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| Status |
Public on Sep 05, 2023 |
| Title |
HiC, -met, rep2 |
| Sample type |
SRA |
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| Source name |
yMD291
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: yMD291
chip antibody: NA
condition: NA
genotype: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, tor1-1, fpr::NAT, bar1, HIS3::REV1pr-tetR-mCherry-REV1pr-LacI-GFP, ADE2::REV1pr-LacI-REV1pr-tetR, Chr15::497047_LacO, Chr15::834487_TetO
treatment: methionine depletion
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| Growth protocol |
Yeast strains were grown in 200 mL synthetic media without methionine to OD660 = 0.3.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard Hi-C protocol was used for the preparation of Hi-C samples
Hi-C libraries were prepared with NEBNext Ultra II DNA Library Prep Kit. Next generation sequencing was performed on NextSeq 2000.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Data processing |
150 bp paired-end reads were aligned to S. cerevisiae genome (sacCer3) and analyzed with HiC-pro.
Assembly: sacCer3
Supplementary files format and content: BED file includes Hi-C bins
Supplementary files format and content: matrix file of Hi-C dataset
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| Submission date |
Sep 05, 2023 |
| Last update date |
Sep 07, 2023 |
| Contact name |
Lu Bai |
| E-mail(s) |
lub15@psu.edu
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| Organization name |
Penn State University
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| Department |
BMB
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| Lab |
Bai
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| Street address |
406 SOUTH FREAR, UNIVERSITY PARK
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| City |
UNIVERSITY PARK |
| State/province |
PENNSYLVANIA |
| ZIP/Postal code |
16802 |
| Country |
USA |
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| Platform ID |
GPL31112 |
| Series (2) |
| GSE242396 |
DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions (HiC) |
| GSE242400 |
DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions |
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| Relations |
| BioSample |
SAMN37286221 |
| SRA |
SRX21638549 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7762059_HiC_S8_10000_iced.matrix.gz |
3.0 Mb |
(ftp)(http) |
MATRIX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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