Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Epidermis
Cell type
A-375
Primary Tissue
Skin
Tissue Diagnosis
Melanoma

Attributes by original data submitter

Sample

source_name
A375
cell type
Melanoma cells
passages
10-15
chip antibody
H3K4me3 (Millipore 04-745)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Formaldehyde was added directly to the growth media for a final concentration of 1% for 10 mins at 37C to initiate chromatin fixation. The entire two-day ChIP procedure was performed using the EZ-Magna ChIP HiSens Chromatin Immunoprecipitation Kit (Millipore 1710460) according to the manufacturer’s protocol. Samples were pulse sonicated with 2 rounds of 10 mins (30s on-off cycles, high frequency) in a rotating water bath sonicator (Diagenode Bioruptor) with 5 mins on ice between each round. To detect histone modifications, antibodies (H3K4me2: Millipore 17-677, H3K4me3: Millipore 04-745, H3K27ac: Millipore 17-683) were optimized individually for each antibody to be 0.5 μL for 1 million cells. 1 μL of IgG (Millipore 12-370) was used for negative control. ChIP samples were prepped with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB E7645S). DNA libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
60672166
Reads aligned (%)
78.3
Duplicates removed (%)
14.2
Number of peaks
23861 (qval < 1E-05)

hg19

Number of total reads
60672166
Reads aligned (%)
78.2
Duplicates removed (%)
14.2
Number of peaks
23665 (qval < 1E-05)

Base call quality data from DBCLS SRA