Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GATA3

Cell type

Cell type Class
Neural
Cell type
CLB-Ga
NA
NA

Attributes by original data submitter

Sample

source_name
CLB-GA
cell type
Neuroblastoma cell line
chip antibody
sc-22206X (goat polyclonal)
treatment
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: Chromatin preparation and ChIP were performed with Ideal ChIP-seq kit for histones or transcription factors according to the supplier's protocol (Diagenode ) ChIP-seq: llumina sequencing libraries were prepared from ChIP and input DNAs using the TruSeq ChIP library preparation kit according to the manufacturer’s protocol. Briefly, DNA were subjected to consecutive steps of end-repair, dA-tailing and ligation to TruSeq indexed Illumina adapters. Size-selection was performed only for the H3K27ac ChIP (100 – 600 bp). After a final amplification step, the resulting DNA libraries were quantified using a qPCR method (KAPA library quantification kit) and sequenced on the Illumina HiSeq2500 instrument (rapid run mode; single reads 100 nts). RNA-seq: Total RNA was extracted from fresh cells or frozen tumors using TRIzol® Reagent (Invitrogen), or AllPrep DNA/RNA Mini Kit (Qiagen) or NucleoSpin RNA kit (Macherey-Nagel; for the SK-N-SH cell line treated with chemotherapy). All samples were subjected to quality control on a Bioanalyzer instrument and only RNA with RIN (RNA Integrity Number) > 6 were used for sequencing. RNA-seq: RNA sequencing libraries were prepared from 1 µg of total RNA using the Illumina TruSeq Stranded mRNA Library preparation kit which allows performing a strand-specific sequencing. A first step of polyA selection using magnetic beads is done to focus sequencing on polyadenylated transcripts. After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing and then ligated to the TruSeq indexed adapters. PCR amplification is finally achieved to create the final cDNA library. After qPCR quantification, sequencing was carried out using 2 x 50 cycles (paired-end reads 50 nts) for all samples (except SH-EP, 2 x 100; Pair1-Relapse and Pair3-Relapse, 2 x 75; Pair2-Relapse, 2 x 150). Sequencing was performed with the Illumina HiSeq2500 instrument (high output mode).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
26758587
Reads aligned (%)
75.9
Duplicates removed (%)
24.0
Number of peaks
6683 (qval < 1E-05)

hg38

Number of total reads
26758587
Reads aligned (%)
76.1
Duplicates removed (%)
23.9
Number of peaks
6684 (qval < 1E-05)

Base call quality data from DBCLS SRA