|
| Status |
Public on Jun 09, 2014 |
| Title |
RNAPolII.shCTRL |
| Sample type |
SRA |
| |
|
| Source name |
HEK293 cells, RNAPolII.shCTRL
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
chip antibody: RNA polymerase II
treatment: control shRNA
|
| Growth protocol |
HEK293 cells were infected with lentiviral supernatant carrying shRNA specific for RECQL5 or CTRL shRNA. Once KD efficiency was assessed by Western Blot, cells were processed for RNA Pol II. ChIP-Seq. HEK293T-rex cells were transfected with the pcDNA4/TO-RECQL5 plasmid, carrying a full length version of RCQL5 under a Doxycycline inducible promoter. Once the doses of Doxycycline for the overexpression where assessed by Western Blot the samples were processed for RNA Pol II ChIP-Seq.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked with formaldehyde 1% final. Nuclei were extracted in low salt conditions and burst in high salt before shearing the DNA to reduce the size to 300-400 bp and performing ChIP with an RNA Pol II specific antibody.
DNA libraries were prepared according to Illumina's instructions and run on a GAIIX sequencer
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Processed data file: RNAPolII.shCTRL_peaks.txt
|
| Data processing |
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie 0.12.7 with default parameters appart from the “--best” option.
BAM files representing the same sample were merged and reads mapping to regions blacklisted for mappability by the Encode project were removed.
Peaks were called against an IgG control using MACS v1.4.2 with the following settings: --gsize (hs), --tsize (36), --mfold (8,30), --pvalue (0.00001)
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files detailing the peaks called by MACS (see supplementary files linked to Series record)
|
| |
|
| Submission date |
Jul 18, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard James Mitter |
| Organization name |
The Francis Crick Institute
|
| Department |
Bioinformatics & Biostatistics
|
| Street address |
1 Midland Road
|
| City |
London |
| State/province |
LONDON |
| ZIP/Postal code |
NW1 1AT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL10999 |
| Series (2) |
| GSE49008 |
Genome wide profiling of RNA Polymerase II upon knock-down or overexpression of RECQL5 |
| GSE49134 |
RECQL5 Controls Transcript Elongation and Suppresses Transcription-Associated Genome Instability |
|
| Relations |
| BioSample |
SAMN02260307 |
| SRA |
SRX326416 |
