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| Status |
Public on Sep 05, 2023 |
| Title |
DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions (MeDIP) |
| Organism |
Saccharomyces cerevisiae |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Here, we present Methyltransferase Targeting-based chromosome Architecture Capture (MTAC), a method that maps the contacts between a target site (viewpoint) and the rest of the genome with high resolution and sensitivity. By targeting M.CviPI DNA methyltransferase to the viewpoint and by detecting differentially methylated regions, MTAC detects hundreds of intra- and inter-chromosomal interactions in the budding yeast genome that cannot be captured by 4C, Hi-C, or Micro-C.
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| Overall design |
MeDIP-seq data of targeted S. cerevisiae strains (LacO array inserted into the corresponding viewpoints) and control strains (No LacO insertion) under different conditions (growth condition, M.CviPI induction time, LacO copy numbers etc.). 4C-seq data of different viewpoints and Hi-C data for chromosome conformation capture in S. cerevisiae. ChIP-seq data for Met4. RNA-seq data of S. cerevisiae cells in -met condition.
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| Contributor(s) |
Li Y, Lee J, Bai L |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Sep 05, 2023 |
| Last update date |
Jan 16, 2024 |
| 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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| Platforms (1) |
| GPL31112 |
NextSeq 2000 (Saccharomyces cerevisiae) |
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| Samples (66)
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| GSM7762063 |
Ctrl, MeDIP, 1hr, 0X, rep1 |
| GSM7762064 |
Ctrl, MeDIP, 1hr, 0X, rep2 |
| GSM7762065 |
YBP2, MeDIP, 1hr, 4X, rep1 |
| GSM7762066 |
YBP2, MeDIP, 1hr, 4X, rep2 |
| GSM7762067 |
YBP2, MeDIP, 1hr, 8X, rep1 |
| GSM7762068 |
YBP2, MeDIP, 1hr, 8X, rep2 |
| GSM7762069 |
YBP2, MeDIP, 1hr, 16X, rep1 |
| GSM7762070 |
YBP2, MeDIP, 1hr, 16X, rep2 |
| GSM7762071 |
YBP2, MeDIP, 1hr, 256X, rep1 |
| GSM7762072 |
YBP2, MeDIP, 1hr, 256X, rep2 |
| GSM7762073 |
Ctrl, MeDIP, 2hr, 0X, rep1 |
| GSM7762074 |
Ctrl, MeDIP, 2hr, 0X, rep2 |
| GSM7762075 |
YBP2, MeDIP, 2hr, 256X, rep1 |
| GSM7762076 |
YBP2, MeDIP, 2hr, 256X, rep2 |
| GSM7762077 |
PUS2, MeDIP, 2hr, 256X, rep1 |
| GSM7762078 |
PUS2, MeDIP, 2hr, 256X, rep2 |
| GSM7762079 |
OLE1, MeDIP, 2hr, 256X, rep1 |
| GSM7762080 |
OLE1, MeDIP, 2hr, 256X, rep2 |
| GSM7762081 |
CDC43, MeDIP, 2hr, 256X, rep1 |
| GSM7762082 |
CDC43, MeDIP, 2hr, 256X, rep2 |
| GSM7762083 |
PCL10, MeDIP, 2hr, 256X, rep1 |
| GSM7762084 |
PCL10, MeDIP, 2hr, 256X, rep2 |
