|
| Status |
Public on May 07, 2021 |
| Title |
100 nM 24 h |
| Sample type |
SRA |
| |
|
| Source name |
breast cancer cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
treatment: PCI-24781
treatment duration: 24h
dose: 100 nM
|
| Treatment protocol |
Cells were treated for 24h or 48h in adherent conditions with 100 nM and 200 nM PCI-24781 or DMSO.
|
| Growth protocol |
MDA-MB-231 cells were cultured in a humidified incubator equilibrated with 5% CO2 at 37 °C. The media (Dulbecco Modified Eagle Medium (DMEM)) was supplemented with 10% fetal bovine serum (FBS), 100 units/mL penicillin, and 100 mg/mL streptomycin
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Complete Genomics |
| |
|
| Data processing |
Typically, base call quality diminishes toward the end of a read. This is characteristic to first- and second-generation sequencing technologies (Sanger, Illumina, SOLiD, 454)
SOAPnuke, a filtering software independently developed by BGI, is used for filtering.
We use Bowtie2 to align the clean reads to the genome sequence, and then use RSEM to calculate the gene expression level of each sample. RSEM is a software package for RNA-seq reads to calculate the expression of genes and transcripts.
Abundance estimates were reported in raw read counts or in FPKM (fragments per thousand nucleotides per million mapped reads).
Genome_build: hg19_ucsc
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
|
| |
|
| Submission date |
May 07, 2020 |
| Last update date |
May 08, 2021 |
| Contact name |
yan wang |
| E-mail(s) |
yanwang@tmu.edu.cn
|
| Organization name |
National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences
|
| Street address |
17 panjiayuan nanli, chaoyang district, Beijing, China
|
| City |
beijing |
| ZIP/Postal code |
100021 |
| Country |
Zimbabwe |
| |
|
| Platform ID |
GPL23525 |
| Series (1) |
| GSE150038 |
HDAC inhibitor PCI-24781 inhibits metastasis in breast cancer |
|
| Relations |
| BioSample |
SAMN14848422 |
| SRA |
SRX8287530 |
