|
| Status |
Public on Jul 29, 2024 |
| Title |
Hi-C WT, DSB 4 hr, right annealing oligos only |
| Sample type |
SRA |
| |
|
| Source name |
WT, DSB 4 hr, right annealing oligos only
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
tissue: S. cerevisiae culture
|
| Treatment protocol |
~1.5x10^9 cells were crosslinked with 3% formaldehyde for 30 minutes at 120 rpm at room temperature, followed by quenching with 330 mM glycine for 30 minutes at 120 rpm.
|
| Growth protocol |
Cells were grown to exponential phase in YP-lactate media and synchronized in G1 with alpha-factor for 3 hours. Cells were washed 3 times in pre-warmed YP-lactate and released in S-phase in YP-lactate supplemented with 2% galactose. For Scc1-AID depletion experiment, 2 mM IAA were added at the time of release. For Pol3/Rfc1-AID depletion, 50 ug/mL doxycycline and 2 mM IAA were added 1 hour post-release.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were spheroplasted with 0.25 mg/mL Zymolyase 100T at 37°C for 30 minutes, crosslinked with 3 mM EGS (ethylene glycol bis(succinimidyl succinate)) at 30°C for 40 minutes at 100 rpm, and quenched with 400 mM glycine for 5 minutes at 100 rpm.
Hi-C and ssHi-C library were generated using the Arima Hi-C+ kit following manufacturer instructions starting from 2-5x10^7 cells, with addition of the annealing oligonucleotide mix at 7 nM each in the lysis buffer prior to incubation at 62°C for 10 minutes.
DNA was fragmented in 300-400 bp DNA fragments using Covaris M220 sonicator. Illumina sequencing libraries were prepared using the Thermofisher Collibri ES DNA Library Prep Kit for Illumina Systems with UD indexes following manufacturer's instructions. For ssHi-C, two rounds of targeted capture using the IDT xGen Hybridization buffer and enhancer using biotinylated oligonucleotides at 0.6 uM each. The library was digested with MfeI and SspI in NEB cutsmart buffer prior to sequencing.
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Reads alignement, contact filtering and PCR duplicate removal was performed using the hicstuff (v3.1.2) pipeline function with mapping quality set to 30 or 20. Hi-C contact matrices in sparse format were binned at 1 kb using hicstuff rebin function and converted to cooler format using hicstuff convert function.
For ssHi-C, sparse matrices generated by hicstuff pipeline function were processed with the sshicstuff pipeline function to isolate fragments of interest
Assembly: S. cerevisiae S288c-R64-2-1 (http://sgd-archive.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-2-1_20150113.tgz)
Supplementary files format and content: Hi-C and unfiltered ssHi-C contact data in cooler format, either per fragment (for ssHiC samples) or binned at 1kb (for HiC samples)
Supplementary files format and content: Unfiltered ssHi-C contact data in graal (sparse) format, per fragment
Supplementary files format and content: Tabulated ssHi-C contact data filtered with ssHiCstuff, binned at 1kb
|
| |
|
| Submission date |
Jul 24, 2024 |
| Last update date |
Jul 29, 2024 |
| Contact name |
Aurele Piazza |
| E-mail(s) |
aurele.piazza@ens-lyon.fr
|
| Organization name |
ENS Lyon
|
| Street address |
46 Allee d'Italie
|
| City |
Lyon |
| ZIP/Postal code |
69007 |
| Country |
France |
| |
|
| Platform ID |
GPL27812 |
| Series (1) |
| GSE272969 |
Mechanism of homology search expansion during recombinational DNA repair |
|
| Relations |
| BioSample |
SAMN42783678 |
| SRA |
SRX25442186 |
