Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Neural
Cell type
Neuro-2a
Tissue
Brain
Cell Type
Neuroblast
Disease
Neuroblastoma

Attributes by original data submitter

Sample

source_name
Zac1 transfected Neuro-2A neuroblastoma cell line
strain
Swiss Albino
cell type
neuroblastoma Neuro-2A
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
16-hours after transfection, cells were fixated using paraformaldehyde, lysated and nuclei were prepared and sonicated. ChIP was performed with an in-house antiZac1 antibody. The protocol described by Kouskouti & Kyrmizi (http://www.epigenome-noe.net/WWW/researchtools/protocol.php?protid=10) was used. Libraries were prepared according to Illumina's instructions using the ChIPseq DNA sample prep kit (IP-102-1001). For each sample, 10ng of DNA was repaired, resulting in blunt end fragments and adenylated on its 3' ends. Illumina's adapters were ligated on adenylated DNA. A sizing step was performed on an agarose gel (fragment size including adapters: 200bp) followed by a 18 cycles PCR to amplify fragments with both adapters. Libraries were validated on a DNA1000 Chip on a Bioanalyzer (Agilent).

Sequencing Platform

instrument_model
Illumina Genome Analyzer

mm10

Number of total reads
9711816
Reads aligned (%)
92.4
Duplicates removed (%)
11.7
Number of peaks
366 (qval < 1E-05)

mm9

Number of total reads
9711816
Reads aligned (%)
92.2
Duplicates removed (%)
12.0
Number of peaks
423 (qval < 1E-05)

Base call quality data from DBCLS SRA