Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Kdm4a

Cell type

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

Attributes by original data submitter

Sample

source_name
ESCs, Jmjd2a, OHT, Jmjd2a ChIP
cell type
Embryonic stem cell (ESC) line
strain/background
C57Bl/6
genotype/variation
Jmjd2a(f/f);Rosa26::CreERT2
treatment
OHT
chip antibody
anti-Jmjd2a (Cell Signaling Technology, #5328)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP) with antibodies specific for Jmjd2a, H3K9me3, H3K36me3, H3K4me3 or H3. Adaptor-ligated libraries were generated from precipitated DNA using the NEBNext® Ultra DNA library kit for Illumina (New England Biolabs E7370L), subjected to gel-selection and PCR-amplified (15x PCR cycles) using indexed multiplex primers for Illumina sequencing (New England Biolabs E7335), and sequenced on a HiSeq 2000 using 50bp single-end sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
35403936
Reads aligned (%)
80.8
Duplicates removed (%)
16.0
Number of peaks
513 (qval < 1E-05)

mm9

Number of total reads
35403936
Reads aligned (%)
80.5
Duplicates removed (%)
16.0
Number of peaks
541 (qval < 1E-05)

Base call quality data from DBCLS SRA