GSM2891282: NY8 input ChIP 1; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
Input control
Antigen
Input control
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
none
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.