Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Med1

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
NS5 Neural Stem Cell
antibody
Med1 (Behtyl Labs #A300-793A)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
NS-5 cells were fixed sequentially with di(N-succimidyl) glutarate and 1% formaldehyde to cross-link chromatin. Chromatin was prepared for sonication with 20 mM Tris-HCl pH8, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100. We used 15 cycles of 30 seconds ON, 30 seconds OFF on a Bioruptor Pico sonication device (Diagenode Cat# B01060001) to shear chromatin to 150-200bp fragments. The resulting chromatin extract was incubated overnight at 4°C with 100ul of Dynal Protein G magnetic beads that had been pre-incubated with approximately 10 μg of the appropriate antibody. Beads were washed 1X with the sonication buffer, 1X with 20 mM Tris-HCl pH8, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1%Triton X-100, 1X with 10 mM Tris-HCl pH8, 250 mM LiCl, 2 mM EDTA, 1% NP40 and 1X with TE containing 50 mM NaCl. Bound complexes were eluted from the beads (50 mM Tris-Hcl, pH 8.0, 10 mM EDTA and 1% SDS) by heating at 65°C for 1 hr with occasional vortexing and crosslinking was reversed by overnight incubation at 65°C. Finally ,DNA was precipitated using phenol:chloroform:isoamyl alcohol (PCI). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
21122393
Reads aligned (%)
95.9
Duplicates removed (%)
38.6
Number of peaks
15621 (qval < 1E-05)

mm9

Number of total reads
21122393
Reads aligned (%)
95.6
Duplicates removed (%)
38.7
Number of peaks
15589 (qval < 1E-05)

Base call quality data from DBCLS SRA