Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NFIC

Cell type

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

Attributes by original data submitter

Sample

GEO Accession
GSM1010880
antibody antibodydescription
Mouse monoclonal IgG, raised against a recombinant protein corresponding to an internal region of NF-1 of human origin. Antibody Target: NFIC
antibody targetdescription
Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.
antibody vendorid
sc-81335
antibody vendorname
Santa Cruz Biotechnology
antibody
NFIC_(SC-81335)
cell description
neuroblastoma, newly promoted to tier 2: not in 2011 analysis, the SK-N-SH line was established from a neuroblastoma in a 4 year old individual.
cell karyotype
cancer
cell lineage
ectoderm
cell organism
human
cell sex
F
cell
SK-N-SH
controlid
SL12791,SL13505
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL14603,SL13313
protocol description
Faster ChIP protocol & AMpure XP size selection for ChIP-seq (Myers)
protocol
v042211.1
replicate
1,2
softwareversion
MACS
treatment description
No special treatment or protocol applies
treatment
None

Sequenced DNA Library

library_name
GSM1010880: HudsonAlpha_ChipSeq_SK-N-SH_NFIC_(SC-81335)_v042211.1
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibTfbs

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
72448814
Reads aligned (%)
76.8
Duplicates removed (%)
8.3
Number of peaks
55728 (qval < 1E-05)

hg38

Number of total reads
72448814
Reads aligned (%)
78.2
Duplicates removed (%)
7.2
Number of peaks
55938 (qval < 1E-05)

Base call quality data from DBCLS SRA