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| Status |
Public on Apr 09, 2019 |
| Title |
S6_BAL |
| Sample type |
SRA |
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| Source name |
bronchoalveolar lavage
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| Organism |
Homo sapiens |
| Characteristics |
cell type: alveolar macrophage
rin: 8.9
age: 69.5
Sex: F
race: AA
packyears: 50.5
smoke: Current
copd: cont
fev1pp: 108.1
fev1_fvc: 0.73
bmi: 32.66
pctemph: 0.89709
perc15: 105
adj_density: 84.074229175
pi10: 2.86
awt: 1.1585167947
wallareapct: 60.629061383
wbc: 7.5
neutrophl_pct: 38
lymphcyt_pct: 50
monocyt_pct: 8
eosinphl_pct: 3
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| Extracted molecule |
total RNA |
| Extraction protocol |
Bronchoalveolar lavage (BAL) was performed in two lung segments with 60ml of normal saline in each segment, and the BAL fluid obtained from each subject was pooled.
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 |
SAMN10620212 |
| Supplementary data files not provided |
| Raw data not provided for this record |
| Processed data are available on Series record |
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