|
| Status |
Public on Mar 03, 2022 |
| Title |
231-P KD-3 |
| Sample type |
SRA |
| |
|
| Source name |
Breast cancer cell-line MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
treatment: PELP1 shRNA
shRNA: Stable tranfection were generated using puromycin selection
|
| Growth protocol |
MDA-MB-231 control-shRNA and PELP1-shRNA cells were cultured in RPMI medium supplemented with 10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from MDA-MB-231 control-shRNA and PELP1-shRNA cells were isolated using RNeasy mini kit (Qiagen). Illumina TruSeq RNA Sample preparation and sequencing was done using UT Health San Antonio sequencing core protocol.
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Illumina bcl2fastq software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. The aligned BAM files sorted (SAMTools) and then processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format. The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count
|
| |
|
| Submission date |
Dec 16, 2021 |
| Last update date |
Mar 03, 2022 |
| Contact name |
YI ZOU |
| E-mail(s) |
zou@uthscsa.edu
|
| Organization name |
UTHSA-GCCRI
|
| Street address |
8403 Floyd Curl Drive
|
| City |
SAN ANTONIO |
| State/province |
TX |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE191066 |
Global genomic and proteomic analysis of TNBC cells identifies the critical role of PELP1 in ribosome biogenesis |
|
| Relations |
| BioSample |
SAMN24139215 |
| SRA |
SRX13427224 |
