Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K36me2

Cell type

Cell type Class
Unclassified
Cell type
Unclassified
NA
NA

Attributes by original data submitter

Sample

source_name
SCC-4 cells & S2 cells (spiked-in)
chip antibody
H3K36me2 (Cell Signaling Tech, #2901)
cell line
SCC-4
cell type
Patient-derived head and neck squamous cell carcinoma cell line
genotype
NSD1 mutant

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were crosslinked with 1% formaldehyde (Sigma). Fixed cell preparations were washed, pelleted and stored at -80°C. Sonication of lysed nuclei (lysed in a buffer containing 1% SDS) was performed on a BioRuptor UCD-300 for 60 cycles, 10s on 20s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and concentrated using Nanosep 10k OMEGA (Pall). Before ChIP reaction 2% of sonicated drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing. ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. Dynalbeads Protein A (Invitrogen) were washed and then incubated with specific antibodies, and 1.5 million cells of sonicated cell lysate combined with protease inhibitors for 10 hr, followed by 20 min wash cycle with provided wash buffers. Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail at 65°C for 30 min followed by 2ul Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers' protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol. KAPA HyperPrep Kit

Sequencing Platform

instrument_model
Illumina HiSeq 4000

dm6

Number of total reads
93741149
Reads aligned (%)
0.6
Duplicates removed (%)
21.7
Number of peaks
464 (qval < 1E-05)

dm3

Number of total reads
93741149
Reads aligned (%)
1.5
Duplicates removed (%)
68.5
Number of peaks
580 (qval < 1E-05)

Base call quality data from DBCLS SRA