Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27me3

Cell type

Cell type Class
Pluripotent stem cell
Cell type
mESC derived neural cells
NA
NA

Attributes by original data submitter

Sample

source_name
mouse embryonic fibroblast cells
cell type
ES-derived neural progenitor cells
chip antibody
CST #9733S

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation was performed following standard protocol. Basically, 8-10 X10^6 cells were crosslinked with 1% formaldehyde at room temperature for 10 min, and then lysed with RIPA buffer containing 0.3 M NaCl. Specific H3K27me3 antibody was added to the sheared chromatin of 200-700 bp size, and rotated at 4°C for overnight. ChIP'd DNA was purified using PCR Purification Kit (Qiagen) and then quantified by Quant-iT dsDNA HS Assay Kit (Invitrogen). Equal amounts of ChIP enriched DNA (5 ng) under each experimental condition (WT and NULL) were prepared for ChIP-Seq libraries. ThruPLEX-FD Prep Kit (Rubicon Genomics, Cat# R400427) was used to construct the sequencing libraries according to the manufacturer's protocol, and the final products were sequenced on the HiSeq2000.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
28962660
Reads aligned (%)
95.5
Duplicates removed (%)
11.3
Number of peaks
131 (qval < 1E-05)

mm9

Number of total reads
28962660
Reads aligned (%)
95.3
Duplicates removed (%)
11.4
Number of peaks
171 (qval < 1E-05)

Base call quality data from DBCLS SRA