 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 14, 2020 |
| Title |
Wiz-del rep2 (Hi-C) |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic stem cells v6.5
|
| Organism |
Mus musculus |
| Characteristics |
genotype: WIZ deletion
cell line: mESC v6.5
|
| Treatment protocol |
ESCs growing in exponential phase were placed in single cell suspension in 1x PBS with 1% formaldehyde. After 2 minutes, crosslinking was quenched with addition of glycine to 150mM
|
| Growth protocol |
V6.5 murine embryonic stem cells (mESCs) (male) were grown on irradiated murine embryonic fibroblasts under standard conditions, as previously described (Dowen et al, 2014)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C libraries were prepared using the Arima Hi-C kit (Arima Genomics) according to manufacturer's specifications, with one modification. Treatment with DNA ligase was performed for one hour instead of the recommended 15 minutes.
Dual-indexed Illumina sequencing libraries were prepared using Kapa Hyper Prep (Kapa Biosciences, cat.#KK8502) according to specifications provided by Arima Genomics, with one modification. Ligation of sequencing adapters was allowed to proceed for 1 hour instead of the recommended 15 minutes.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
collisions_Wiz-del.txt; inter_30_Wiz-del.hic; merged_loops_Wiz-del.bedpe; contact_domains_25kb_Wiz-del.bedpe
|
| Data processing |
Initial data processing, including merging of replicates, alignment, filtering, and generation of Hi-C contact maps, was perfomed using the Juicer wrapper from the Lieberman-Aiden lab.
Contact domains were called from merged, Knight-Ruiz balanced contact maps at 25kb resolution using the Arrowhead algorithm with default parameters.
Loops were called from merged, Knight-Ruiz balanced contact maps at 5kb, 10kb, and 25kb resolution using the HiCCUPs algorithm with default parameters except: -p 8,4,2 -i 14,10,6
Genome_build: mm10
Supplementary_files_format_and_content: Hi-C matrices are provided in .hic format. Loop and domain calls are provided in .bedpe format.
|
| |
|
| Submission date |
Sep 11, 2019 |
| Last update date |
Apr 14, 2020 |
| Contact name |
Jill Dowen |
| E-mail(s) |
jilldowen@unc.edu
|
| Organization name |
UNC Chapel Hill
|
| Street address |
250 Bell Tower Drive, CB 7100 3360 Genome Sciences Building
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE137274 |
A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity [Hi-C] |
| GSE137285 |
A WIZ/Cohesin/CTCF complex anchors DNA loops to define gene expression and cell identity |
|
| Relations |
| BioSample |
SAMN12730497 |
| SRA |
SRX6831907 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
