|
| Status |
Public on Sep 07, 2023 |
| Title |
PML knockdown, MDA231, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cell type: Human breast cancer
genotype: PML knockdown
treatment: shPML
|
| Treatment protocol |
Silencing of PML was performed via lentiviral shRNA
|
| Growth protocol |
DMEM, 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNAeasy mini kit (Qiagen)
RNA libraries were prepared using the TruSeq stranded mRNA protocol (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
X5_shpml
|
| Data processing |
Base-calling was performed on NovaSeq 6000 Illumina machine.
Sequencing adapters were removed using trimmomatic v0.39.
Trimmed sequence reads were mapped to the human genome assembly GRCh38 (hg38) using the STAR aligner v2.5.3a.
Annotation of genomic features was performed using the featureCounts tool v1.6.4 using the GENCODE v31 Gene transfer format (GTF). Differential gene expression was evaluated in R/BioConductor using the DeSeq2 package.
Assembly: hg38
Supplementary files format and content: tab delimited text of normalized counts
|
| |
|
| Submission date |
Feb 25, 2023 |
| Last update date |
Sep 07, 2023 |
| Contact name |
Rosa Bernardi |
| E-mail(s) |
bernardi.rosa@hsr.it
|
| Organization name |
San Raffaele Scientific Institute
|
| Street address |
via Olgettina 60
|
| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE226111 |
PML modulates epigenetic composition of chromatin to regulate expression of pro-metastatic genes in triple-negative breast cancer [RNA-seq] |
| GSE226210 |
PML modulates epigenetic composition of chromatin to regulate expression of pro-metastatic genes in triple-negative breast cancer |
|
| Relations |
| BioSample |
SAMN33443339 |
| SRA |
SRX19503560 |
