|
| Status |
Public on Nov 30, 2018 |
| Title |
NET_Dox_r1_2 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 Flp-in T-REx pcDNA5 Avitag TFIISDN
|
| Organism |
Homo sapiens |
| Characteristics |
growth conditions: DMEM 10% FCS, +hygromycin, +blasticidin, +doxycycline
antibody: Mouse 8WG16 anti-pol II (Thompson et al, 1990)
molecule: Nascent RNA
|
| Treatment protocol |
TFIISdn expression was induced with 2ug/ml doxycycline for 24 hrs
|
| Growth protocol |
DMEM 10% FCS, +200 ug/ml hygromycin, +6.5 ug/ml blasticidin, +pen/strep
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pol II-associated nascent RNA was isolated by IP
10-20ng of RNA was used with the Lexogen small RNA-seq kit (#052)
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
anti-pol II mNET-seq
NET_Dox_r1.F.bw
NET_Dox_r1.R.bw
|
| 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
|
| |
|
| Submission date |
Sep 19, 2018 |
| Last update date |
Nov 30, 2018 |
| Contact name |
Ryan Sheridan |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Street address |
12801 East 17th Avenue
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE120201 |
Widespread backtracking by RNA pol II is a major effector of gene activation, 5’ pause release, termination and transcription elongation rate |
|
| Relations |
| BioSample |
SAMN10093459 |
| SRA |
SRX4717814 |
