Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PITX3

Cell type

Cell type Class
Neural
Cell type
SH-SY5Y
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

source_name
SHSY5Y cells stably expressing mouse Pitx3-3Fn
cell line
SHSY5Y
cell type
Midbrain Dopamine Neurons
chip antibody
Pulichino et al. 2003

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP experiment was performed as previously reported with few modifications (Langlais et al, Molecular Cell 2012). Briefly, human SHSY5Y cells stably expressing mouse Pitx3-3Fn were grown to 90% confluence, fixed in 1% formaldehyde/PBS for 5min at room temperature, washed, scraped off from the petri and sonicated to yield chromatin fragments with average size of 300-600bp. Sheared chromatin was incubated overnight at 4˚C along with 1:1 mix of Dynabeads-Protein A:Dynabeads-Protein G (Invitrogen) already coupled to primary antibody and thoroughly washed. Primary antibodies that were used were against the native form of Pitx3 (rabbit polyclonal, home-made) and Pitx3-Flag forms (mouse FlagM2, Sigma), including also rabbit (G2018, Sigma) or mouse (I5381, Sigma) IgG as controls for specific antibodies. Immunoprecipitated chromatin was washed, de-crosslinked, and then briefly treated with proteinase K and RNAse A. DNA from input, specific antibody and IgG was then purified using Qiaquick PCR purification kit (Qiagen). Immunoprecipitated DNA was sent for sequencing on Illumina GAIIx or Hi-Seq 2000 according to McGill University and Genome Quebec Innovation Centre protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
36384395
Reads aligned (%)
88.8
Duplicates removed (%)
8.3
Number of peaks
23301 (qval < 1E-05)

hg38

Number of total reads
36384395
Reads aligned (%)
90.1
Duplicates removed (%)
7.5
Number of peaks
23403 (qval < 1E-05)

Base call quality data from DBCLS SRA