GSM6064729: siCtrl ChIP rep5; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
TFs and others
Antigen
HIF1A
Cell type
Cell type Class
Pancreas
Cell type
PANC-1
Tissue
Pancreas/Duct
Disease
Epithelioid Carcinoma
Attributes by original data submitter
Sample
source_name
PDAC cell line (ATCC)
protocol
Hypoxia
sirna
siCtrl
cell line
Panc1
fraction
ChIP-DNA
antibody
Antibody HIF-1α (D2U3T) Rabbit mAb #14179 (CellSignaling-Technologies) was used for ChIP
Sequenced DNA Library
library_name
GSM6064729
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed in paraformaldehyde (3.7%) for 5 minutes under hypoxia, then glycine was added for 7 minutes to quench the reaction. Cells were collected by scraping and spun down at 500g for 5 minutes. The pellet was frozen for subsequent ChIP reaction. The NEBNext® Ultra™ II DNA Library Prep Kit from NEB ( New England Biolabs, Ipswich, MA) in the succeeding steps. ChIP samples (1 ng) were end-repaired and adenylated. Adapters containing the index for multiplexing were ligated to the fragmented DNA samples. Fragments containing adapters on both ends were enriched by PCR. The quality and quantity of the enriched libraries were measured using Qubit® (1.0) Fluorometer and the Tapestation (Agilent, Waldbronn, Germany). The product is a smear with an average fragment size of approximately 300 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The libraries were sequenced single read 100 bp using the Illumina Novaseq 6000 (Illumina, Inc, California, USA). Reads were quality-checked with fastqc which computes various quality metrics for the raw reads.