 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 05, 2019 |
| Title |
HiC_Retina_P0-Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
retina
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: retina
developmental stage: postnatal day 0
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
In situ Hi-C protocol was performed using retinal cells, with minor modification to the original protocol (Rao et al., 2014). Two to five million cells were crosslinked with 1% formaldehyde for 10 min at room temperature, then digested with 125 units of MboI overnight followed by labeling with biotinylated nucleotides and proximity ligation.
After reverse crosslinking, ligated DNA was purified and sheared to 300-500 bp using a Covaris LE220.
The DNA fragments containing ligation junctions were pulled down with streptavidin beads followed by Illumina compatible library construction and paired end sequencing.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
hic_Retina_P0.inter_30.hic
Proc.HiC_Retina_P0.tgz
|
| Data processing |
Basecalls performed using CASAVA
All HiC data have been processed by the Juicer pipeline (version 1.5) against mouse genome mm9. We confirmed the data were reproducible before merging the files from technical or biological replicates using HiC-spector (version 201706028 from github).
All 5 samples had more than 4.9 billion contacts and 3 samples had >7.5 billion contacts providing a resolution less than 1 kb. Stable loops were identified using HiCCUPS from Juicer at 5kb and 10kb resolution. The highest quality (MAPQ > 30), 370~640 loops were called from each sample and those that were less than 3 Mb were included in the visualization online.
Using Juicebox tools from Juicer pipeline, we extracted contact matrixes from .hic file created by Juicer and call TADs or Loops as below. File name suffix "HiCCUPS.loops": Loops called using HiCCUPS (default parameters and "--ignore_sparsity") come with Juicer pipeline(Durand, Cell Syst, 2016). File name suffix "ArrowHead.5000_blocks": TADs called using Arrowhead(default parameters and "--ignore_sparsity") come with Juicer pipeline(Durand, Cell Syst, 2016). File name suffix "DOM.DC.NONE.100K.bed": TADs called using DomainCaller(Dixon, Nature, 2012. Default parameters using matlab2017b) at 100kb resolution on raw contacts. File name suffix "DOM.DC.VC_SQRT.100K.bed": TADs called using DomainCaller(Dixon, Nature, 2012. Default parameters using matlab2017b) at 100kb resolution on VC_SQRT(Rao, 2014, Cell) normalized contacts. File name suffix "NONE.100K.bed": TADs called using Armatus(Filippova, Algorithms Mol Biol, 2014. Parameters "-m -g 0.2 -s 0.1") at 100kb resolution on raw contacts. File name suffix "KR.100K.bed": TADs called using Armatus(Filippova, Algorithms Mol Biol, 2014. Parameters "-m -g 0.2 -s 0.1") at 100kb resolution on Knight-Ruiz (Rao et al, 2014, Cell) normalized contacts. File name suffix "VC_SQRT.100K.bed": TADs called using Armatus(Filippova, Algorithms Mol Biol, 2014. Parameters "-m -g 0.2 -s 0.1") at 100kb resolution on VC_SQRT (Rao et al, 2014, Cell) normalized contacts. File name suffix "100K.VCS-KR.vote.bed": TADs merged "VC_SQRT.100K.bed" and "KR.100K.bed" after removing TADs called in "KR.100K.bed" overlapping TADs called in "VC_SQRT.100K.bed"
Genome_build: mm9(MGSCv37)
Supplementary_files_format_and_content: HiC file version: 8; multiple bed files instructed in README.txt.
|
| |
|
| Submission date |
Aug 06, 2019 |
| Last update date |
Oct 24, 2019 |
| Contact name |
Beisi Xu |
| E-mail(s) |
beisi.xu@stjude.org
|
| Organization name |
St Jude Children's Research Hosipital
|
| Department |
Center for Applied Bioinformatics
|
| Street address |
262 Danny Thomas Pl
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE87064 |
The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis |
| GSE135465 |
Nucleome Dynamics during Retinal Development[Hi-C_Mm] |
|
| Relations |
| BioSample |
SAMN12505193 |
| SRA |
SRX6657343 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
