 |
 |
GEO help: Mouse over screen elements for information. |
|
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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
 |