Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
JMJD6

Cell type

Cell type Class
Kidney
Cell type
293
Primary Tissue
Kidney
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
HEK293T cell
cell line
Human Embryonic Kidney 293 cells
chip antibody
JMJD6
chip antibody details
ab10526 (Abcam)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Fixation was stopped by adding Glycine (0.125M) and incubating for 5 min at RT, followed by washing with PBS twice. Chromatin DNA was sheared to 300–500 bp average in size through sonication. Resultant was immunoprecipitated with control IgG or specific antibodies overnight at 4°C, followed by incubation with protein G magnetic beads (Invitrogen) for an additional 2 h. After washing and elution, the protein–DNA complex was reversed by heating at 65°C overnight. For samples fixed with glutaraldehyde, proteinase K (0.3mg/ml) (Ambion) was added during de-crosslinking. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen) the libraries were constructed following Illumina’s Chip-Seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
58309756
Reads aligned (%)
87.6
Duplicates removed (%)
7.1
Number of peaks
7297 (qval < 1E-05)

hg38

Number of total reads
58309756
Reads aligned (%)
89.4
Duplicates removed (%)
5.8
Number of peaks
7306 (qval < 1E-05)

Base call quality data from DBCLS SRA