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Sample GSM1479457 Query DataSets for GSM1479457
Status Public on Jan 06, 2015
Title lib245
Sample type SRA
 
Source name Whole Blood
Organism Homo sapiens
Characteristics age: 24
cellcount: 2000000
celltype: CD4
collectiondate: May 23 2012
diseasestatus: Type 1 Diabetes
donorid: 34
gender: F
index: 15
race: White
samplename: 34_CD4T
smoker: --
time since last flare (months): --
time since steroid dose: --
time since symptom onset (yrs): --
years since diagnosis: 7
Extracted molecule total RNA
Extraction protocol 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).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiScanSQ
 
Data processing fastq files were created from .bcl files via Illumina's CASAVA 1.8.2
reads were aligned to Hg19 via Omicsoft sequence aligner (OSA) version 2.0.1
gene counts were generated by HTSeq version 0.5.4p3
TMMs were generated with Bioconductor package EdgeR
Genome_build: Hg19
Supplementary_files_format_and_content: tab delimited file contains TMM normalized counts
 
Submission date Aug 14, 2014
Last update date Jan 04, 2024
Contact name Stephanie Osmond
E-mail(s) sosmond@benaroyaresearch.org
Organization name Benaroya Research Institute
Street address 1201 9th Ave
City Seattle,
State/province WA
ZIP/Postal code 98101
Country USA
 
Platform ID GPL15456
Series (1)
GSE60424 Next generation sequencing of human immune cell subsets across diseases
Relations
BioSample SAMN02990341
SRA SRX680565

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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