NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4521164 Query DataSets for GSM4521164
Status Public on May 07, 2021
Title 100 nM 48 h
Sample type SRA
 
Source name breast cancer cell
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
treatment: PCI-24781
treatment duration: 48h
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 SAMN14848421
SRA SRX8287531

Supplementary file Size Download File type/resource
GSM4521164_100_nM_48h.txt.gz 407.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap