GSM2773938: HGEP 2 H3K27me3 (biological replicate 1); Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
Unclassified
Antigen
Unclassified
Cell type
Cell type Class
Others
Cell type
Gingival epithelial cells
NA
NA
Attributes by original data submitter
Sample
source_name
cultured cells
biomaterial_provider
CELLnTEC (Switzerland)
cell line
HGEP
cell type
primary human gingival epithelial cell line
experiment type
ChIP-seq
ip-target
H3K27me3
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
SCC25 and HGEP cells were fixed with 1% formaldehyde for 10 min. For histone ChIP-seq we used the Chromatin Shearing Optimization Kit-Low SDS (Diagenode) with 10 million cells per cell line and 40 cycles sonication (30 sec ON, 30 sec OFF, High) in the Bioruptor Plus (Diagenode). After RNase and proteinase K incubation, chromatin shearing was confirmed as a DNA smear between 100-300 bp on a 1.5% agarose gel. Histone ChIP DNA was prepared with the Auto Histone ChIP-seq kit protein G Kit (Diagenode), with 3 μg H3K4me1, 2 μg H3K4me3, 2.4 μg H3K27ac, 2 μg H3K27me3 and 2.4 μg H3K36me3 premium polyclonal antibody (Diagenode) per 1 million cells with the SX-8G IP-Star® Compact System (Diagenode). 1% input sample for each cell line was used as a control for background experimental noise. ChIP and input DNA were quantified with the Quant-iT PicoGreen ds DNA Assay Kit (Invitrogen). ChIP-seq libraries were made with the ThruPLEXTM-FD Prep Kit (Rubicon Genomics), purified and size-selected with a 2% agarose Pippin cassette (Sage Science). Libraries were quantified with the Quant-iT PicoGreen ds DNA Assay Kit (Invitrogen) and the KAPA Library Quantification Kit (Kapa Biosystems). Quality control was performed with the Agilent Technologies 2100 Bioanalyzer. Libraries were normalized based on qPCR and pooled with the TruSeq SR Cluster Kit v3-cBot-HS (Illumina). Pooled samples were multiplexed and sequenced with the HiSeq 2500 v3 (Illumina).