Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Placenta
Cell type
Trophoblast stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
shKdm5b_TSC
genotype/variation
shKdm5b
cell type
differentiated TS cell
differentiation day
day 2
chip antibody
NULL

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays. ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
28347558
Reads aligned (%)
97.7
Duplicates removed (%)
41.6
Number of peaks
491 (qval < 1E-05)

mm9

Number of total reads
28347558
Reads aligned (%)
97.3
Duplicates removed (%)
41.7
Number of peaks
531 (qval < 1E-05)

Base call quality data from DBCLS SRA