Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SIX5

Cell type

Cell type Class
Blood
Cell type
GM12878
Tissue
blood
Lineage
mesoderm
Description
B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

Attributes by original data submitter

Sample

source_name
GM12878
biomaterial_provider
GM12878
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell description
B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus
antibody antibodydescription
Six5 (K-20) Goat polyclonal IgG, 200?g/ml. Epitope mapping near the C-terminus of Six5 of human origin. Recommended for detection of Six5 of human origin by WB, IF and ELISA. Antibody Target: SIX5
antibody targetdescription
The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2.
antibody vendorname
Santa Cruz Biotechnology
antibody vendorid
sc-55706
protocol description
one 15-cycle round of PCR (Myers)
controlid
SL1394,SL1395
labexpid
SL1200,SL1061
replicate
1,2
softwareversion
MACS
antibody targetdescription
The protein encoded by this gene is a homeodomain-containing transcription factor that appears to function in the regulation of organogenesis. This gene is located downstream of the dystrophia myotonica-protein kinase gene. Mutations in this geneare a cause of branchiootorenal syndrome type 2.
antibody vendorname
Santa Cruz Biotech
antibody vendorid
sc-55706
treatment
None
treatment description
No special treatment or protocol applies
protocol
PCR1x
protocol description
1-cycle of PCR (Myers)
controlid
SL1394
labexpid
SL1061
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM803338: HudsonAlpha_ChipSeq_GM12878_SIX5_PCR1x
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
82953168
Reads aligned (%)
36.2
Duplicates removed (%)
41.7
Number of peaks
5571 (qval < 1E-05)

hg38

Number of total reads
82953168
Reads aligned (%)
37.4
Duplicates removed (%)
45.0
Number of peaks
5210 (qval < 1E-05)

Base call quality data from DBCLS SRA