Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Digestive tract
Cell type
Ganglionic gut
NA
NA

Attributes by original data submitter

Sample

source_name
Enteric precursor cells
strain
CD1
age
P7
tissue
ganglionic gut
cell type
Enteric precursor cells
chip antibody
none (input)
pool number
Pool2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed with 1% formaldehyde and was sonicated in a Bioruptor System (Diagenode, USA). ChIP assay was performed with the Magna Chip Hisens Kit (Millipore,USA) according to manufacturer’s instructions and using the Anti-Dnmt3b antibody-ChIP Grade (Abcam, USA). 10% of samples volume/reaction was kept as controls (input) before immunoprecipitation. ChIP and input samples were processed with the ChIP-Seq DNA sample prep kit (Illumina, USA), following the manufacturer’s instructions. Size-selection was then performed by agarose gel electrophoresis to isolate fragments with size between 200 and 300bp. Afterwards, purified libraries were amplified by PCR and size range was subsequently checked in the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent, USA). Quantification was performed in the 7500-Real Time PCR System (Applied Biosystems) with the Library Quantification Kit (Kapa Biosystems). After proper dilutions, 4 nM libraries were processed, to obtain pools at a final concentration of 8 pM following the instructions of the Miseq Reagent kit V2. (50 cycles) (Illumina, USA).

Sequencing Platform

instrument_model
Illumina MiSeq

mm10

Number of total reads
1073199
Reads aligned (%)
90.8
Duplicates removed (%)
27.8
Number of peaks
58 (qval < 1E-05)

mm9

Number of total reads
1073199
Reads aligned (%)
90.2
Duplicates removed (%)
29.6
Number of peaks
64 (qval < 1E-05)

Base call quality data from DBCLS SRA