|
| Status |
Public on Sep 11, 2017 |
| Title |
LREXJQ1_rep3_RNASeq |
| Sample type |
SRA |
| |
|
| Source name |
LREXJQ1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LREX' tumor
treatment: JQ1
|
| Growth protocol |
Standard growth conditions as outlined in methods of paper
|
| Extracted molecule |
total RNA |
| Extraction protocol |
ChIP protocol outlined in methods of paper; Tumors harvested and flash frozen in liquid nitrogen, RNA was extracted via lysing in MP Biomedical Lysing Matrix tubes in homogenizer, then Trizol extraction, followed by cleanup using Qiagen RNEasy columns
ChIP-seq and RNA-seq libraries prepared using standard KAPA Hyper Library and Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
counts_RNASeq.txt
|
| Data processing |
For ChIPSeq, reads were aligned to the human genome (hg19) using Bowtie (v1.1.1) with default parameters and the results were converted to bam files by Samtools. Reads mapped to a single genomic location were kept and redundant ones were filtered out.
For ChemSeq, reads were aligned to the human genome (hg19) using Bowtie (v1.1.1) with default parameters and the results were converted to bam files by Samtools. Reads mapped to a single genomic location were kept and redundant ones were filtered out.
For RNASeq, reads were aligned to the human genome (hg19) using STAR (v2.4.2a). The number of RNA-seq fragments mapped to each gene was determined for all genes in the GENCODE database (v19) using the HTSeq.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIPSeq and ChemSeq, Tdf files were generated from the bam files by Igvtools with default parameters for visualization in IGV. For RNASeq, counts were generated by HTSeq.
|
| |
|
| Submission date |
Sep 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Deyou Zheng |
| E-mail(s) |
deyou.zheng@einstein.yu.edu
|
| Organization name |
Albert Einstein College of Medicine
|
| Street address |
1301 Morris Park Ave
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE103449 |
Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer |
|
| Relations |
| BioSample |
SAMN07604380 |
| SRA |
SRX3159255 |
