|
| Status |
Public on Jul 04, 2019 |
| Title |
Ctrl_rep_2 |
| Sample type |
SRA |
| |
|
| Source name |
Human pulmonary artery endothelial cells (hPAECs)
|
| Organism |
Homo sapiens |
| Characteristics |
passages: 3-5
cell type: Human pulmonary artery endothelial cells (hPAECs)
condition: Ctrl
|
| Growth protocol |
PAECs, at passage number 3–5 from control subjects, infected by lentivirus expressing control shGFP or shBmpr2 to silent BMPR2 signaling were treated with control AdGfp vector or AdAlox5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN).
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) and subjected to sequencing on 1–2 Illumina HiSeq 2000 lanes to obtain an average of approximately 100-150 million uniquely mapped reads for each sample (Stanford Personalized Medicine Sequencing Core).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
RNA-seq sample processing was performed according to Bulk RNA-seq pipeline as part of the ENCODE Uniform Processing Pipeline.
Paired end reads were mapped to human genome hg38 using STAR program.
The quantification of genes and transcripts is done with the RSEM program
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited files generated by RSEM detailing quantification of genes in expected count, TPM, FPKM.
|
| |
|
| Submission date |
Jul 03, 2019 |
| Last update date |
Jul 07, 2019 |
| Contact name |
Peter Kao |
| E-mail(s) |
[email protected]
|
| Organization name |
Stanford University School of Medicine
|
| Department |
Pulmonary and Critical Care Medicine
|
| Street address |
300 Pasteur Drive
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE133749 |
Human pulmonary artery endothelial cells (hPAECs) with downregulated BMPR2 signaling demonstrate a unique gene expression signature after exposure to overexpression of AdAlox5 |
|
| Relations |
| BioSample |
SAMN12207080 |
| SRA |
SRX6401685 |
