|
| Status |
Public on May 24, 2017 |
| Title |
RNA pol II tNET-seq Rpb1 H1108Y Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr H1108Y
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
growth conditions: DMEM 10% FCS,+hygromycin+blasticidin+doxycycline+a-amanitin
antibody: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)
|
| Treatment protocol |
Amr Rpb1 was induced with doxycycline (2.0 mg/ml) for 12-16 hr then treated with a-amanitin (2.5 mg/ml) for a further 42 hr before cross-linking and harvesting for ChIP-seq.
|
| Growth protocol |
Rpb1 WT and mutant cells were grown in DMEM 10% FCS, 200μg/ml hygromycin B, 6.5μg/ml blasticidin, and pen/strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cross-linked Chromatin was sonicated with a Bioruptor
IP's were prepared from DNAseI solublilized nuclear extracts (~1.5X 10E7 cells). RNA was purified by Trizol extraction and processed using the KAPA RNA-seq kit (#07962169001) to create stand-specific random-primed libraries
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
nascent nuclear RNA
Anti-pol II tNET-seq
processed data file: H1108Y_tNetSeq_merge_negative_bedgraph.tdf, H1108Y_tNetSeq_merge_positive_bedgraph.tdf
|
| Data processing |
Library strategy: tNET-Seq
Single-end 50 base reads (after removing barcodes) or 125 base reads (after removing barcodes and trimming adaptor sequences) were mapped to the hg19 UCSC human genome or sacCer3 yeast genome with Bowtie version 0.12.5 for ChIP-seq and with Hisat2 version 2.0.4 for t-NET-seq
Genome_build: GRCh37/hg19 assembly or SacCer_Apr2011/sacCer3
Supplementary_files_format_and_content: bigwig or TDF format
|
| |
|
| Submission date |
Apr 14, 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 |
GPL11154 |
| Series (1) |
| GSE97827 |
RNA pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD phosphorylation and transcriptional direction |
|
| Relations |
| BioSample |
SAMN06758138 |
| SRA |
SRX2737677 |
