|
| Status |
Public on Jul 07, 2021 |
| Title |
BDXNY-Xen-mitotic-dilution-IGG-R1-T1 |
| Sample type |
SRA |
| |
|
| Source name |
Individual Xenopus
|
| Organism |
Xenopus laevis |
| Characteristics |
protocol: Hi-C
enzyme: DpnII
cell line: Xenopus sperm
antibody: IGG
treatment: Depletion of protein in Egg extract with described antibody, before fixation samples were diluted
protocol: Egg extract added to demembranated sperm nuclei to make reconstituted mitotic chromosomes.
|
| Treatment protocol |
Extract was either depleted with specific antibody or with control IGG
|
| Growth protocol |
Egg extract was isolated from Xenopus Eggs
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
half million sperm was used as input for reconstituting chromosomes
Hi-C was performed as described in detail in supplemental methods, DpnII enzyme.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Hi-C FASTQ sequencing files were mapped to the Xenopus Leavis 9.2 Genome
publicly available distiller-nf mapping pipeline (https://github.com/mirnylab/distiller-nf) and downstream
analysis tools pairtools (https://github.com/mirnylab/pairtools) and cooltools
(https://github.com/mirnylab/cooltools).
Genome_build: Xenopus laevis 9.2
Supplementary_files_format_and_content: multicooler files (.mcool) for all interactions
|
| |
|
| Submission date |
Jan 08, 2021 |
| Last update date |
Jul 07, 2021 |
| Contact name |
Bastiaan Dekker |
| E-mail(s) |
bastiaan.dekker@umassmed.edu
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Systems Biology
|
| Lab |
Dekker lab
|
| Street address |
368 Plantation street
|
| City |
Worcester |
| State/province |
Massachusetts |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL22393 |
| Series (1) |
| GSE164434 |
Linker histone H1.8 inhibits chromatin-binding of condensins and DNA topoisomerase II to tune chromosome compaction and individualization |
|
| Relations |
| BioSample |
SAMN17257713 |
| SRA |
SRX9805847 |
