Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

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

Attributes by original data submitter

Sample

source_name
iPSC
chip antibody
None
antibody catalog number
None
cell type
SNEL #4
young_id
10112013_C2T2JACXX_3.TGACCA

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Library construction protocol: Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
39519028
Reads aligned (%)
95.3
Duplicates removed (%)
12.0
Number of peaks
539 (qval < 1E-05)

mm9

Number of total reads
39519028
Reads aligned (%)
95.0
Duplicates removed (%)
12.0
Number of peaks
646 (qval < 1E-05)

Base call quality data from DBCLS SRA