Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Lung
Cell type
NCI-H1299
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma Non-Small Cell

Attributes by original data submitter

Sample

source_name
H1299 cells
cell line
H1299
cell type
Non-small cell lung cancer cell line
passages
10-15
treatment
None
chip antibody
H3K4me3 (C42D8, Cell Signaling Technology)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation (ChIP) was performed with the SimpleChIP Enzymatic Chromatin IP Kit (Magnetic Beads) (#9003, Cell Signaling Technology, Danvers, MA) according to the manufacturer's instructions. Briefly, cells were cross‐linked with 1% formaldehyde (Sigma‐Aldrich) and lysed. Chromatin was digested with micrococcal nuclease into 150-900bp DNA/protein fragments. The fragments were immunoprecipitated with antibodies against H3K4me3 (C42D8, Cell Signaling Technology), H3K27me3 (C36B11, Cell Signaling Technology), or normal rabbit IgG with protein G magnetic beads. Cross-links were reversed, and purified DNAs were then subjected to next-generation sequencing (NovaSeq 6000 System).

Sequencing Platform

instrument_model
Illumina NovaSeq 6000

hg38

Number of total reads
20672445
Reads aligned (%)
91.4
Duplicates removed (%)
9.4
Number of peaks
6107 (qval < 1E-05)

hg19

Number of total reads
20672445
Reads aligned (%)
90.8
Duplicates removed (%)
9.8
Number of peaks
5927 (qval < 1E-05)

Base call quality data from DBCLS SRA