRP092059

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
GSE89177_RAW.tar 223.1 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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