|
| Status |
Public on May 24, 2017 |
| Title |
ChIP-seq H3 Cter R749H pol II |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 Flp-in T-REx pcDNA5 Rpb1 Amr R749H
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
growth conditions: DMEM 10% FCS,+hygromycin+blasticidin+doxycycline+a-amanitin
antibody: rabbit anti H3 Cter (Zhang et al EMBO J, 24: 2379, 2005 )
|
| 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 |
genomic DNA |
| Extraction protocol |
cross-linked Chromatin was sonicated with a Bioruptor
1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, gel purification of ~200bp fragments, and amplification (18cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Chromatin IP against histone H3 Cter
|
| Data processing |
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 |
SAMN06758186 |
| SRA |
SRX2737639 |
