Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Neural
Cell type
SK-N-SH
Primary Tissue
Brain
Tissue Diagnosis
Neuroblastoma

Attributes by original data submitter

Sample

source_name
SK-N-SH_RA
biomaterial_provider
ATCC
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell description
neuroblastoma cell line, treatment: differentiated with retinoic acid, (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)
antibody antibodydescription
Rabbit polyclonal. Antibody Target: CTCF
antibody targetdescription
CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
antibody vendorname
Millipore
antibody vendorid
07-729
controlid
SL2905
labexpid
SL2914,SL2906
replicate
1,2
softwareversion
MACS
antibody antibodydescription
rabbit polyclonal
antibody targetdescription
CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
antibody vendorname
Millipore
antibody vendorid
07-729
treatment
None
treatment description
No special treatment or protocol applies
protocol
v041610.2
protocol description
2x10^7 cells, fragmentation by probe-in sonicator, one 15-cycle round of PCR (Myers)
controlid
SL2905
labexpid
SL2906
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM803333: HudsonAlpha_ChipSeq_SK-N-SH_RA_CTCF_v041610.2
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
38944213
Reads aligned (%)
54.3
Duplicates removed (%)
28.7
Number of peaks
45685 (qval < 1E-05)

hg38

Number of total reads
38944213
Reads aligned (%)
55.4
Duplicates removed (%)
27.9
Number of peaks
45780 (qval < 1E-05)

Base call quality data from DBCLS SRA