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
Cell Line
strain background
C57BL/6
cell line
Mull_M_Y-Cr143.01
cell type
iPSCs from mature Muller cell MakeRetina Cr143.01
chip antibody
none (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
After removal of IRMEFs, iPS cells were collected after washing with PBS. Then cells were subjected to crosslinking in 1% formaldehyde (Thermo scientific, 28906) for 10 minutes at room temperature, followed by the addition of glycine at the final concentration of 0.125 M to quench the reaction. After centrifuge, cells were washed with cold PBS, counted and pelleted as 10 million cells for each nuclei preparation. The nuclei were isolated and prepared for shearing using TruChIP chromatin shearing kit (Covaris, 520127) according to manufacturer's protocol. After shearing, ChIP was performed using the iDeal ChIP-seq kit (Diagenode, C01010051). The antibodies used were: anti-H3K4me3 (Diagenode, C15410003-50), anti-H3K4me2 (Abcam, ab7766), anti-H3K4me1 (Abcam, ab8895), anti-H3K9/14ac (Diagenode, C15410200), anti-H3K27ac (Abcam, ab4729), anti-H3K36me3 (Active Motif, 61101), anti-H3K27me3 (Active Motif, 39155), and anti-CTCF (Active Motif, 61311). After de-crosslinking, DNA was extracted using MinElute PCR-purification kit (Qiagen, 28006) or Agencourt AMPure XP beads (Beckman Coulter, A63881) and subjected to library preparation using NEBNext ChIP-Seq Library Prep Master Mix Set for illumina (NEB, E6240L). The ChIP experiments and library preparation for antibodies including anti-RNA polymerase II (Abcam, ab5095), anti-Brd4 (Bethyl Laboratories, A301-985A) and anti-H3K9me3 (Active Motif, 39161), were performed by Active Motif.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
39409340
Reads aligned (%)
98.3
Duplicates removed (%)
11.6
Number of peaks
677 (qval < 1E-05)

mm9

Number of total reads
39409340
Reads aligned (%)
98.0
Duplicates removed (%)
11.6
Number of peaks
733 (qval < 1E-05)

Base call quality data from DBCLS SRA