|
| Status |
Public on Sep 14, 2018 |
| Title |
Hap1_NELFA_deg_TMP_control_PolII_151203_R1 |
| Sample type |
SRA |
| |
|
| Source name |
Hap1 NELFA-degron (Sheridan and Bentley Biotechniques 60:69-74, 2016)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line/genotype: Hap1 NELFA-degron (Sheridan and Bentley Biotechniques 60:69-74, 2016)
spike in: NA
growth conditions: IMDM 10% FCS, 10mM trimethoprim (note NELFA degron not induced)
antibody: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)
experiment: Chromatin IP against RNA pol II
|
| Treatment protocol |
In some experiments HCT116 were treated with 10mM NM-PP1 for 24 hr before cross-linking and harvesting for ChIP-seq, this drug treament should have no effect on these cells.
|
| Growth protocol |
HCT116 cells were grown in McCoy's medium 10% FCS 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 4000 |
| |
|
| Data processing |
Single-end 50 base reads (after removing barcodes) or 151 base reads (after removing barcodes) were mapped to the hg19 UCSC human genome with Bowtie2 version 2.3.2 (trim from 3 prime to 50 base pairs)
Genome_build: GRCh37/hg19 assembly
|
| |
|
| Submission date |
Jul 12, 2018 |
| Last update date |
Sep 16, 2018 |
| Contact name |
David Bentley |
| E-mail(s) |
[email protected]
|
| Phone |
3037243237
|
| Organization name |
UCD AMC
|
| Department |
BMG
|
| Lab |
Bentley
|
| Street address |
12801 E. 17th Ave, RC1 So. RM 10401D
|
| City |
Aurora |
| State/province |
Colorado |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE117006 |
Dynamic turnover of paused pol II complexes at human promoters |
|
| Relations |
| BioSample |
SAMN09650968 |
| SRA |
SRX4385559 |
