Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pluripotent stem cell
Cell type
mESC derived neural cells
NA
NA

Attributes by original data submitter

Sample

source_name
neural progenitor cells
cell type
ESC-derived clonal neural progenitor cells
genotype
Smchd1-/-
antibodies
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Total RNA was extracted using standard Trizol protocol. ChIP/CHART-enriched and input DNA were extracted with phenol:chloroform. RNA-seq libraries were generated by dUTP-mediated directional RNA-seq based on NEBNext Ultra directional RNA library preparation protocol. ChIP-seq and Hi-C libraries were generated by NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina. CHART-seq libraries were generated by NEBNext Ultra DNA Library Prep Kit for Illumina.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
47692586
Reads aligned (%)
97.4
Duplicates removed (%)
8.5
Number of peaks
583 (qval < 1E-05)

mm9

Number of total reads
47692586
Reads aligned (%)
97.2
Duplicates removed (%)
9.2
Number of peaks
590 (qval < 1E-05)

Base call quality data from DBCLS SRA