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
Trophoblast Stem Cells
antibody
None
knock-in
none
shRNA
pLKO vector
strain
129/SvEv

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed in 1% paraformaldehyde for 10 minutes, harvested, and the nuclei were isolated and lysed. The nuclear lysate was sonicated and underwent immunoprecipitation using 50 µl of dynabeads (Invitrogen) coupled to 5 µl of Active Motif α-H2BK5Ac antibody per sample. DNA-protein crosslinks were reversed overnight at 65C, and samples were ribonuclease and proteinase treated before DNA was purified using Min Elute columns (Qiagen). Preparation of libraries was performed using 50 ng of ChIP or TSWT input DNA and the KAPA HyperPrep kit with Illumina TruSeq indexed adapters. Dual SPRI size selection was performed after 18 cycles of amplification according to the manufacturer’s protocol. The average library size was ~300 bp. 12-plex libraries were sequenced (1 X 75 bp) using an Illumina NextSeq500 ranging from 7.1-8.9 X 107 reads per sample.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
139684193
Reads aligned (%)
92.8
Duplicates removed (%)
11.2
Number of peaks
730 (qval < 1E-05)

mm9

Number of total reads
139684193
Reads aligned (%)
92.6
Duplicates removed (%)
11.2
Number of peaks
884 (qval < 1E-05)

Base call quality data from DBCLS SRA