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Sample GSM3011784 Query DataSets for GSM3011784
Status Public on May 09, 2018
Title mRNA_lupus_LH__TBR_4
Sample type SRA
 
Source name Human whole blood
Organism Homo sapiens
Characteristics tissue: whole blood
diagnosis: Lupus
vascular phenotype: High TBR
Extracted molecule total RNA
Extraction protocol Peripheral blood was collected by venipuncture in PAXgene Blood RNA Tubes (BD Diagnostics) and stored at -80C. RNA was isolated using Paxgene Blood RNA Kit (Qiagen, Inc.)
cDNA libraries were prepared using the TruSeq® Stranded mRNA NeoPrep™ Kit (Illumina). RNA seq data were generated on Illumina HiSeq 2500 or 3000 instruments according to the manufacturer's instructions
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description exp ID: 161220_0011_s09
sample name: S09
Data processing alignment: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of 50 bases were mapped to hg19 using TopHat 2.1.1
RPKM calculation: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Partek6.6
Genome_build: hg19
Supplementary_files_format_and_content: excel for a RPKM file
 
Submission date Feb 15, 2018
Last update date May 09, 2018
Contact name Hong-wei Sun
Organization name NIAMS
Department Office of Science & Technology
Lab Biodata Mining & Discovery Section
Street address 9000 Rockville Pile
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL21290
Series (1)
GSE110685 Low density granulocytes and their gene signature associate with vascular inflammation and coronary atheroclerosis in systemic lupus erythematosus patients
Relations
BioSample SAMN08546675
SRA SRX3703089

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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