Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TRIM28

Cell type

Cell type Class
Blood
Cell type
BJAB
Primary Tissue
Blood
Tissue Diagnosis
Lymphoma B-cell

Attributes by original data submitter

Sample

source_name
B cell
cell line
BJAB B-cell line
cell type
Cell line derived from Burkitt's lymphoma
passage
Multiple
chip antibody
TRIM28
chip antibody vendor
Abcam

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Approximately 30 to 50 million cells were cross-linked in 1% formaldehyde for 5 mins and quenched with 1 M Tris pH 8.0. Cells were washed twice with cold PBS and placed in 1 ml Low Salt Buffer (150 mM NaCl, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.5% NP-40, 1% Triton X-100) with complete protease inhibitor mixture (Roche Applied Science). Cells were sonicated for 15 mins (20 sec. on, 40 sec. off) with a Sonicator Ultrasonic Processor XL (Misonix Incorporated). Lysate was spun down at 13200 rpm for 20 mins and immunoprecipitation performed with 10 µg 8WG16 (Covance, MMS-126R), normal mouse IgG (Santa Cruz, sc-2025), normal rabbit IgG (Santa Cruz, sc-2027), SPT5 (Santa Cruz sc-28878), TRIM28/TIF1b (Abcam ab622553), OGA/NCOAT (Santa Cruz sc-376429), or O-GlcNAc (RL2; Santa Cruz sc-59624) overnight at 4°C. 50 µl protein G beads (Roche), pre-blocked with 0.5% BSA, and were incubated with the lysate for 3 hrs at 4°C. Beads were washed for 5 mins 4 times with RIPA Buffer (10 mM Tris, pH 7.6; 150 mM NaCl; 1 mM EDTA; 1% Triton X-100; 0.1% Sodium deoxycholate; 0.1% SDS) and once with Rinse Buffer (10 mM Tris, pH 7.6; 50 mM NaCl; 1 mM EDTA). The cross-link is reversed in 100 µl Elution Buffer 1 (10 mM Tris, pH 7.6; 1 mM EDTA; 1% SDS) for 10 min at 65°C. 150 µl Elution Buffer 2 (10 mM Tris, pH 7.6; 1 mM EDTA; 0.67% SDS) is added and treated with RNase A (Roche Applied Science) for 30 min at 37°C, and then with Proteinase K (Roche Applied Science) overnight at 65°C. DNA is recovered using a MinElute PCR Purification Kit (QIAGEN). DNA was quantified by Qubit dsDNA High Sensitivity Quantification. Libraries were constructed with 25 ng DNA using the KAPA Hyper Prep Kit (KAPA Biosystems) with NEXTflex DNA Barcodes (BIOO Scientific). Libraries were constructed with 25 ng DNA using the KAPA Hyper Prep Kit (KAPA Biosystems) with NEXTflex DNA Barcodes (BIOO Scientific).

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
82643537
Reads aligned (%)
80.8
Duplicates removed (%)
17.1
Number of peaks
43471 (qval < 1E-05)

hg38

Number of total reads
82643537
Reads aligned (%)
82.7
Duplicates removed (%)
15.7
Number of peaks
44086 (qval < 1E-05)

Base call quality data from DBCLS SRA