Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

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
wild type NSC
strain background
mixed C57BL/6 x DBA
cell type
forebrain-derived neural stem cells (NSCs)
genotype/variation
wild type
passages
passage 3 to 7
chip antibodies
Ab8894 (Abcam) for H3K4me1.

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For each line, neurospheres were dissociated and 4 million single cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Reaction was quenched with 0.125 M Glycine, cells were washed with cold PBS and lysed according to Vermunt et al., 2016. Nuclei pellets were resuspended in 160μl sonication buffer and divided over two microtubes for shearing in the Covaris S series with the following settings for 12 cycles of 60 seconds: intensity 3, duty cycle 20%, 200 cycles/bursts. Chromatin immunoprecipitation steps after sonication were performed as described previously (Vermunt et al., 2016) using 50 μl DynaI protein G beads that were preincubated with 5 μg Ab4729 (Abcam) for H3K27ac or 5 μg Ab8894 (Abcam) for H3K4me1. Whole cell extract of 4 million cells was split onto both antibodies, resulting in the use of 2 million cells per ChIP. Libraries were made using the Illumina Truseq DNA library protocol and sequencing was done at the MIT BioMicro Center (http://openwetware.org/wiki/BioMicroCenter).

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

mm10

Number of total reads
44996585
Reads aligned (%)
98.1
Duplicates removed (%)
5.5
Number of peaks
60550 (qval < 1E-05)

mm9

Number of total reads
44996585
Reads aligned (%)
98.0
Duplicates removed (%)
5.6
Number of peaks
60566 (qval < 1E-05)

Base call quality data from DBCLS SRA