Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pluripotent stem cell
Cell type
hESC derived mesendodermal cells
NA
NA

Attributes by original data submitter

Sample

source_name
ES derived mesoderm
tissue
ES derived mesoderm
differentiation time
day02
genotype
H9 MLC2v:H2B
matched input
N/A
chip antibody
none (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq experiments for all histone marks at all time points were performed as previously described (PMID: 22763441). Detailed protocols for ChIP-seq including antibodies used and antibodies validations performed are available at www.encodedcc.org associated with each experiment described here. They can also be found at the links below. Standard ChIP-seq, Tissue fixation & sonication: https://www.encodeproject.org/documents/3125496b-c833-4414-bf5f84dd633eb30d/@@download/attachment/Ren_Tissue_Fixation_and_Sonication_v060614.pdf, Immunoprecipitation: https://www.encodeproject.org/documents/89795b31-e65a-42ca-9d7bd75196f6f4b3/@@download/attachment/Ren%20Lab%20ENCODE%20Chromatin%20Immunoprecipitation%20Protocol_V2.pdf, Library preparation: https://www.encodeproject.org/documents/4f73fbc3-956e-47ae-aa2d41a7df552c81/@@download/attachment/Ren_ChIP_Library_Preparation_v060614.pdf.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
84296807
Reads aligned (%)
98.8
Duplicates removed (%)
8.0
Number of peaks
2162 (qval < 1E-05)

hg19

Number of total reads
84296807
Reads aligned (%)
97.9
Duplicates removed (%)
9.8
Number of peaks
1817 (qval < 1E-05)

Base call quality data from DBCLS SRA