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Sample GSM3523511 Query DataSets for GSM3523511
Status Public on Apr 09, 2019
Title S17_PB
Sample type SRA
 
Source name peripheral blood
Organism Homo sapiens
Characteristics cell type: whole blood
rin: 9.1
age: 60.8
Sex: F
race: NHW
packyears: 46.5
smoke: Former
copd: cont
fev1pp: 108.3
fev1_fvc: 0.82
bmi: 31.72
pctemph: 0.285715
perc15: 96
adj_density: 94.678130038
pi10: 1.72
awt: 0.6588944197
wallareapct: 36.48347095
wbc: 7.9
neutrophl_pct: 60
lymphcyt_pct: 31
monocyt_pct: 6
eosinphl_pct: 2
Extracted molecule total RNA
Extraction protocol Whole blood was collected in a PaxGene RNA tube on the day of bronchoscopy.
Total RNA was extracted using the AllPrep kit (Qiagen, Valenica, CA). RNA quality was assessed on a BioAnalyzer (Agilent, Santa Clara, CA). Extracted RNA samples with RNA integrity number (RIN) greater than six and a concentration greater than or equal to 20 μg/ul were sequenced.
Libraries were QCed by quantification with picogreen, size analysis on an Agilent Bioanalyzer (Agilent, Santa Clara, CA) and qPCR quantitation against a standard curve. Paired end reads with nominal 75 bp length were generated on an Illumina HiSeq 2500 flow cell. Sequencing was performed to an average depth of 20 million reads.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description gene_count_table.tsv
Data processing The quality control pipeline included FastQC and RNA-SeQC. Adapter trimming was performed using Skewer.
STAR aligner version 2.4.0h was used to map the reads to the GRCH38 genome reference.
The Python framework HTSeq was used to produce gene-level counts with the Ensembl version 81 gene annotation.
The samples retained for analysis each had more than 7 million total reads, and greater than 70% of reads mapped to the reference genome, with less than 10% of R1 reads in the sense orientation.
Only data for genes mapped to autosomal chromosomes were retained, leaving counts for 54,243 of the 65,988 transcripts available for analysis.
Genome_build: GRCH38
Supplementary_files_format_and_content: Gene-level counts
 
Submission date Dec 20, 2018
Last update date Apr 09, 2019
Contact name Jarrett Morrow
Organization name Brigham and Women's Hospital
Department Channing Division of Network Medicine
Street address 181 Longwood Ave.
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL16791
Series (1)
GSE124180 RNA-sequencing across three matched tissues highlights gene expression signatures in COPD
Relations
BioSample SAMN10620185

Supplementary data files not provided
Raw data not provided for this record
Processed data are available on Series record

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