Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
BAP1

Cell type

Cell type Class
Breast
Cell type
CAL-51
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
CAL51
cell type
breast cancer cell
passages
Low passages (6-10)
sample type
BAP1_FL_CAL51_BAP1_WT_R1
chip antibody
BAP1_FL (homemade)
genotype/variation
wild type BAP1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit. ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg of total RNA was used as starting material. Libraries were validated using the Agilent DNA 1000 Kit

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
39853425
Reads aligned (%)
89.8
Duplicates removed (%)
7.9
Number of peaks
3105 (qval < 1E-05)

hg38

Number of total reads
39853425
Reads aligned (%)
91.0
Duplicates removed (%)
7.2
Number of peaks
3300 (qval < 1E-05)

Base call quality data from DBCLS SRA