| GSM7762085 |
SHC1, MeDIP, 2hr, 256X, rep1 |
| GSM7762086 |
SHC1, MeDIP, 2hr, 256X, rep2 |
| GSM7762087 |
LSM4, MeDIP, 2hr, 256X, rep1 |
| GSM7762088 |
LSM4, MeDIP, 2hr, 256X, rep2 |
| GSM7762089 |
VHR1, MeDIP, 2hr, 256X, rep1 |
| GSM7762090 |
VHR1, MeDIP, 2hr, 256X, rep2 |
| GSM7762091 |
MBR1, MeDIP, 2hr, 256X, rep1 |
| GSM7762092 |
MBR1, MeDIP, 2hr, 256X, rep2 |
| GSM7762093 |
MNR2, MeDIP, 2hr, 256X, rep1 |
| GSM7762094 |
MNR2, MeDIP, 2hr, 256X, rep2 |
| GSM7762095 |
LHS1, MeDIP, 2hr, 256X, rep1 |
| GSM7762096 |
LHS1, MeDIP, 2hr, 256X, rep2 |
| GSM7762097 |
TRP2, -met, MeDIP, 2hr, 256X, rep1 |
| GSM7762098 |
TRP2, -met, MeDIP, 2hr, 256X, rep2 |
| GSM7762099 |
Ctrl, -met, MeDIP, 2hr, 0X, rep1 |
| GSM7762100 |
Ctrl, -met, MeDIP, 2hr, 0X, rep2 |
| GSM7762101 |
TRP2, +met, MeDIP, 2hr, 256X, rep1 |
| GSM7762102 |
TRP2, +met, MeDIP, 2hr, 256X, rep2 |
| GSM7762103 |
Ctrl, +met, MeDIP, 2hr, 0X, rep1 |
| GSM7762104 |
Ctrl, +met, MeDIP, 2hr, 0X, rep2 |
| GSM7762105 |
MATa, D, MeDIP, 2hr, 256X, rep1 |
| GSM7762106 |
MATa, D, MeDIP, 2hr, 256X, rep2 |
| GSM7762107 |
Ctrl_a, D, MeDIP, 2hr, 0X, rep1 |
| GSM7762108 |
Ctrl_a, D, MeDIP, 2hr, 0X, rep2 |
| GSM7762109 |
MATa, G, MeDIP, 2hr, 256X, rep1 |
| GSM7762110 |
MATa, G, MeDIP, 2hr, 256X, rep2 |
| GSM7762111 |
Ctrl_a, G, MeDIP, 2hr, 0X, rep1 |
| GSM7762112 |
Ctrl_a, G, MeDIP, 2hr, 0X, rep2 |
| GSM7762113 |
MATalpha, D, MeDIP, 2hr, 256X, rep1 |
| GSM7762114 |
MATalpha, D, MeDIP, 2hr, 256X, rep2 |
| GSM7762115 |
Ctrl_alpha, D, MeDIP, 2hr, 0X, rep1 |
| GSM7762116 |
Ctrl_alpha, D, MeDIP, 2hr, 0X, rep2 |
| GSM7762117 |
MATalpha, G, MeDIP, 2hr, 256X, rep1 |
| GSM7762118 |
MATalpha, G, MeDIP, 2hr, 256X, rep2 |
| GSM7762119 |
Ctrl_alpha, G, MeDIP, 2hr, 0X, rep1 |
| GSM7762120 |
Ctrl_alpha, G, MeDIP, 2hr, 0X, rep2 |
| GSM7762121 |
Mlp1_M.CviPI, MeDIP, rep1 |
| GSM7762122 |
Mlp1_M.CviPI, MeDIP, rep2 |
| GSM7762123 |
M.CviPI, MeDIP, rep1 |
| GSM7762124 |
M.CviPI, MeDIP, rep2 |
| GSM8016823 |
Ctrl, MLP1/2 mutant, MeDIP, 2hr, 0X, rep1 |
| GSM8016824 |
Ctrl, MLP1/2 mutant, MeDIP, 2hr, 0X, rep2 |
| GSM8016825 |
YBP2, MLP1/2 mutant, MeDIP, 2hr, 256X, rep1 |
| GSM8016826 |
YBP2, MLP1/2 mutant, MeDIP, 2hr, 256X, rep2 |
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| This SubSeries is part of SuperSeries: |
| GSE242400 |
DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions |
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| Relations |
| BioProject |
PRJNA1013710 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE242398_Deseq2_output.xlsx |
10.0 Mb |
(ftp)(http) |
XLSX |
| GSE242398_RAW.tar |
573.9 Mb |
(http)(custom) |
TAR (of BIGWIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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