Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
NFIC

Cell type

Cell type Class
Liver
Cell type
Hep G2
Primary Tissue
Liver
Tissue Diagnosis
Carcinoma Hepatocellular

Attributes by original data submitter

Sample

GEO Accession
GSM1010741
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
hepatocellular carcinoma
cell karyotype
cancer
cell lineage
endoderm
cell organism
human
cell sex
M
cell
HepG2
controlid
SL6019
datatype description
Chromatin IP Sequencing
datatype
ChipSeq
lab description
Myers - Hudson Alpha Institute for Biotechnology
lab
HudsonAlpha
labexpid
SL7554,SL7102
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
GSM1010741: HudsonAlpha_ChipSeq_HepG2_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
83345338
Reads aligned (%)
67.7
Duplicates removed (%)
11.7
Number of peaks
27196 (qval < 1E-05)

hg38

Number of total reads
83345338
Reads aligned (%)
68.7
Duplicates removed (%)
10.9
Number of peaks
27387 (qval < 1E-05)

Base call quality data from DBCLS SRA