Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Oligodendrocyte progenitor
NA
NA

Attributes by original data submitter

Sample

source_name
pooled wt and Zfp191 null oligodendrocyte and oligodendrocyte progenitor cells
strain
C57BL/6
developmental stage
postnatal day (P) 7,
genotype
pooled wildtype and Zfp191- null
tissue
brain
cell type
pooled OPC and OLG
antibody
none (input)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For ChIP (done by ActiveMotif), the equivalent of 22 microgram DNA was precleared with protein A agarose beads (Invitrogen). and incubated with 20 ul of an antibody against ZNF24 (Sigma, HPA024062, Lot. A71676, 0.16 ug/ul). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and bound fraction was purified by phenol-chloroform extraction and ethanol precipitation. Illumina sequencing libraries were prepared from the ChIP and Input DNAs using standard Illumina PE adaptors (Bentley et al., Nature 2008) by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina NextSeq 500 (75 nt reads, single end). Reads were aligned to the mouse genome (mm10).

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
39400342
Reads aligned (%)
97.3
Duplicates removed (%)
17.2
Number of peaks
562 (qval < 1E-05)

mm9

Number of total reads
39400342
Reads aligned (%)
97.1
Duplicates removed (%)
17.2
Number of peaks
587 (qval < 1E-05)

Base call quality data from DBCLS SRA