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Series GSE60424 Query DataSets for GSE60424
Status Public on Jan 06, 2015
Title Next generation sequencing of human immune cell subsets across diseases
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary This study compared whole transcriptome signatures of 6 immune cell subsets and whole blood from patients with an array of immune-associated diseases. Fresh blood samples were collected from healthy subjects and subjects diagnosed type 1 diabetes, amyotrophic lateral sclerosis, and sepsis, as well as multiple sclerosis patients before and 24 hours after the first treatment with IFN-beta. At the time of blood draw, an aliquot of whole blood was collected into a Tempus tube (Invitrogen), while the remainder of the primary fresh blood sample was processed to highly pure populations of neutrophils, monocytes, B cells, CD4 T cells, CD8 T cells, and natural killer cells. RNA was extracted from each of these cell subsets, as well as the whole blood samples, and processed into RNA sequencing (RNAseq) libraries (Illumina TruSeq). Sequencing libraries were analyzed on an Illumina HiScan, with a target read depth of ~20M reads. Reads were demultiplexed, mapped to human gene models (ENSEMBL), and tabulated using HTSeq. Read count data were normalized by the TMM procedure (edgeR package).
 
Overall design We performed whole genome RNAseq profiling of immune cell subsets and whole blood from subjects with an array of immune-associated diseases.
 
Contributor(s) Speake C, Linsley PS, Whalen E, Chaussabel D, Presnell SR, Mason MJ, Gersuk VH, O'Brien KK, Nguyen Q, Greenbaum CJ, Buckner JH, Malhotra U
Citation(s) 25314013
Submission date Aug 14, 2014
Last update date May 15, 2019
Contact name Scott Presnell
E-mail(s) SPresnell@benaroyaresearch.org
Organization name Benaroya Research Institute
Department Systems Immunology
Street address 1201 Ninth Ave.
City Seattle
State/province WA
ZIP/Postal code 98101
Country USA
 
Platforms (1)
GPL15456 Illumina HiScanSQ (Homo sapiens)
Samples (134)
GSM1479433 lib221
GSM1479434 lib222
GSM1479435 lib223
Relations
BioProject PRJNA258216
SRA SRP045500

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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
GSE60424_GEOSubmit_FC1to11_normalized_counts.txt.gz 2.3 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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