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Sample GSM4120013 Query DataSets for GSM4120013
Status Public on Apr 13, 2020
Title Hi-C Chd4 cKO2
Sample type SRA
 
Source name Hi-C Chd4 cKO
Organism Mus musculus
Characteristics developmental stage: P22
genotype/variation: Chd4 cKO
tissue: Cerebellum
Extracted molecule genomic DNA
Extraction protocol Nuclei were digested and blunt-end ligated in the presence of a biotinylated nucleotide. Ligation complexes were then isolated from sonicated DNA by streptavidin pull-down.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description hicKo2
Data processing HiC-Pro (v2.10.0) was used to generate contact matrices using the mm10 mouse genome as reference (Servant et al., 2015). Valid pairs determined by HiC-Pro was used as input to generate Hi-C contact matrices at 1, 5, 10, 20, 40, 150, 500 kb and 1 million base pair resolutions. addNorm function from Juicer (v1.5.6) was used to perform genome-wide normalization (Durand et al., 2016). Observed over expected (O/E) and Knight-Ruiz (KR)-normalized Hi-C contacts from genomic bins were extracted using juicer-tools (v1.8.9) dump. For visualization of contact matrices in figures S3A and S3E, KR-normalized Hi-C contacts were extracted from genomic bins using juicer-tools (v1.8.9) straw then scaled to the same sequencing depth (Figures S3A, S3E); otherwise, KR-normalized, Observed/Expected Hi-C contacts were extracted from genomic bins using juicer-tools (v1.8.9) dump. Visualization of the Pearson’s matrix was performed using Juicebox (v1.9.8) at 40kb resolution (Durand et al., 2016). The similarity of biological replicates was compared using unnormalized contacts across all chromosomes at 1Mb resolution.
Genome_build: mm10
Supplementary_files_format_and_content: Txt files represent the output from Diffbind. Bed files represent the MACS2-called DHS sites at or outside of transcription start sites. Bedpe files represent the Hi-C domains and loops called by Arrowhead and HiCCUPS, respectively. Hic files represent the binarized Hi-C matrices from individual replicates or the pooled sum of all replicates.
 
Submission date Oct 14, 2019
Last update date Apr 13, 2020
Contact name Jared V Goodman
E-mail(s) jvgoodman@wustl.edu
Organization name Washington University in St. Louis School of Medicine
Street address 4523 Clayton Ave
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
 
Platform ID GPL19057
Series (1)
GSE138822 The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain
Relations
BioSample SAMN13026696
SRA SRX6988635

Supplementary file Size Download File type/resource
GSM4120013_koRep2.hic 2.2 Gb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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