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Sample GSM5060465 Query DataSets for GSM5060465
Status Public on Sep 15, 2021
Title CX-5461 ES
Sample type SRA
 
Source name ES cells
Organism Mus musculus
Characteristics cell type: CX-5461 treated ES cells
Growth protocol Mouse ES cells were cultured on 0.1% gelatin-coated plates with MEF feeder cells in LIF/2i media for 2 days.
Extracted molecule genomic DNA
Extraction protocol 10^6 cells were cross-linked for 10 min with 1% final concentration fresh formaldehyde and quenched by 0.2M glycine for 5 min. The cross-linked cells were subsequently lysed in lysis buffer. Extracted nuclei were re-suspended with 150 μl 0.1% SDS and incubated at 65°C for 10 min, then SDS were quenched by 120 μl water and 30 μl 10% Triton X-100, and incubated at 37 °C for 15 min.
Purified DNA was sheared to a length of ~400 bp. Point ligation junctions were pulled down by Dynabeads MyOne Streptavidin C1(Thermofisher) according to manufacturers` instructions. The Hi-C library for Illumina sequencing was prepared by NEBNext Ultra II DNA library Prep Kit for Illumina (NEB) according to manufacturers` instructions. The final library was sequenced on the Illumina HiSeq X Ten platform (San Diego, CA, United States) with 150PEmode. Two replicates were generated for one group material.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Data processing Basecalls performed using CASAVA version 1.8
Short sequencing reads were first independently mapped to mouse mm10 reference genome using the bowtie2 aligner with end-to-end algorithm and ‘-very-sensitive’ option. To rescue the chimaeric fragments spanning the ligation junction, the ligation site was detected and the 5’ fraction of the reads was aligned back to the reference genome. Unmapped reads, multiple mapped reads and singletons were then discarded. Pairs of aligned reads were then assigned to MboI restriction fragments. Read pairs from uncut DNA, self-circle ligation and PCR artefacts were filtered out and the valid read pairs involving two different restriction fragments were used to build the contact matrix. Valid read pairs were then binned at a 40kb and 150kb resolution by dividing the genome into bins of equal size.
The binned interaction matrices were then corrected using Knight–Ruiz matrix balancing method using HiCExplorer (https://hicexplorer.readthedocs.io/en/latest/) (Version 3.3) hicCorrectMatrix command with --correctionMethod KR option. The Observed/Expected (O/E) Hi-C matrix and Pearson Hi-C matrix was obtained by HiCExplorer hicTransform command with --method obs_exp_norm and --method pearson option, respectively.
Aggregate analyses of OE matrices at MERVL were performed in 40kb matrices in a 2mb window around the central region. Visualization of Hi-C matrix was carried out by R software.
Genome_build: mm10
Supplementary_files_format_and_content: text generated using HiC-Pro
 
Submission date Feb 02, 2021
Last update date Sep 15, 2021
Contact name Hua Yu
E-mail(s) huayu@zju.edu.cn
Phone 18758008246
Organization name Zhejiang University
Street address 866 Yuhangtang Rd
City Hangzhou
ZIP/Postal code 310058
Country China
 
Platform ID GPL17021
Series (2)
GSE166032 rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin [Hi-C]
GSE166041 rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin
Relations
BioSample SAMN17764768
SRA SRX10008819

Supplementary file Size Download File type/resource
GSM5060465_CX-5461.allValidPairs.txt.gz 1.1 Gb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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