|
| Status |
Public on Aug 31, 2024 |
| Title |
p53KO, Day 21 rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
MCF7
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
cell type: breast cancer cell
genotype: TP53 knockout
treatment: abemaciclib
|
| Treatment protocol |
MCF7 cells were treated with 50 nM abemaciclib (Selleck) for indicated days.
|
| Growth protocol |
MCF7 cells were maintained in DMEM supplemented with 10% fetal bovine serum and antibiotics in humidified atmosphere with 5% CO2 at 37℃.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by using Rneasy Mini kit (Qiagen).
NEBNext Ultra II RNA Library Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X |
| |
|
| Data processing |
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file.
Assembly: GRCh38
Supplementary files format and content: Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file.
|
| |
|
| Submission date |
Jul 16, 2024 |
| Last update date |
Aug 31, 2024 |
| Contact name |
Rei Kudo |
| E-mail(s) |
reikudobc@gmail.com
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
HOPP
|
| Lab |
Chandarlapaty Lab
|
| Street address |
417 E 68th Street
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL34281 |
| Series (1) |
| GSE272312 |
Effect of abemaiclicb and deletion of TP53 on gene expression in MCF7 cells at different timepoints |
|
| Relations |
| BioSample |
SAMN42513260 |
| SRA |
SRX25338962 |
