Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PRKCQ

Cell type

Cell type Class
Blood
Cell type
Jurkat
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Lymphocytic

Attributes by original data submitter

Sample

source_name
Jurkat cell line
treatment
PMA and Ionomycin
cell line
Jurkat T-cell leukemia cell line
chip antibody
PKCtheta (SantaCruz, catalog# sc-212, lot# K0713)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP samples were prepared with anti-PKC-theta (sc-212, SantaCruz), according to the protocol supplied by Upstate Biotechnology. 10ng of PKC-theta immunoprecipitated ChIP-DNA, and the corresponding total input (TI), were used to prepare the ChIP-seq DNA library using the NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina® (New England BioLabs Inc, NEB#E6240L) according to the manufacturer’s instructions. ChIP-DNA size was selected with AMPure XP beads (Beckman Coulter, Inc., Part #: A63881). The selected DNA was repaired with NEBNext End Repair Enzyme Mix and Buffer, followed by treatment with Klenow fragment (3’-5’ exo-) to generate “A” base overhangs. Subsequent adaptor ligation of the dA-tailed DNA was performed with 1.5μM NEBNext adaptor primers, Quick Ligation Reaction Buffer, and Quick T4 DNA ligase. AMPure beads were used to isolate library fragments ranging between 175 and 225bp in size and the purified DNA was combined with the NEBNext High-Fidelity 2X PCR Master mix, 25μM Universal PCR primer, and 25μM index primer for multiplexing purposes (New England BioLabs Inc, NEBNext® Multiplex Oligos for Illumina®, NEB#E7335L). A total of 15 cycles were used for PCR amplification of the adaptor-ligated DNA. The resultant ChIP-DNA library was subjected to DNA purification with AMPure beads. The quality of the ChIP-DNA library was assessed on a Bioanalyzer. A total of 2nM was captured on the Illumina flow cell for cluster generation

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
56364387
Reads aligned (%)
45.6
Duplicates removed (%)
53.0
Number of peaks
1533 (qval < 1E-05)

hg38

Number of total reads
56364387
Reads aligned (%)
47.8
Duplicates removed (%)
51.2
Number of peaks
1630 (qval < 1E-05)

Base call quality data from DBCLS SRA