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| Status |
Public on Apr 03, 2017 |
| Title |
IM_SL_Rep3 |
| Sample type |
SRA |
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| Source name |
interstitial macrophage sea level
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: lung
tissue compartment: interstitial
cell type: macrophage
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| Treatment protocol |
mice remained at sea level or were exposed to simulated altitude of 18,000 feet
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mice lung was digested, macrophages were facs sorted and RNA was isolated using trizol extraction and qiagen Rneasy MinElute kit
RNA libraries were prepared for sequencing using standard Illumina protocols with Nugen ovation amplication kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Derived sequences were analyzed by applying a custom computational pipeline consisting of the open-source gSNAP, Cufflinks, and R for sequence alignment and ascertainment of differential gene expression (CITES). In short, reads generated were mapped to the mouse genome (mm10) by gSNAP, expression (FPKM) derived by Cufflinks, and differential expression analyzed with ANOVA in R.
Genome_build: mm10
Supplementary_files_format_and_content: csv files containing average FKPM data (3 samples) for control sea level macrophage and hypoxic macrophage counterpart (IM D4 or D14, AM D4 or D14). Fold change, P value, q value and individual FKPM values for each sample also listed
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| Submission date |
Oct 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
steve C pugliese |
| E-mail(s) |
steven.pugliese@ucdenver.edu
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| Phone |
2158808239
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| Organization name |
University of Colorado
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| Department |
Medicine
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| Lab |
Kurt Stenmark
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| Street address |
12700 East 19th Avenue
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| City |
denver |
| State/province |
CO |
| ZIP/Postal code |
80206 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE87602 |
Activation of Lung Macrophages in Hypoxic Pulmonary Hypertension |
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| Relations |
| BioSample |
SAMN05861147 |
| SRA |
SRX2209868 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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