Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Lung
Cell type
Lung
MeSH Description
Either of the pair of organs occupying the cavity of the thorax that effect the aeration of the blood.

Attributes by original data submitter

Sample

source_name
Lung normal tissue
tissue
Lung normal
antibody
H3K4me3

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cell or Chopped tissue pellets were homogenized in PBS containing proteinase inhibitor. The nuclei were checked by phase-contrast microscopy to maximize the yield of nuclei (~5x107). With sufficient lysis in 25% sucrose, 0.2% NP-40/TBS, the pellets were layered on 50% [w/v] sucrose/TBS, and then centrifuged at 21,000 g, 30 min, 4°C. The nuclei pellets were resuspended in digestion buffer (0.32 M sucrose, 50 mM Tris-HCl (pH 7.5), 4 mM MgCl2, 1 mM CaCl2), and digested with MNase for ~10 min to generate mainly mononucleosomes that were immunoprecipitated with anti-H3K4me3 antibody (ab8580, Abcam). After incubation over night, Protein A Dynal magnetic beads were washed 6 times using modified RIPA buffer (50 mM Tris-HCL pH 7.8, 1 mM EDTA, 0.25% Na Deoxycholate, 1% NP-40, 0.5 M LiCl). The DNA was eluted in 1% SDS and 0.1M NaHCO3 and reversed cross-linking at 65°C, over night. The library was generated using NEBNext ChIP-Seq Library Prep Master Mix Set, and amplified with 10 PCR cycles. The library was prepared by size selection for mononucleosome fragments.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
34545390
Reads aligned (%)
99.3
Duplicates removed (%)
28.2
Number of peaks
34424 (qval < 1E-05)

hg19

Number of total reads
34545390
Reads aligned (%)
98.9
Duplicates removed (%)
29.0
Number of peaks
34337 (qval < 1E-05)

Base call quality data from DBCLS SRA