|
| Status |
Public on Feb 04, 2021 |
| Title |
PARP 7 KD with SiRNA 3 Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
PARP 7 KD with siRNA 3
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: OVCAR4
sirna: PARP7 siRNA3
|
| Treatment protocol |
OVCAR4 cells were transfected with control or PARP7-specific siRNAs at a final concentration of 30 nM in 10 cm diameter culture dishes. Twenty-four hours later, the cells were collected and plated at a density of 20,000 cells per well in a 24-well plate.
|
| Growth protocol |
OVCAR4 cells were purchased from the American Type Cell Culture (ATCC). They were maintained in RPMI (Sigma-Aldrich, R8758) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Fresh cell stocks were regularly replenished from original stocks and tested for mycoplasma.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Two biological replicates of total RNA were isolated from each siRNA-mediated knockdown. Total RNA was isolated using the RNeasy kit (Qiagen, 74106) according to the manufacturer’s instructions. The total RNA was then enriched for polyA+ RNA using Dynabeads Oligo(dT)25 (Invitrogen).
The polyA+ RNA was then used to generate strand-specific RNA-seq libraries as described previously (Zhong et al., 2011). The RNA-seq libraries were subjected to QC analyses (final library yield, and the size distribution of the final library DNA fragments) and sequenced using an Illumina HiSeq 2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
PARP7_SiRNA3_R2
polyA-RNA-seq
processed data file: SiRNA3.Forward.bw
processed data file: SiRNA3.Reverse.bw
|
| Data processing |
The RNA-seq reads were aligned to the hg38 human reference genome using TopHat a fast splice junction mapper for RNA-Seq reads using the ultra high-throughput short read aligner Bowtie (Langmead et al, 2009).
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and bigwig files were generated to for presentation as browser tracks using custom R scripts.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.bw: BigWig files
|
| |
|
| Submission date |
Jun 26, 2020 |
| Last update date |
Feb 04, 2021 |
| Contact name |
W. Lee Kraus |
| E-mail(s) |
lee.kraus@utsouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd.
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-8511 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE153395 |
Substrate Identification Using a Chemical Genetics Approach Reveals a Role for PARP-7-Mediated MARylation in Controlling Microtubule Stability in Ovarian Cancer Cells |
|
| Relations |
| BioSample |
SAMN15390197 |
| SRA |
SRX8624935 |
