Sample information curated by ChIP-Atlas

Antigen

Antigen Class
RNA polymerase
Antigen
RNA polymerase II

Cell type

Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA

Attributes by original data submitter

Sample

source_name
Embryonic Stem Cell
cell line
J1
antibody
3e10-5, Chromotek
genotype/variation
Taf5l KO

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin Immunoprecipitation (ChIP) was performed as described previously (Kim et al., 2009; Das et al., 2014). For bioChIP reactions, streptavidin beads (Dynabeads MyOne Streptavidin T1- Invitrogen) were used for the precipitation of chromatin, and 2% SDS was applied for first washing step. All other steps were same as conventional ChIP protocol. 2-10 ng of purified ChIP DNA was used to prepare sequencing libraries, using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB) and NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) according to the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
30310582
Reads aligned (%)
95.6
Duplicates removed (%)
81.2
Number of peaks
1793 (qval < 1E-05)

mm9

Number of total reads
30310582
Reads aligned (%)
95.4
Duplicates removed (%)
81.4
Number of peaks
1780 (qval < 1E-05)

Base call quality data from DBCLS SRA