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| Status |
Public on Apr 09, 2019 |
| Title |
S17_PB |
| Sample type |
SRA |
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| Source name |
peripheral blood
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| 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
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
gene_count_table.tsv
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| 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
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| Submission date |
Dec 20, 2018 |
| Last update date |
Apr 09, 2019 |
| Contact name |
Jarrett Morrow |
| Organization name |
Brigham and Women's Hospital
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| Department |
Channing Division of Network Medicine
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| Street address |
181 Longwood Ave.
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE124180 |
RNA-sequencing across three matched tissues highlights gene expression signatures in COPD |
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| 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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