GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM2411256 Query DataSets for GSM2411256
Status Public on Dec 05, 2017
Title Hi-C E3.5ICM_rep2
Sample type SRA
Source name Embryo
Organism Mus musculus
Characteristics strain: C57BL/6N x PWK/PhJ
developmental stage: E3.5
tissue: Inner cell mass
Treatment protocol C57BL/6N female mice were induced for superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin and 5 IU of human chorionic gonadotrophin (44-48 hours apart) and mated to DBA/2N males.
Extracted molecule genomic DNA
Extraction protocol After trypsin and pancreatic enzyme digestion followed by mechanical dissection to separate epiblast and visceral endoderm, embryonic cells were washed with PBS and incubated in lysis buffer. Hi-C libraries were prepared using a protocol described in Du et al., Nature, 2017, 547(7662):232.
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model HiSeq X Ten
Description HI-C
processed data file: Hi-C_processed_data_files.tar.gz.
Data processing Basecalls were performed using CASAVA version 1.8.
Sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the mm9 reference genome in a two-step approach with Bowtie2. Next, the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb bin size was used and a 40Kb bin size was used for examination of local domain level contacts. The raw contact counts were normalized with iterative correction.
Genome build: mm9.
Processed data files format and content: The compartment files contain the values which indicate compartment A (more than 0) or compartment B (less than 0) in 100kb bin in the genome. The matrix txt file includes the interaction frequency between the two bins (represented by the number in the bed file) in first two columns. These files are available in a tar archive on the series record.
Submission date Nov 30, 2016
Last update date May 15, 2019
Contact name Wei Xie
Organization name Tsinghua University
Street address Zhongguancun north street
City Beijing
ZIP/Postal code 100084
Country China
Platform ID GPL21273
Series (1)
GSE76505 Dynamic epigenomic landscapes during early lineage specification in mouse embryos
BioSample SAMN06090783
SRA SRX2385124

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap