Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K36me3

Cell type

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

Attributes by original data submitter

Sample

source_name
ES-E14TG2a
developmental stage
embryonic stem cell, blastocyst derived
chip antibody
H3K36me3
strain
E14
transfection
control siRNA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIPSeq,cells were cross-linked in 1% formaldehyde and lysate to extract nuclei. The chromatin was sonicated to 250 bp fragments. Lysates were cleared from sonicated nuclei and used for immunoprecipitation. For RNASeq, RNA was extracted according to TRIzol protocol (invitrogen). For ChIPSeq, 10ng of immuno-precipitated DNA fragments were used to prepare ChIP-seq libraries with Ovation SP Ultralow DR Multiplex system (Nugen) following the manufacturer’s protocol. the NEBNext RNA library prep kit (New England BioLabs) and Ovation SP Ultralow DR Multiplex system (Nugen) were used to process RNA-Seq samples following the manufacturer’s protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
32121166
Reads aligned (%)
97.5
Duplicates removed (%)
10.3
Number of peaks
504 (qval < 1E-05)

mm9

Number of total reads
32121166
Reads aligned (%)
97.2
Duplicates removed (%)
10.3
Number of peaks
522 (qval < 1E-05)

Base call quality data from DBCLS SRA