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| Status |
Public on Sep 05, 2023 |
| Title |
Ctrl_a, D, MeDIP, 2hr, 0X, rep1 |
| Sample type |
SRA |
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| Source name |
yLB121a-sw
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: yLB121a-sw
chip antibody: anti-5-methylcytosine(Thermo Fisher, 33D3)
condition: 2hr, 2nM Beta-estradiol
genotype: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, GAL10pr::GAL10pr-HO::URA3
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| Treatment protocol |
β-estradiol (Sigma, 50-28-2) was added to a final concentration of 2 nM for 1/2 hrs, allowing the LacI-NLS-M.CviPI fusion protein to express. For MATa and MATalpha viewpoint, glucose (D) or galactose(G) was added according to the experimental conditions.
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| Growth protocol |
Yeast strains were grown in 50 mL synthetic media with/without methionine at 30°C to OD660 = 0.3.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard MeDIP protocol for preparation of methylated genomic DNA
MeDIP-Seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L). Next generation sequencing was performed on NextSeq 2000 (Illumina).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Description |
Deseq2_output.xlsx
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| Data processing |
Paired-end reads of 50 bp or 150 bp were processed with fastp (version 0.23.2) to remove low quality reads. Processed reads were aligned to S. cerevisiae genome (sacCer3) with BWA (version 0.7.17). Aligned bam files were deduplicated with Picard MarkDuplicates (version 3.0.0). bigwig files were generated by deeptools bamCoverage (version 3.5.1) for visualization purposes. To detect differentially methylated NDRs, aligned reads on each NDR were counted by Subread featureCounts (version 2.0.3) using a list of NDR coordinates generated from a previous study, with the following parameters “-p -O”. Fold change and P-value were generated by DEseq2 (1.38.0) without outliers filtering. log2 (Fold Change) > 0.7 and the adjusted P-value < 0.05 were used as the cutoff for identifying differentially methylated regions.
Assembly: sacCer3
Supplementary files format and content: table generated by DEseq2
Supplementary files format and content: bigwig
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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) |
| GSE242398 |
DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions (MeDIP) |
| GSE242400 |
DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions |
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| Relations |
| BioSample |
SAMN37286149 |
| SRA |
SRX21638505 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7762107_MATa_1_D_C.bigwig |
6.1 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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