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| Status |
Public on Sep 18, 2015 |
| Title |
RNA_Compound A 2h_1 |
| Sample type |
SRA |
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| Source name |
RNA_Compound A 2h_1
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| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
cancer: Breast adenocarcinoma
type: TNBC
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| 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.
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| Growth protocol |
The TNBC cell line MDA-MB-231 were obtained from the American Type Culture Collection, and cultured in DMEM 10% FBS.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
RNA-seq replicate 1
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| 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.
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| Submission date |
May 31, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Xun Lan |
| E-mail(s) |
xlan@stanford.edu
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| Phone |
7738345917
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| Organization name |
Stanford University
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| Department |
Genetics
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| Lab |
Pritchard's Lab
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| Street address |
318 Campus Dr. Room S240
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE56022 |
Ligand-dependent genomic function of glucocorticoid receptor in triple-negative breast cancer |
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| Relations |
| BioSample |
SAMN03753691 |
| SRA |
SRX1044407 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1700780_CpdA_2h_S1_RPKM.txt.gz |
131.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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