|
| Status |
Public on Oct 02, 2023 |
| Title |
Hi-C WT replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
fission yeast cut14-208 mutant cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: condensin cut14-208 mutant
tagged protein: cnd2 tagged with GFP
chip antibody: N/A
|
| Treatment protocol |
None
|
| Growth protocol |
cells exponentailly growing in synthetic PMG medium at 30°C were shifted at 33°C and arrested in metaphase by depletion of the Slp1 protein (APC co-activator) for 3hours, fixed and processed for Hi-C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C protocol
NextFlex DNA Barcoding & PCR mastermix
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Treated for Hi-C
|
| Data processing |
Raw data was processed through the hicstuff pipeline http://doi.org/10.5281/zenodo.4066363 3.1 version
Genome_build: fission yeast genome version ASM294v2
Supplementary_files_format_and_content: Hi-C matrices in .txt format. Supplementary files (available on the series record) include information for interpreting data in the Hi-C matrices: info_contigs.txt and fragments_list.txt
GCA_000002945_Saccharomyces_cerevisiae.fasta correspond to a modified version of the ASM294v2 version of fission yeast genome from NCBI, concatenated with budding yeast genome (R64 - sacCer3). Briefly, the**telomere 2 R*(*Tel2R) sequence from plasmid pNSU70 (Sugawara, NF. Ph.D. thesis. Harvard University, Cambridge, Massachusetts) was aligned with ASM294v2 using Blast, and nucleotides 4137 to 7223 of pNSU70 were added to the end of the current sequence of chromosome 2 to create a TEL2R-extended version of the fission yeast ASM294v2 genome. Next, this TEL2-R extended version of ASM294v2 was concatenated with budding yeast genome (R64 - sacCer3) to create the files GCA_000002945_Saccharomyces_cerevisiae.fasta and GCA_000002945.bed.
|
| |
|
| Submission date |
Feb 04, 2022 |
| Last update date |
Oct 02, 2023 |
| Contact name |
Pascal BERNARD |
| E-mail(s) |
[email protected]
|
| Organization name |
CNRS
|
| Department |
LBMC
|
| Lab |
ENS de Lyon
|
| Street address |
46 allée d'Italie
|
| City |
Lyon |
| ZIP/Postal code |
F-69364 |
| Country |
France |
| |
|
| Platform ID |
GPL28961 |
| Series (1) |
| GSE196149 |
Condensin positioning at telomeres by shelterin proteins drives sister-telomere disjunction in anaphase |
|
| Relations |
| BioSample |
SAMN25653251 |
| SRA |
SRX14045328 |
