Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
HNF1A

Cell type

Cell type Class
Pancreas
Cell type
NY8
NA
NA

Attributes by original data submitter

Sample

source_name
NY8
cell type
pancreatic cancer-derived cells
cell line
NY8
chip antibody
HNF1A (goat polyclonal C-19 from Santa Cruz Biotechnology)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
A confluent 15cm culture plate of cells (NY8 or NY15) was used per immunoprecipitation. Cells were fixed with 1% formaldehyde for 10 minutes. Nuclei were collected and chromatin sheared to 1-10 nucleosomes using the SimpleChIP Plus Enzymatic Chromatin IP kit and protocol (Cell Signaling). HNF1A was immunoprecipitated overnight with goat polyclonal antibody C-19 (Santa Cruz) and 60µL magnetic protein G beads. Beads were washed and immunoprecipitated DNA was reverse crosslinked/purified per the SimpleChIP Plus Enzymatic Chromatin kit protocol. 10 to 500 ng of ChIPped DNA was prepared as a standard Illumina library using IntegenX Prep X (was Wafergen now Takara) reagents on the Apollo 324 instrument, where the fragments are end-repaired, A-tailed, and adapter ligated. Then the samples are PCR amplified and pooled. Final libraries were checked for quality and quantity by TapeStation (Agilent, Santa Clara, CA) and qPCR using Kapa's library quantification kit for Illumina Sequencing platforms (catalog # KK4835) (Kapa Biosystems,Wilmington MA).  They were clustered on the cBot (Illumina) and sequenced on a 50 cycle single end run on a HiSeq 2500 in High Output mode using version 4 reagents according to manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
72997928
Reads aligned (%)
95.6
Duplicates removed (%)
18.6
Number of peaks
1857 (qval < 1E-05)

hg19

Number of total reads
72997928
Reads aligned (%)
94.5
Duplicates removed (%)
20.4
Number of peaks
1455 (qval < 1E-05)

Base call quality data from DBCLS SRA