Illumina HiSeq 2500 sequencing; Epigenetic regulation and transcriptional repression by Tet1 in the early post-implantation mouse embryo: ChIP seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
No description
Antigen
NA
Cell type
Cell type Class
Pluripotent stem cell
Cell type
ES cells
NA
NA
Attributes by original data submitter
Sample
ENA first public
2017-05-15
ENA last update
2017-03-08
ENA-CHECKLIST
ERC000011
External Id
SAMEA103898511
INSDC center alias
Laboratory for Translational Genetics VIB Center for Cancer Biology (CCB) Department of Human Genetics, KULeuven
INSDC center name
Laboratory for Translational Genetics VIB Center for Cancer Biology (CCB) Department of Human Genetics, KULeuven
INSDC first public
2017-05-15T17:01:33Z
INSDC last update
2017-03-08T15:32:13Z
INSDC status
public
Submitter Id
E-MTAB-5562:BT1138
broker name
ArrayExpress
cell line
ESC derived cell line
cell type
epiblast-like cells
common name
house mouse
genotype
pPyCAGIP vector expressing JMJD8(27-271)-V5/His
sample name
E-MTAB-5562:BT1138
sex
male
strain
C57BL/6
Sequenced DNA Library
library_name
BT1138_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
WT cells were collected from a B6 incipient congenic (N5; >95% B6) blastocyst-derived embryonic stem cell line (wt) converted in vitro to epiblast-like cells. homozygous cells for Tet1 gene trap GT(RRG140) were collected from B6 incipient congenic (N5; >95% B6) blastocyst-derived embryonic stem cell line (KO) converted in vitro to epiblast-like cells. Cells were trypsinized and fixed in freshly prepared 1% para-formaldehyde at room temperature for 10 min and quenched with 1.25M glycine. Nuclei were isolated and chromatin was sheared to 200-500bp using Bioruptor sonicator for 20 cycles (30s ON, 30s OFF). Sheared chromatin was immunoprecipated using appropriate antibody and incubated overnight with Dyna beads Protein G (10004D). Immunocomplexes were washed for 5 minutes each with the following buffers: 1X low salt buffer (20mM Tris pH 8.1, 150mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), 1X high salt buffer (20mM Tris pH 8.1, 500mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), 1X LiCl buffer (10mM Tris pH 8.1, 250mM LiCl,1mM EDTA, 1% deoxycholate, 1% NP-40) and 2X TE buffer (+ 50mM NaCl). Chromain was eluted with elution buffer (50 mM Tris-Hcl, pH 8.0, 10 mM EDTA and 1% SDS) and reverse cross-linked by incubation at 65 °C in 5M NaCl buffer over night. DNA was purified using Zymo ChIP DNA Clean & Concentrator Kit (D5205) for library preparation. Library was prepared using NEBNext Ultra DNA Library Prep Kit and sequenced on an Illumina HiSeq 2500