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| Status |
Public on Nov 30, 2018 |
| Title |
polII_Dox_DRB10m_1 |
| Sample type |
SRA |
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| Source name |
HEK293 Flp-in T-REx pcDNA5 Avitag TFIISDN
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| Organism |
Homo sapiens |
| Characteristics |
growth conditions: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline, +DRB
antibody: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)
molecule: Genomic DNA
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| Treatment protocol |
TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs, followed by treatment with 100 uM DRB for 3 hrs, cells were washed with PBS and incubated in -DRB media for 10 min
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| Growth protocol |
DMEM 10% FCS, +200 ug/ml hygromycin, +6.5 ug/ml blasticidin, +pen/strep
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| 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, SPRI bead purification of ~200bp fragments, and amplification (15-18 cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Chromatin IP of RNA pol II
polII_Dox_DRB10m.bw
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| Data processing |
Libraries that were sequenced multiple times were combined into a single fastq file
Adapters were trimmed using cutadapt version 1.16
Reads were aligned to the hg19 UCSC human genome (Feb. 2009) with Bowtie2 version 2.3.2 basepair. Samples containing a yeast spike-in were also aligned to sacCer3 (April 2011).
PCR duplicates were removed using Picard Tools version 2.18.7. Custom software was used to remove duplicates from NET-seq libraries: https://github.com/sheridar/TFIISdn_paper.
Read coordinates were centered assuming a fragment size of 90-180 bp
Genome_build: GRCh37/hg19 assembly or SacCer_Apr2011/sacCer3
Supplementary_files_format_and_content: BigWig
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| Submission date |
Sep 19, 2018 |
| Last update date |
Nov 30, 2018 |
| Contact name |
Ryan Sheridan |
| E-mail(s) |
[email protected]
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| Organization name |
University of Colorado Anschutz Medical Campus
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| Street address |
12801 East 17th Avenue
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| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE120201 |
Widespread backtracking by RNA pol II is a major effector of gene activation, 5’ pause release, termination and transcription elongation rate |
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| Relations |
| BioSample |
SAMN10093479 |
| SRA |
SRX4717785 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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