|
| Status |
Public on Apr 28, 2022 |
| Title |
A673 BARD1 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
A673 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: BARD1 siRNA
replicate: 1
|
| Treatment protocol |
30nM BARD1siRNA SMART pool (Dharmacon) or non-targeting control siRNA (Dharmacon) was transfected into cells using Lipofectamine RNAiMAX and optiMEM media. RNA was extracted at hour 72 post-transfection.
|
| Growth protocol |
cells cultured in RPMI with 10%FBS at 37C and 5% CO2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Quagen RNeasy PLUS mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
FastQC v0.11.5 was used to perform QC of fastq files
fastp v0.20.0 was used for adapter and quality trimming, --qualified_quality_phred 15 --length_required 20
transcript quantification was performed using salmon v0.13.1, --validateMappings --rangeFactorizationBins 4 --gcBias --seqBias
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing counts and transcripts per million
|
| |
|
| Submission date |
Aug 24, 2021 |
| Last update date |
Apr 28, 2022 |
| Contact name |
Kelly M Bailey |
| Organization name |
University of Pittsburgh
|
| Department |
Pediatrics
|
| Street address |
Rangos Research Building 4401 Penn Ave
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15224 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE182677 |
BARD1 loss enhances GBP1 expression and tumor sensitivity to DNA damage in Ewing sarcoma |
|
| Relations |
| BioSample |
SAMN20960426 |
| SRA |
SRX11895992 |
