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
retina
strain
C57BL/6
cell type
mature retinal-derived iPSCs 3302
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP with iDeal ChIP-seq kit (Diagenode # C01010051), MinElute PCR-purification kit (QIAGEN #28006), quantified using the Quant-iT PicoGreen ds DNA assay (Life Technologies #Q33120) Libraries were prepared from 5-10 ng DNA using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina with NEBNext High-Fidelity 2x PCR Master Mix according to the manufacturer’s instructions (New England Biolabs, Ipswich, MA) with the following modifications: A 1:1 Ampure cleanup was added after adaptor ligation a total of 2 times.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
84357023
Reads aligned (%)
97.6
Duplicates removed (%)
45.7
Number of peaks
722 (qval < 1E-05)

mm9

Number of total reads
84357023
Reads aligned (%)
97.4
Duplicates removed (%)
45.7
Number of peaks
824 (qval < 1E-05)

Base call quality data from DBCLS SRA