|
| Status |
Public on Oct 30, 2019 |
| Title |
293FlpIN_pcDNA5_Xrn2D235A_DRB_WashOut_T5_PolII |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 Flp-in T-REx pcDNA5 HA-Xrn2 D235AshXrn2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
growth conditions: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline, +DRB
antibody: Rabbit anti pan CTD (Schroeder et al Genes Dev. 14:2435, 2000)
treatment: Xrn2 D235A expression was induced with 2ug/ml doxycycline for 24 hrs, DRB (100mM) was added for 2.5 hr. then washed out for 5 min
|
| Growth protocol |
DMEM 10% FCS, +200 ug/ml hygromycin, +6.5 ug/ml blasticidin, +pen/strep
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cross-linked chromatin was sonicated with a Bioruptor or Covaris Ultrasonicator
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.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Pol II ChIP-seq
|
| 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.
Read coordinates were centered assuming a fragment size of 90-180 bp
Genome_build: GRCh37/hg19 assembly
Supplementary_files_format_and_content: BigWig
|
| |
|
| Submission date |
Jul 12, 2019 |
| Last update date |
Oct 31, 2019 |
| Contact name |
David Bentley |
| E-mail(s) |
David.Bentley@ucdenver.edu
|
| 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 |
GPL16791 |
| Series (1) |
| GSE134198 |
Control of RNA pol II speed by PNUTS-PP1 and Spt5 dephosphorylation facilitates termination by a “sitting duck torpedo” mechanism |
|
| Relations |
| BioSample |
SAMN12261740 |
| SRA |
SRX6435357 |
