Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Pancreas
Cell type
Beta-TC-6
Tissue
Pancreas
Cell Type
Beta Cell
Disease
Insulinoma

Attributes by original data submitter

Sample

source_name
input control
biomaterial_provider
ATCC Cat #CRL-11506
cell line
BetaTC6

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Beta-TC6 cells (~40-160 million) were fixed for 30 minutes in 2mM DSG and for 10 minutes in 1% formaldehyde and then either frozen at -80ûC or processed immediately. Nuclei were isolated in buffer containing 1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8.0, and protease inhibitors and sonicated using a Diagenode Bioruptor to shear chromatin to 200-1000bp fragments. Protein-DNA complexes were incubated with antibodies against BMAL1 and CLOCK (affinity-purified guinea pig IgGs as described above), H3K4Me2 (Abcam), H3K27Ac (Active Motif), H2AZ (Active Motif), or PDX1 (Novus Biologicals) and immunoprecipitated with IgG paramagnetic beads (Invitrogen). Eluted chromatin was isolated using MinElute PCR purification columns (Qiagen). Sequencing libraries were generated using KAPA DNA Library Preparation kits (Kapa Biosystems, KK8504) according to manufacturer's instructions. Library concentrations were assessed by both a Bioanalyzer (Agilent) and qPCR-based quantification (Kapa Biosystems)

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
35933181
Reads aligned (%)
96.6
Duplicates removed (%)
56.7
Number of peaks
2637 (qval < 1E-05)

mm9

Number of total reads
35933181
Reads aligned (%)
96.4
Duplicates removed (%)
56.8
Number of peaks
2573 (qval < 1E-05)

Base call quality data from DBCLS SRA