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Sample GSM1700778 Query DataSets for GSM1700778
Status Public on Sep 18, 2015
Title RNA_Dexamethasone 4h_1
Sample type SRA
 
Source name RNA_Dexamethasone 4h_1
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
cancer: Breast adenocarcinoma
type: TNBC
Treatment protocol For hormone responsive experiments, MDA-MB-231 cells were maintained in phenol red-free RPMI medium with 5% charcoal-stripped FBS for 3 days, and then treated with vehicle and different ligands.
Growth protocol The TNBC cell line MDA-MB-231 were obtained from the American Type Culture Collection, and cultured in DMEM 10% FBS.
Extracted molecule total RNA
Extraction protocol After treatment with 100 nM Dex, 10 uM CpdA or vehicle for 1 h, MDA-MB-231 cells were crosslinked with 1% formaldehyde for 10 min. Sonicated chromatin was enriched by immunoprecipatation with an anti-GR antibody. MDA-MB-231 cells were treated with 100 nM Dex, or 10 M CpdA for 2h and 4h, respectively. RNA was extracted using the RNeasy Mini Kit.
For ChIP-exo, T4 DNA polymerase, T4 PNK, and Klenow DNA Polymerase were used together for end polishing. The ligation step was performed with less reducing agent. Protein A Dynal magnetic beads were washed using modified RIPA buffer (50mM Tris-HCL pH 7.8, 1mM EDTA, 0.25% Na Deoxycholate, 1% NP-40, 0.5M LiCl). The library was amplified with only 10 or 12 PCR cycles, and prepared without gel-based size selection. For RNA-seq, libraries were constructed using the Illumina Truseq RNA Sample Prep Kit according to the manufacturer’s protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description RNA-seq replicate 1
Data processing ChIP-exo Alignment: Sequence reads were obtained and mapped to the human (hg19) genomes using the Bowtie. All reads mapping with two or fewer mismatches were retained. Only reads with unique mapping location is used for downstream analysis.
RNA-Seq: Read alignment was conducted using TopHat 2.0.13, and relative transcript abundances and differentially expressed genes were determined using Partek Genomics Suite (v6.6) with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files are in bigwig format. Each file is the reads counts of all 5 bp bins in the human genome for that sample.
 
Submission date May 31, 2015
Last update date May 15, 2019
Contact name Xun Lan
E-mail(s) xlan@stanford.edu
Phone 7738345917
Organization name Stanford University
Department Genetics
Lab Pritchard's Lab
Street address 318 Campus Dr. Room S240
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL16791
Series (1)
GSE56022 Ligand-dependent genomic function of glucocorticoid receptor in triple-negative breast cancer
Relations
BioSample SAMN03753689
SRA SRX1044405

Supplementary file Size Download File type/resource
GSM1700778_Dex_4h_S1_RPKM.txt.gz 131.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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