|
Status |
Public on Nov 01, 2017 |
Title |
S173_DX-Lung Dx Controls-140812_I270_FCC4MR9ACXX_L1_RHUMjlxTAAORRAAPEI-206 |
Sample type |
SRA |
|
|
Source name |
Blood
|
Organism |
Homo sapiens |
Characteristics |
tissue: blood sample_code: S173_DX subject: 173 disease state: Lung Dx Controls treatmentresult: NA time: DX timetonegativity: NA mgit: 50 xpert: 40 tgrv: NA
|
Extracted molecule |
total RNA |
Extraction protocol |
Paxgene RNA GlobinClear Globin transcript reduction followed by Illumina mRNA-Seq
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Alignment STAR version STAR_2.3.1d Sequenced reads were filtered for low-quality sequence and the presence of 'N's, then mapped to hg19 whole genome STAR_2.3.1d Junctions counts were calculated by using an in house script to count the number of reads mapped to all splice junctions in the genome Gene counts were calculated by usingHTSEQ to map the read counts to the gene names Genome_build: hg19 Supplementary_files_format_and_content: tab delimited file including the raw junction counts for all the detected junctions in the genome (number of reads mapped to the splice junctions in all samples) Supplementary_files_format_and_content: tab delimited file including the raw gene counts for all the detected genes in the genome
|
|
|
Submission date |
Nov 01, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Daniel Zak |
E-mail(s) |
danielzak000@gmail.com
|
Organization name |
2Seventy Bio
|
Lab |
Data Sciences
|
Street address |
188 East Blaine Street, Suite 300
|
City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98102 |
Country |
USA |
|
|
Platform ID |
GPL11154 |
Series (1) |
GSE89403 |
A blood RNA signature for predicting the treatment outcome in the Tuberculosis Treatment Response Cohort |
|
Relations |
BioSample |
SAMN05963153 |
SRA |
SRX2314877 |