|
| Status |
Public on Mar 30, 2023 |
| Title |
Mouse_deltaGCR_HiC |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic craniofacial tissue
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Embryonic craniofacial tissue
genotype: Homozygous for deletion
developmental stage: E11.5
|
| Treatment protocol |
Tissue crosslinked and frozen immediately after collection
|
| Growth protocol |
Timed matings and harvest of tissue according to approved University of Connecticut Health Center IACUC protocols
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclear extraction-see accompanying manuscript
as per Belaghzal, H., Dekker, J., and Gibcus, J.H. (2017). Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation. Methods 123, 56–65.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
HiC from mouse E11.5 craniofacial tissue (Homozygous for a deletion on Chr 6)
|
| Data processing |
HiC-Pro (v. 2.10.0)
hicexplorer (v. 3.7.1)
convert data processed by HiC-Pro to .hic format: java -Xmx48g -jar ${JUICERTOOLS} pre ${SAMPLE}.bsorted.pairs.gz ${SAMPLE}.hic ${GENOME_SIZE} -f ${REFILE}" > ${JOB_NAME}.slurm
mm10 or hg19
.hic files compatible with juicer or .fastq files for analysis with other hic pipelines
|
| |
|
| Submission date |
Mar 10, 2022 |
| Last update date |
Mar 30, 2023 |
| Contact name |
Justin Cotney |
| Organization name |
UConn Health
|
| Department |
Genetics and Genome Sciences
|
| Street address |
400 Farmington Avenue
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06030-6403 |
| Country |
USA |
| |
|
| Platform ID |
GPL21626 |
| Series (1) |
| GSE198297 |
Chromatin state and chromatin architecture in mouse embryonic craniofacial tissue, neural crest cell culture model and human primary craniofacial tissue |
|
| Relations |
| BioSample |
SAMN26559553 |
| SRA |
SRX14427320 |
