Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ctcf

Cell type

Cell type Class
Neural
Cell type
Neural Stem Cells
MeSH Description
Self-renewing cells that generate the main phenotypes of the nervous system in both the embryo and adult. Neural stem cells are precursors to both NEURONS and NEUROGLIA.

Attributes by original data submitter

Sample

source_name
Neural stem cells
strain
C57BL/6 x FVB/N
cell type
E14.5 mouse brain derived neural stem cells
genotype/variation
Smchd1 wild-type
gender
male
chip antibody
Ctcf (Millipore, 07-729, lot 2452497)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, nuclei were isolated from formaldehyde crosslinked NSCs and chromatin was fragmented by sonication. Chromatin immunoprecipitation was performed with corresponding antibodies for Ctcf, Smchd1, H3K4me3 and H3K27me3. DNA was extracted from the immunoprecipitated fraction following reverse-crosslinking. For MBD-seq, genomic DNA was extracted using an AllPrep DNA/RNA Mini Kit (Qiagen) and methylated DNA was isolated via binding to the methyl-CpG binding domain of human MBD2 protein coupled beads using the MethylMiner methylated DNA enrichment kit (Life Technologies) according to the manufacturer’s instructions. Sequencing libraries was generated with Illumina's TruSeq DNA Sample Preparation Kit or Ovation Ultralow system (NuGen) according to manufacturer's instruction.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
20511748
Reads aligned (%)
91.6
Duplicates removed (%)
69.5
Number of peaks
659 (qval < 1E-05)

mm9

Number of total reads
20511748
Reads aligned (%)
91.5
Duplicates removed (%)
69.7
Number of peaks
601 (qval < 1E-05)

Base call quality data from DBCLS SRA