|
| Status |
Public on Sep 27, 2020 |
| Title |
Bewo shGPX4 Exp B |
| Sample type |
SRA |
| |
|
| Source name |
Bewo shGPX4, following ferrostatin-1 withdrawal
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BeWo placental cell line
treatment: shGPX4
|
| Treatment protocol |
ferroptosis activation was induced by ferrostatin-1 withdrawal
|
| Growth protocol |
BeWo cells were maintained in F12K Kaighn’s modified medium (Gibco) supplemented with 10% bovine growth serum and ferrostatin-1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with Qiagen RNeasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols at Novogene Corporation
The samples were sequenced using PE150 sequencing on a Novaseq 6000 with S4 flowcell.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
fer3_geo.csv: Column "shGPX4.B"
|
| Data processing |
After evaluating the basecall quality and removing the adatpers, the reads were aligned to GRCh38 human genome assembly using the software STAR (version 2.5.2a).
Read count for each gene was calculated using STAR.
Additional data analysis steps: Libraries were normalized using the median of the ratios method implemented in R package DESeq2
Generalized linear model with Negative binomial distribution (implemented in DESeq2) was used to test if a gene is differentially expressed between shControl and shGPX4
P values of the tests were adjusted using the Benjamini & Hochberg's method to control the false discovery rate.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file that reports reads per gene for each sample
|
| |
|
| Submission date |
Mar 27, 2020 |
| Last update date |
Sep 27, 2020 |
| Contact name |
Ofer beharier |
| E-mail(s) |
behariero@mwri.magee.edu
|
| Phone |
4125968853
|
| Organization name |
MWRI
|
| Street address |
204 Craft Ave
|
| City |
Pittsburgh |
| ZIP/Postal code |
15213 |
| Country |
USA |
| |
|
| Platform ID |
GPL27644 |
| Series (1) |
| GSE147625 |
Sub-lethal stimulation of ferroptosis leads to trophoblast dysfunction |
|
| Relations |
| BioSample |
SAMN14468227 |
| SRA |
SRX8011964 |
