|
| Status |
Public on Aug 01, 2024 |
| Title |
MCF7_WT_med |
| Sample type |
SRA |
| |
|
| Source name |
MCF-7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
cell type: breast cancer cell line
genotype: WT
treatment: medium
|
| Growth protocol |
Cells were cultured in DMEM (Gibco) or RPMI-1640 medium (Gibco), supplemented with 10% heat-inactivated fetal bovine serum (Sigma) and 50 units/ml penicillin-streptomycin (Gibco).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated with the Nucleospin RNA kit (Macherey-Nagel). cDNA conversion of mRNA was performed with AMV Reverse Transcriptase (Roche) and OdT primers.
RNA-sequencing library preparation was performed with TruSeq Stranded Total RNA with Ribo-Zero Gold
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Quality control of the RNA-sequencing reads as well as adapter clipping, read alignment and gene expression quantification was done using the BIOWDL RNAseq pipeline v4.0.0 (https://doi.org/10.5281/zenodo.3975552).
Reads were aligned to the human reference genome (hg38 build) using STAR v2.7.5a, followed by gene expression quantification by htseq-count v0.12.4.
For expression quantification gencode v35 (corresponding to Ensembl 101) was used for gene annotation.
Assembly: human reference genome (hg38 build)
Supplementary files format and content: Tab-delimited text file containing the raw counts per sample
|
| |
|
| Submission date |
Dec 12, 2023 |
| Last update date |
Aug 01, 2024 |
| Contact name |
Tom van Wezel |
| Organization name |
Leiden University Medical Center
|
| Department |
Pathology
|
| Street address |
Albinusdreef 2
|
| City |
Leiden |
| ZIP/Postal code |
2333 ZA |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE250000 |
Bulk RNA-sequencing of transduced colorectal cancer cell line HCT-116 and breast cancer cell line MCF-7 overexpressing full-lenght p53β or p53β-stop-lost. |
|
| Relations |
| BioSample |
SAMN38790901 |
| SRA |
SRX22868006 |
