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Sample GSM3579861 Query DataSets for GSM3579861
Status Public on Jan 25, 2019
Title 680kinv.B10 [Capture Hi-C]
Sample type SRA
 
Source name 680kinv.B10
Organism Mus musculus
Characteristics cell type: mESC
hybrid cells: cas/129
Growth protocol Mouse ESCs were maintained on 1% gelatin coated dishes. Hybrid cells (Cas/129) were grown in DMEM supplemented with 2i plus LIF. ESC to NPC differentiation was carried out as previously described (Abranches et al., 2009). mESCs were plated on 0.1% gelatin-coated dishes in serum-free ESGRO Complete Clonal Grade medium (Millipore Inc.) at high density. After 24 hours, cells were passaged to RHB-A media (Stem Cell Science Inc.) at the density of 1x10^4cells/cm2 and maintained for 12 days with media changed every other day.
Extracted molecule genomic DNA
Extraction protocol Capture Hi-C enriching 45488946-50879849 on chromosome 16 was performed as previously described (Dryden et al., 2014). Hi-C libraries from 25 million cells were constructed with 4 base cutter MboI, and target enrichment was performed using Agilent SureSelect RNA oligo system with custom designed capture probes (50bp RNA targeting Mbo1 fragments containing at least 1 SNP). Capture Hi-C libraries were then sequenced on Illumina NextSeq 550 with 150bp pair end.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model NextSeq 550
 
Data processing Reads were trimmed by Trim Galore! (https://github.com/FelixKrueger/TrimGalore).
Mapped to mm10 using HiCUP v0.5.9 (Wingett et al., 2015).
Allele parsed using SNPsplit v0.3.0 (Krueger and Andrews, 2016).
Capture Hi-C heatmaps were plotted in R using interaction matrix for 10kb windows.
Genome_build: mm10
Supplementary_files_format_and_content: *mat: Tab-delimited text
 
Submission date Jan 25, 2019
Last update date Jan 26, 2019
Contact name David M Gilbert
Organization name Florida State University
Department Biology
Lab Gilbert
Street address 319 Stadium Drive
City Tallahassee
State/province FL
ZIP/Postal code 32306-4295
Country USA
 
Platform ID GPL21626
Series (2)
GSE114139 Identification of cis elements for temporal and spatial control of DNA replication
GSE114619 Identification of cis elements for temporal and spatial control of DNA replication [Capture Hi-C]
Relations
BioSample SAMN10820084
SRA SRX5292021

Supplementary file Size Download File type/resource
GSM3579861_680k.inv.B10.G1.linear_mm10.ENRICHED_REGION_10KB.mat.gz 539.4 Kb (ftp)(http) MAT
GSM3579861_680k.inv.B10.G2_mm10.ENRICHED_REGION_10KB.mat.gz 540.1 Kb (ftp)(http) MAT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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