Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
RUNX1

Cell type

Cell type Class
Gonad
Cell type
Epididymis
MeSH Description
The convoluted cordlike structure attached to the posterior of the TESTIS. Epididymis consists of the head (caput), the body (corpus), and the tail (cauda). A network of ducts leaving the testis joins into a common epididymal tubule proper which provides the transport, storage, and maturation of SPERMATOZOA.

Attributes by original data submitter

Sample

source_name
Epididymis
cell type
Primary human epididymis cells
chip antibody
RUNX1 (Abcam ab23980)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were lysed in lysis buffer (5mM PIPES pH 8.0, 85mM KCL, 0.5% NP-40, 1x Protese Inhibitor Cocktail (Roche)). Nuclei were isolated by centrifugation, lysed in RIPA buffer (1x PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, Protease Inhibitor Cocktail), and sonicated. Protein-DNA complexes were isolated with the AR antibody. DNA ends were blunted using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. Next, DNA was incubated with Klenow exo- to add 5' adenine overhangs. Multiplex adaptors were then ligated to the ends and converted to dsDNA using 5 cycles of PCR. DNA was size-selected to contain fragments between 200 and 300bp and PCR amplified for 5 cycles. DNA was purified with 1.2x AMPsureXP beads. Sequencing was preformed on an Illumina Hi-Seq.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
31414008
Reads aligned (%)
85.8
Duplicates removed (%)
9.5
Number of peaks
14699 (qval < 1E-05)

hg38

Number of total reads
31414008
Reads aligned (%)
86.4
Duplicates removed (%)
9.1
Number of peaks
14773 (qval < 1E-05)

Base call quality data from DBCLS SRA