|
| Status |
Public on Aug 01, 2017 |
| Title |
RNAseq HCT116 Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
genotype: wildtype
|
| Treatment protocol |
WT HCT116 and Cdk7as cells were treated with 10mM NM-PP1 for 24 hr before cross-linking and harvesting for ChIP-seq or RNA-seq
|
| Growth protocol |
McCoy's 10% FCS, 10mM NM-PP1, 24hr
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ribosomal RNA was removed using the NEB ribosome removal kit and libraries were prepared using the NEB ultra directional kit, with RNA fragmentation for 8 min and 15 PCR cycles.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
rRNA depleted total RNA
|
| Data processing |
Single-end 50 base reads (after removing barcodes) or 151 base reads (after removing barcodes and trimming adaptor sequences) were mapped to the hg19 UCSC human genome with Bowtie version 0.12.5 for ChIP-seq and with Hisat2 version 2.0.4 for RNA-seq
Genome_build: GRCh37/hg19 assembly
Supplementary_files_format_and_content: bigwig files for ChIP-seq, TDF files for RNA-seq
|
| |
|
| Submission date |
Jun 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
David L. Bentley |
| E-mail(s) |
david.bentley@ucdenver.edu
|
| Organization name |
U. Colorado School of Medicine
|
| Department |
Biochemistry and Mol. Genetics
|
| Street address |
12801 E. 17th Ave
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE100040 |
Human TFIIH kinase CDK7 regulates transcription-associated epigenetic modification |
|
| Relations |
| BioSample |
SAMN07247116 |
| SRA |
SRX2922520 |
