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Sample GSM1820485 Query DataSets for GSM1820485
Status Public on Aug 20, 2015
Title PIN_RNB_IP_E_PR3
Sample type SRA
 
Source name PIN_RNB DIS3 cells RNA Pol II CHIP replicate 3
Organism Homo sapiens
Characteristics cell type: HEK293
genotype: PIN RNB mutant 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 SAMN03856970
SRA SRX1092991

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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