Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ARNTL

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
Non-malignant Neural Stem Cell
tumor type
n/a
antibody
BMAL1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
BMAL1 ChIP assays were performed with 107 cells using Magna ChIP-seq kit (Millipore, 17-10085) according to manufacturer's instruction. Briefly, cells were fixed with 1% formaldehyde at room temperature for 10 minutes, and subsequently quenched with 0.125M glycine. Then, the cells were washed with cold PBS and suspended with lysis buffer supplemented with Protease Inhibitor Cocktail II. Chromatin was sonicated to obtain DNA fragments with an average length of 200-500 bp for sequencing by Bioruptor Plus sonication device (Diagenode) followed by centrifugation for clearing. Soluble fraction of sheared chromatin was diluted 10-fold with ChIP dilution buffer and incubated with BMAL1 antibody (Cell Signaling Technology) and EZ-Magna ChIP A/G magnetic beads overnight at 4°C with rotation. Chromatin-captured beads were washed once with low salt wash buffer, once with high salt wash buffer, once with LiCl wash buffer and twice with TE buffer for 5 min each by rotation at 4°C. Beads were resuspended in elution buffer and removed by magnet. Proteinase K was added to the eluted DNA followed by incubation at 62°C for 4 hours with shaking. Then the eluted DNA was incubated at 95°C for 10 min to remove RNA. Reverse-crosslinked DNA was purified by using purification columns. Eluted DNA was used to do quantitative PCR (qPCR) or sequencing library preparation. ChIP quantitative RT-PCR was performed by using SYBR Green PCR Master Mix (ABI, 4309155). qPCR primers were listed as Table S1. Then sequencing libraries were prepared by using ThruPLEX® NGS Library Preparation Kits (Rubicon Genomics, R400427) according to manufacturer's instruction. ChIP-seq libraries were sequenced on Illumima HiSeq platform by Genewiz. Then sequencing libraries were prepared by using ThruPLEX® NGS Library Preparation Kits (Rubicon Genomics, R400427) according to manufacturer's instruction. ChIP-seq libraries were sequenced on Illumima HiSeq platform by Genewiz.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
14086835
Reads aligned (%)
34.9
Duplicates removed (%)
53.4
Number of peaks
12595 (qval < 1E-05)

hg38

Number of total reads
14086835
Reads aligned (%)
36.3
Duplicates removed (%)
51.9
Number of peaks
12686 (qval < 1E-05)

Base call quality data from DBCLS SRA