Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMCHD1

Cell type

Cell type Class
Neural
Cell type
hTERT RPE-1
Primary Tissue
Eye
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

sample_name
DRS003044
sample comment
SMCHD1 ChIP-seq in hTERT-RPE1. The human SMCHD1-specific mouse monoclonal antibody was raised against an SMCHD1 fragment (amino acids 1645–2006), expressed in and purified from E. coli as a His6-fusion protein.

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq libraries were prepared according to the manufacturer's instructions (Illumina). Briefly, immunoprecipitated DNA was end-repaired using a mix of Klenow DNA polymerase, T4 DNA polymerase and T4 polynucleotide kinase (NEB), tailed with an 'A' base using Klenow Fragment 3'-5' exo minus (NEB), and ligated with the Illumina single-end adaptor, using a DNA ligation Kit (TaKaRa). Adaptor-ligated fragments of approximately 300 bp were purified using the E-gel SizeSelect system (Life Technologies), and were subjected to 18 cycles of PCR amplification using KOD FX polymerase (TOYOBO). To remove the remaining PCR primers, the amplified products were further purified using AMPure XP Kits (Beckman Coulter). Libraries were quantified using a BioAnalyzer 2100 with a High Sensitivity DNA Kit (Agilent).

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
38935687
Reads aligned (%)
33.5
Duplicates removed (%)
64.6
Number of peaks
1470 (qval < 1E-05)

hg38

Number of total reads
38935687
Reads aligned (%)
35.6
Duplicates removed (%)
63.0
Number of peaks
1817 (qval < 1E-05)

Base call quality data from DBCLS SRA