Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Neural progenitor cells
NA
NA

Attributes by original data submitter

Sample

source_name
Neural progenitor cells
strain
FVB/N
cell type
Primary adult neural progenitor cell
passages
4-9
chip antibody
No Antibody

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was cross-linked with 1% formaldehyde for 10 min, followed by quenching with 0.125 M glycine for 5 min. Cells were washed and incubated in swelling buffer (10 mM HEPES pH 7.8, 1.5 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT, 0.5 mM PMSF) for 15 min on ice, followed by nuclei isolation by dounce homogenization. Nuclei were pelleted and resuspended in RIPA buffer (1% NP-40, 0.5% sodium deoxycholate, 1% SDS in PBS pH 7.4), and chromatin was sheared with a Vibra-Cell Sonicator VC130 (Sonics) six times for 30 sec at 60% amplitude. Single end libraries were generated according to the manufacturer’s instructions (Illumina).

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

mm10

Number of total reads
41291632
Reads aligned (%)
92.5
Duplicates removed (%)
14.7
Number of peaks
577 (qval < 1E-05)

mm9

Number of total reads
41291632
Reads aligned (%)
92.3
Duplicates removed (%)
14.7
Number of peaks
669 (qval < 1E-05)

Base call quality data from DBCLS SRA