Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

Cell type Class
Pancreas
Cell type
MIN6B1
NA
NA

Attributes by original data submitter

Sample

source_name
Pancreatic beta cell line
cell line
MIN6
tissue
Pancreatic beta cell line

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq was done following a ChIPmentation protocol (PMID 26280331). Min6 cells were crosslinked with 1% formaldehyde at room temperature followed by glycine quenching. To isolate nuclei, the cells were lysed with Lysis buffer I (50 mM HEPES; pH 7.5, 140mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% Nonidet‐40, 0.25% Triton X-100 and protease inhibitor cocktail) for 10 minutes at 4°C. The collected nuclei were then washed with a lysis buffer II (200mM NaCl, 1mM EDTA pH8.0, 0.5mM EGTA pH8.0, 10mM Tris-Cl pH8.0 and protease inhibitor cocktail) for 20 minutes at room temperature. The nuclei pellets were resuspended in lysis buffer III (10mM Tris-Cl pH8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine and protease inhibitor cocktail) for sonication. The chromatin was sheared for 10 cycles (15 seconds on and 45 seconds off at constant power 3) on Branson 450 sonifier.  250ug of chromatin was used for each pulldown (NIPBL, Bethyl Laboratories, A301-778A). First, 50ul of Dynabeads M-280 (Life Technologies, Sheep Anti-Rabbit IgG, Cat# 11204D) was washed three times with 0.5mg/ml of BSA/PBS on ice and then incubated with designed antibody for at least 2 hours at 4°C. The beads/antibody complexes were then washed with BSA/PBS. The pulldown was down in binding buffer (1% Trixon-X 100, 0.1% Sodium Deoxycholate and protease inhibitor cocktail in 1X TE) by mixing the beads/antibody complexes and chromatin. After pulling down for overnight, the beads/antibody/chromatin complexes were washed with RIPA buffer (50mM HEPES pH8.0, 1% NP-40, 0.7% Sodium Deoxycholate, 0.5M LiCl, 1mM EDTA and protease inhibitor cocktail). The beads complexes were then subjected to ChIPmentation by incubating with homemade Tn5 transposase in tagmentation reaction buffer (10mM Tris-Cl pH8.0 and 5mM MgCl2) for 10 minutes at 37°C. To remove free DNA, beads were washed twice with 1x TE  on ice. The pulldown DNA was recovered by reversing crosslink for overnight followed by PCRClean DX beads purification.  To generate ChIP-seq libraries, PCR was applied to amplify the pulldown DNA with illumina nextera primers. Size selection was then done with PCRClean DX beads to choose the fragments ranging from 100bp to 1000bp. All ChIP-seq libraries were sequenced on illumine HiSeq2500 platform (1x50bp).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
14220140
Reads aligned (%)
98.3
Duplicates removed (%)
16.2
Number of peaks
491 (qval < 1E-05)

mm9

Number of total reads
14220140
Reads aligned (%)
98.1
Duplicates removed (%)
16.2
Number of peaks
481 (qval < 1E-05)

Base call quality data from DBCLS SRA