|
| Status |
Public on Oct 31, 2018 |
| Title |
NPC_CHD7_29_A |
| Sample type |
SRA |
| |
|
| Source name |
Neural progenitor cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: CHD7 shRNA#29
replicate #: 1
|
| Treatment protocol |
Cells were infected with lentivirus containing shRNA targeting CHD7 and grown for 72 hours with puromycin to select for the plasmid.
|
| Growth protocol |
Cells were grown in DMEM/F12, 1% pen/strep, 1% sodium pyruvate and 10ug recombinant EGF and FGF. Maintained at 37C with 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted with TRIzol.
NEBNext Ultra RNA Library Prep Kit for Illumina with polyA selection
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
adapter trimming using trimgalore v0.4.1
fastqc v0.10.1 for quality score assessment
star version v2,5,2b for alignment
ht-seq-gene v 0.5.3 to consoldiate reads to features
Genome_build: hg37
Supplementary_files_format_and_content: raw count table at the gene level for all 12 samples
|
| |
|
| Submission date |
Sep 08, 2018 |
| Last update date |
Oct 31, 2018 |
| Contact name |
Sara Cooper |
| E-mail(s) |
sjcooper@hudsonalpha.org
|
| Phone |
256-327-9491
|
| Organization name |
HudsonAlpha Institute
|
| Street address |
601 Genome Wau
|
| City |
Huntsville |
| State/province |
AL |
| ZIP/Postal code |
35806 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE119688 |
CHD7 is Suppressed in the Perinecrotic/Ischemic Microenvironment and is a Novel Regulator of Angiogenesis |
|
| Relations |
| BioSample |
SAMN10022652 |
| SRA |
SRX4662934 |
