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
strain
C57BL/6N
cell type
TSC
cell differentiation state
Undifferentiated
chip-antibody
None

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-enriched DNA was obtaind by using ChIP-IT Express Enzymatic (Active Motif, Cat No. 53009) and S40Gc specific antibody (20B2) The ends of 50 ng of ChIP-enriched DNA and Input DNA were repaired using T4 DNA polymerase (New England Biolabs) and phosphorylated with T4 polynucleotide kinase (New England Biolabs). A single adenine base was added to the 3 prime-end with Klenow fragments (New England Biolabs). TruSeq DNA adapters (Illumina) were ligated to the fragments with T4 DNA ligase (New England Biolabs). Ligation products between 200 and 600 bp were purified on AMpure XP beads (Beckman Coulter Inc.) to remove unligated adapters and subjected to 14 cycles of PCR amplification by KAPA Library Amplification Kit (KAPA BIOSYSTEMS). Completed libraries were quantified using an Agilent 2000 BioAnalyzer system.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
17232963
Reads aligned (%)
98.2
Duplicates removed (%)
4.3
Number of peaks
169 (qval < 1E-05)

mm9

Number of total reads
17232963
Reads aligned (%)
98.1
Duplicates removed (%)
4.4
Number of peaks
123 (qval < 1E-05)

Base call quality data from DBCLS SRA