Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Rnf2

Cell type

Cell type Class
Placenta
Cell type
Trophoblast stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
F1 C/B trophoblast stem cells
parent of origin
CAST/EiJ mother X C57BL/6J father
passage number
18-25
genotype/variation
Kcnq1ot1 truncation
chip antibody
RING1B (Cell Signaling #5694)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For all ChIPs except EZH2, cells were crosslinked in 0.6% formaldehyde. For Ezh2 ChIPs, cells were crosslinked in 1.5mM EGS (ethylene glycol bis(succinimidyl succinate); ThermoFisher Pierce) in PBS for 30 minutes and then in 0.6% formaldehyde. Whole cell lysates were sonicated and chromatin extracts were immunoprecipitated using the specified antibody. Purified immunoprecipitated DNA was prepared for sequencing on the Illumina platform using Next Reagents (NEB).

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
54626230
Reads aligned (%)
96.1
Duplicates removed (%)
23.7
Number of peaks
10362 (qval < 1E-05)

mm9

Number of total reads
54626230
Reads aligned (%)
95.8
Duplicates removed (%)
23.6
Number of peaks
10384 (qval < 1E-05)

Base call quality data from DBCLS SRA