 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Oct 18, 2017 |
| Title |
HiC_ES_4 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells (ES)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: embryonic stem cells (ES)
strain/genotype: Oct4-GFP
sorting: GFP+/G0G1+
|
| Growth protocol |
E14Tg2a, Oct4-GFP and Sox1-GFP feeder-free or Tau-GFP (grown on irradiated CF-1 MEF feeders (Tebu-Bio, Cat.N: GSC-6001G)) cell lines were maintained as described in (Gaspard et. al., 2009). In brief, cells were cultured in DMEM (ThermoFished, Cat.N:21969-035), suppelemented with 15% FBS (ES-qualified, ThermoFished, Cat.N:16141-079) 1,000 U ml of LIF (Millipore, Cat.N: ESG1106), 0.1 mM of non-essential amino acids (ThermoFished, Cat.N: 11140-035), 1 mM of glutamax (ThermoFisher, Cat.N: 35050-038), 50U of penicillin and streptomycin (ThermoFirsher, Cat.N: 15070-063) and 0.1 mM of 2-mercaptoethanol (ThermoFisher, Cat.N: 31350-010). Media was changed every day and cells were passaged every two days using StemPro Accutase (ThermoFisher, Cat.N: A11105-01).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
HiC and library preparation was carried out using the in-situ method as described previously (Rao et. al., 2014) with minor modifications. In order to maximize library complexity, FACS-purified samples were split into batches of 1x10^6 cells and processed separately. In brief, cells were digested overnight at 37C using 500U of DpnII. After biotin filling, proximity ligation was carried out for 4 hours at 18C with 2000U T4 DNA Ligase. After reverse-crosslinking, DNA was purified using ethanol precipitation and sheared to 300-400bp fragments using Covaris S220 sonicator.
Ligation fragments containing biotin were immobilized on MyOne Streptavidin T1 beads (ThermoFished Cat.N: 65602), end-repaired and a-tailed as described. NEXTflex adaptors (Bioo Scientific, Cat.N: 514101) were then ligated and fragments were PCR amplified using KAPA HiFi Library Ampification Kit (Kapa Biosystems, Cat.N: KK2620) for 6-8 cycles. DNA was then double-size selected using AMPure XP beads (Agencourt, Cat.N: A63881) in order to isolate fragments between 300 and 800bp.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Library strategy: HiC
Hi-C data was processed using the Cwalks pipeline (http://compgenomics.weizmann.ac.il/tanay/?page_id=690). In brief, raw sequencing reads were mapped independently to the mm10 reference genome using Bowtie2 in local alignment mode. The uniquely mapped (MAPQ > 36) reads were translated into a pair of fragment-ends (fends) by associating each read with its downstream fend. PCR duplicates and reads mapping to the same restriction fragment were excluded.
supplementary_files_format_and_content:Each processed file represent pairwise information of the observed genome contacts and can be further analyzed using the "Shaman" pipeline (https://bitbucket.org/tanaylab/shaman).
assembly: mm10
|
| |
|
| Submission date |
Mar 11, 2017 |
| Last update date |
Apr 06, 2023 |
| Contact name |
Boyan Bonev |
| E-mail(s) |
boyan.bonev@igh.cnrs.fr
|
| Organization name |
Institute of Human Genetics - CNRS
|
| Lab |
Giacomo Cavalli
|
| Street address |
141 rue de la Cardonille
|
| City |
Montpellier |
| ZIP/Postal code |
34396 |
| Country |
France |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE96107 |
Multi-scale 3D genome rewiring during mouse neural development |
|
| Relations |
| Reanalyzed by |
GSE161259 |
| Reanalyzed by |
GSE161378 |
| Reanalyzed by |
GSE229113 |
| BioSample |
SAMN06564302 |
| SRA |
SRX2636669 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2533821_gc_es4.tar.gz |
4.0 Gb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
