Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GATA3

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
Human ALL Cell Line
cell line
JURKAT
chip antibody
Cell Signaling: 5852

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA was extracted from MLL-AF9 murine leukemic cells lysed in TRI, and collected on Direct-Zol miniprep columns with on-column DNAse digestion. 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
27815790
Reads aligned (%)
87.7
Duplicates removed (%)
7.0
Number of peaks
17072 (qval < 1E-05)

hg38

Number of total reads
27815790
Reads aligned (%)
89.2
Duplicates removed (%)
6.0
Number of peaks
16864 (qval < 1E-05)

Base call quality data from DBCLS SRA