|
| Status |
Public on Oct 25, 2023 |
| Title |
Frog sperm biol. rep. 2 |
| Sample type |
SRA |
| |
|
| Source name |
Xenopus laevis sperm isolated from testes by density gradient centrifugation (DGC)
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue: Xenopus laevis sperm isolated from testes by density gradient centrifugation (DGC)
cell type: Xenopus laevis sperm
|
| Treatment protocol |
Some of the frog sperm samples were de-membranated. Two of the XL177 samples were crosslinked in either PBS or Xenopus egg extract (ULSS). Some of the pronuclei samples were treated by adding recombinant CTCF protein.
|
| Growth protocol |
Xenopus laevis XL177 cells were cultured at 16-20º C in medium containing 65% Leibovitz’s L-15 (Thermo Fisher Scientific, #11415064), 15% FBS (Gibco, 10270106), 20% H2O, 100 U/ml Penicillin and 100 µg/ml Streptomycin (Sigma, P0781). Pronuclei were generated by incubating de-membranated Xenopus laevis sperm in Xenopus egg extract. Human, mouse and frog sperm cells were isolated by density gradient centrifugation or swim-up.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Hi-C was performed according to the previously described in situ Hi-C protocol (Rao et al., Cell 2014).
Hi-C libraries were prepared according to the previously described in situ Hi-C protocol (Rao et al., Cell 2014).
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalling software: Illumina RTA
Hi-C preprocessing of PE fastq files using hicup version 0.7.1
bowtie2 version 2.2.5 mapping against hg19, mm9 and Xenopus laevis v9.2 reference assemblies
truncating, mapping, filtering and deduplicating of Hi-C raw data through hicup process, conversion to input files for HOMER software and juicer tools.
Analyzing Hi-C data with Homer for TAD detection and insulation scores.
juicer tools pre version 1.22.01 to derive .hic files (Aiden Lab) containing Hi-C matrices for usage with Juicebox and juicer tools for further Hi-C processing like loop a.k. corner peak calling using hiccups subroutine.
Assembly: hg19, mm9 and Xenopus laevis v9.2
Supplementary files format and content: hic files: contain Hi-C matrices for usage with Juicebox, made with juicer tools pre command.
|
| |
|
| Submission date |
Jul 11, 2023 |
| Last update date |
Oct 25, 2023 |
| Contact name |
Roman R Stocsits |
| E-mail(s) |
[email protected]
|
| Organization name |
IMP - Research Institute of Molecular Pathology
|
| Lab |
Jan-Michael Peters' Lab
|
| Street address |
Campus-Vienna-Biocenter 1
|
| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL18936 |
| Series (2) |
| GSE237050 |
Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei |
| GSE237051 |
Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei |
|
| Relations |
| BioSample |
SAMN36405488 |
| SRA |
SRX20980225 |
