|
| Status |
Public on Oct 06, 2023 |
| Title |
Sample.6 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB 231 cells, sip53
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB 231
cell type: TNBC cell line
genotype: TP53 knockdown
time: 48h
|
| Treatment protocol |
Silencing was performed for 48h.
|
| Growth protocol |
MDA-MB 231 TNBC cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen) with DNAse treatment.
RNA libraries for RNA-seq were prepared using Illumina TruSeq stranded mRNA library construction Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were trimmed for adapters, polyA read-through, and low-quality tails (quality <Q20) using BBDuk (version 37.02; sourceforge.net/projects/bbmap/).
Reads were subsequently aligned to the human reference genome (hg38) using STAR (version 2.7.3a; ref Dobin et al., 2013) with default parameters.
Raw gene counts were obtained using the featureCounts function of the Rsubread R package (version 2.0.1; ref Liao et al., 2014) and the Gencode gene annotation for hg38 genome.
Gene counts were normalized to counts per million mapped reads (cpm) using the edgeR package (version 3.28.1; ref Robinson et al., 2010); only genes with a CPM greater than 1 in at least 2 samples were further retained for differential analysis. Differential gene expression analysis was performed using the DESeq function of the DESeq2 package.
Assembly: hg38
Supplementary files format and content: Expression matrix of raw counts for each sample
|
| |
|
| Submission date |
Sep 29, 2022 |
| Last update date |
Oct 06, 2023 |
| Contact name |
Silvio Bicciato |
| E-mail(s) |
silvio.bicciato@unipd.it
|
| Phone |
+39-049-827-6108
|
| Organization name |
University of Padova
|
| Department |
Molecular Medicine
|
| Street address |
via U. Bassi 59/b
|
| City |
Padova |
| ZIP/Postal code |
35131 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE214493 |
Effect of silencing of p53 on gene expression in MDA-MB 231 TNBC cell line. [sip53] |
| GSE214494 |
Mutant p53 regulates serine-glycine synthesis and essential amino acids intake |
|
| Relations |
| BioSample |
SAMN31097753 |
| SRA |
SRX17757613 |
