Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TP63

Cell type

Cell type Class
Others
Cell type
JHU-029
Primary Tissue
Unknown
Tissue Diagnosis
Unknown

Attributes by original data submitter

Sample

source_name
JHU-029
cell line
JHU-029
chip antibody
p63 (H129, Santacruz)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
JHU029 cells were subjected to additional cross-linking protein-protein interaction with 2 mM EGS followed by cross-linking with 1% (v/v) formaldehyde. Cells were then lysed in RIPA buffer for 1-2hr at 40C. Nuclear lysates were sonicated and the sonicated chromatin was precleared with ProteinG sepharose beads (GE healthcare) pre-blocked with BSA and sonicated salmon sperm DNA. Samples were incubated with 2 μg of p63 antibody (H129, Santacruz) for overnight at 40C and with beads for additional 2 hrs. Beads were washed in wash buffer. After the wash, beads were incubated for 3 hrs at 550C, then overnight at 650C in TE buffer containing SDS, RNase A, Proteinase K. DNA was purified via Qiaquick PCR purification kit (28106, Qiagen) as per manufacturer’s instructions. Percentage of input was calculated by using 10% as standard. Libraries were prepared for ChIP-sequencing using Illumina kit (cat number, 1005709, 1003473).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
53816463
Reads aligned (%)
20.0
Duplicates removed (%)
69.5
Number of peaks
13600 (qval < 1E-05)

hg38

Number of total reads
53816463
Reads aligned (%)
20.9
Duplicates removed (%)
68.4
Number of peaks
13755 (qval < 1E-05)

Base call quality data from DBCLS SRA