Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Embryo
Cell type
Neural tissue
NA
NA

Attributes by original data submitter

Sample

ENA first public
2019-02-23
ENA last update
2019-02-13
ENA-CHECKLIST
ERC000011
External Id
SAMEA5335941
INSDC center alias
Wellome Sanger Institute
INSDC center name
Wellome Sanger Institute
INSDC first public
2019-02-23T17:02:14Z
INSDC last update
2019-02-13T13:54:27Z
INSDC status
public
Submitter Id
E-MTAB-7252:hiPSC-EPSC_H3K4me3
broker name
ArrayExpress
cell line
C5
cell type
somatic cell
common name
human
developmental stage
late embryo
organism part
neural tissue
sample name
E-MTAB-7252:hiPSC-EPSC_H3K4me3
sex
mixed

Sequenced DNA Library

library_name
hiPSC-EPSC_H3K4me3_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The C5 hiPSC was reprogrammed from the somatic cells derived from post-mortem human fetal neural tissue which was acquired at the time of surgical termination of pregnancy in the day surgery unit of Addenbrookes Hospital, Cambridge. Full informed consent was obtained from participating mothers. All generated lines are unlinked anonymous.. All ​related procedures and experiments were approved by the hospital and Sanger institute. M10 cells were derived from pig fetus fibroblast by reprogramming. Those pig fetus fibroblast cells were derived from a 28-day normal healthy male pig fetus skin. K3 cells were derived from 5-day preimplantation embryos, again, healthy male. All the related embryos and fetus experiments were approved by the Niedersaechsisches Landesamt fuer Verbraucherschutz und Lebensmittelsicherheit, LAVES, Oldenburg Germany. Abbreviations used: PFF means the pig fetus fibroblast. Emb means the origin is 5-day embryos. Parth means parthenogenetic embryos, PGCLC means the primordial germ cell-like cells differentiated from K3 cells. Cells were grown to a final concentration of 5x107 cells for each ChIP-seq experiment. Cells were chemically cross-linked at room temperature by the addition of formaldehyde to 1% final concentration for 10 minutes and quenched with 0.125 M final concentration of glycine. Cross-linked cells were re-suspended in sonication buffer (50mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 1% TritonX-100, 0.1% Na-deoxycholate, 0.1% SDS) and sonicated using a Diagenode Bioruptor for three 10-minute rounds using pulsing settings (30 sec ON; 1 min OFF). 10 µg of sonicated chromatin was then incubated overnight at 4ºC with 5 µg of Flag antibody conjugated to magnetic beads. Following the IP, beads were washed twice with RIPA buffer (50mM Tris-HCl pH8, 150 mM NaCl, 2mM EDTA, 1% NP-40, 0.1% Na-deocycholate, 0.1% SDS), low salt buffer (20mM Tris pH 8.1, 150mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), high salt buffer (20mM Tris pH 8.1, 500mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), LiCl buffer (10mM Tris pH 8.1, 250mM LiCl, 1mM EDTA, 1% Na-deoxycholate, 1% NP-40), and 1X TE. Finally, DNA was extracted by reverse crosslinking at 65ºC overnight with proteinase K (20ug/µL) and 1% SDS followed by phenol:chloroform:isoamyl alcohol purification and ethanol precipitation. Libraries were constructed as indicated above and sequenced using Illumina HiSeq 2500. ChIPed DNA was purified using Qiagen MinElute PCR Purification Kit. Library DNA was purified using AmpureXP beads using 1:1 ratio. Libraries were constructed using Diagenode MicroPlex ChIP kit.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
35230866
Reads aligned (%)
73.5
Duplicates removed (%)
14.9
Number of peaks
23178 (qval < 1E-05)

hg19

Number of total reads
35230866
Reads aligned (%)
73.3
Duplicates removed (%)
15.3
Number of peaks
23192 (qval < 1E-05)

Base call quality data from DBCLS SRA