Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TCF4

Cell type

Cell type Class
Blood
Cell type
CAL-1
NA
NA

Attributes by original data submitter

Sample

source_name
Cal-1 TCF4 mAb
cell line
Cal-1
cell type
BPDCN (blastic plasmacytoid dendritic cell neoplasm) cells
disease state
BPDCN (blastic plasmacytoid dendritic cell neoplasm)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
TCF4 mAb Extraction Other: For the TCF4 ChIP-Seq, 5x10(7) exponentially growing cells were collected by centrifugation, resuspended in room temperature RPMI without FBS ( 2x10(6) cells/ml) and cross-linked with 1% formaldehyde for 5 min at RT. Cross-linking was quenched by addition of 125 mM Glycine for 5 min at RT. Cross-linked cells were first washed with ice-cold PBS and then resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% Sodium Deoxycholate) to a final concentration of 5x10(6) cell/ml. DNA was sheared with a Misonix XL sonicator, by performing 12 x 45'' sonication cycles at power setting of 5. For the immune precipitation reaction, 2.0x10(7) chromatin cell equivalents were incubated overnight with rabbit monoclonal TCF4 antibody developed by Epitomics. The following day, chromatin/antibody complexes were incubated with 50 ul of Protein G magnetic beads (Invitrogen) for 4 h at 4C. Protein G bound complexes were washed 4 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNAse A (0.2 ug/ul). Reverse cross-link was performed overnight at 65C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN). ChIP DNA was used to generate ChIP-Seq libraries with the NEXTflexTM Illumina ChIP- Seq Library Prep Kit (Bio Scientific), according to manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg19

Number of total reads
37550794
Reads aligned (%)
65.2
Duplicates removed (%)
10.7
Number of peaks
47850 (qval < 1E-05)

hg38

Number of total reads
37550794
Reads aligned (%)
66.0
Duplicates removed (%)
10.1
Number of peaks
47871 (qval < 1E-05)

Base call quality data from DBCLS SRA