Illumina HiSeq 2500 sequencing; Cyclin D1 ChIP-seq in H9 undifferentiated human pluripotent stem cells
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
No description
Antigen
NA
Cell type
Cell type Class
Pluripotent stem cell
Cell type
hESC H9
NA
NA
Attributes by original data submitter
Sample
ENA first public
2016-02-01
ENA last update
2018-03-09
ENA-CHECKLIST
ERC000011
External Id
SAMEA3498901
INSDC center alias
Wellcome Trust-Medical Research Council Stem Cell Institute, Anne McLaren Laboratory, Department of Surgery, University of Cambridge
INSDC center name
Wellcome Trust-Medical Research Council Stem Cell Institute, Anne McLaren Laboratory, Department of Surgery, University of Cambridge
INSDC first public
2016-02-01T17:01:35Z
INSDC last update
2018-03-09T02:31:57Z
INSDC status
public
Submitter Id
E-MTAB-3807:Cyclin D1 ChIP replicate 1
broker name
ArrayExpress
cell line
H9
cell type
embryonic stem cell
common name
human
sample name
E-MTAB-3807:Cyclin D1 ChIP replicate 1
Sequenced DNA Library
library_name
Cyclin D1 ChIP replicate 1
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
hESCs were washed with PBS and detached from the plate by incubating them for 10 min at 37 °C in Cell Dissociation Buffer (Gibco). ChIP was carried out as described before (Bienvenu et al. 2010; Casimiro et al. 2012; Pauklin and Vallier 2013), except that crosslinking was performed in solution in PBS if samples were sorted by FACS. Data for each cell cycle was normalized to IgG control of each cell cycle phase. We used additional controls as follows: 1) Input of each cell cycle phase and 2) primers for a chromatin region downstream of Smad7 locus known to be negative for histone marks. All of these controls supported our results indicating an enrichment of Cyclin D proteins to neuroectoderm and endoderm loci in late G1 phase. Antibodies for Cyclin D ChIP have been used previously (Landis et al. 2006). Two biological replicates and one input DNA as control sample were sequenced at the Cambridge Institute NGS service of the University of Cambridge using Illumina HiSeq. Nucleic acid libraries were constructed by the Cambridge SCI Sequencing facility