|
| Status |
Public on Aug 20, 2015 |
| Title |
WT_IP_E_PR3 |
| Sample type |
SRA |
| |
|
| Source name |
WT DIS3 cells RNA Pol II CHIP replicate 3
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HEK293
genotype: WT DIS3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments for RNA polymerase II were performed with MNase treatment and anti-RNA Polymerase II antibody (clone 8WG16, BioLegend).
KAPA Hyper Prep Kit (Kapa Biosystems)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNA Pol II ChIP
|
| Data processing |
Reads were mapped to the human reference genome hg19 (GRCh37) using the short read aligner program Bowtie2.
Quality control, duplicate read removal, filtering, extending and counting reads and visualization was perfrormed using custom scripts implementing elements of the SAMtools (version 0.1.19 and 1.2.1), BEDTools (version 2.23.0) and RseQC (version 2.6) packages.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Count table (tab seperated)
|
| |
|
| Submission date |
Jul 13, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Andrzej Dziembowski |
| E-mail(s) |
andrzejd@ibb.waw.pl
|
| Phone |
+48 22 5922033
|
| Organization name |
Institute of Biochemistry and Biophysics Polish Academy of Sciences
|
| Lab |
Laboratory of RNA Biology and Functional Genomics
|
| Street address |
Pawinskiego 5A
|
| City |
Warszawa |
| ZIP/Postal code |
02-106 |
| Country |
Poland |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE64332 |
Human DIS3 shapes the RNA polymerase II transcriptome degrading variety of unwanted transcripts. |
|
| Relations |
| BioSample |
SAMN03856964 |
| SRA |
SRX1092985 |
