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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 28, 2023 |
| Title |
Sequencing of N6-methyl-deoxyadenosine at single-base resolution across the mammalian genome |
| Organisms |
Escherichia coli; Mus musculus; synthetic construct; Escherichia coli K-12 |
| Experiment type |
Other
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
While DNA N6-methyl-deoxyadenosine (6mA) is abundant in bacteria and protists, its presence and function in mammalian genomes have been less clear. We present Direct-Read 6mA sequencing (DR-6mA-seq), an antibody-independent method to measure 6mA at base-resolution with high sensitivity. DR-6mA-seq employs a unique mutation-based strategy to reveal 6mA sites as misincorporation signatures without any chemical or enzymatic modulation of 6mA. We validated DR-6mA-seq through successful mapping of the well-characterized G(6mA)TC motif in the E. coli DNA and identified 6mA sites in the mammalian mitochondrial DNA. As expected, when applying DR-6mA-seq to mammalian systems, we found that genomic DNA (gDNA) 6mA abundance is in general low in most mammalian tissues and cells; however, we did observe distinct gDNA 6mA sites in mouse testis and glioblastoma cells. DR-6mA-seq provides an enabling tool to detect 6mA at single-base resolution with high sensitivity for a comprehensive understanding of DNA 6mA in eukaryotes.
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| Overall design |
Three biological replicates were generated.
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| Contributor(s) |
Feng X, Cui X, Zhang L, He C |
| Citation(s) |
38215754 |
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| Submission date |
Sep 21, 2022 |
| Last update date |
Apr 01, 2024 |
| Contact name |
Xiaolong Cui |
| E-mail(s) |
xiaolong.cui@northwestern.edu
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| Organization name |
Northwestern University
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| Department |
Department of Preventive Medicine
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| Street address |
680 N Lake Shore Drive
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
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| Platforms (4)
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| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL25368 |
Illumina NovaSeq 6000 (Escherichia coli) |
| GPL26526 |
Illumina NovaSeq 6000 (synthetic construct) |
| GPL26856 |
Illumina NovaSeq 6000 (Escherichia coli K-12) |
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| Samples (67)
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| GSM6595704 |
E.coli rep2 B |
| GSM6595705 |
E.coli rep2 F |
| GSM6595706 |
E.coli rep2 H |
| GSM6595707 |
E.coli rep3 B |
| GSM6595708 |
E.coli rep3 F |
| GSM6595709 |
E.coli rep3 H |
| GSM6640519 |
Mouse testis rep1 B |
| GSM6640520 |
Mouse testis rep1 F |
| GSM6640521 |
Mouse testis rep1 H |
| GSM6640522 |
Mouse testis rep2 B |
| GSM6640523 |
Mouse testis rep2 F |
| GSM6640524 |
Mouse testis rep2 H |
| GSM6640525 |
N cell line rep1 B |
| GSM6640526 |
N cell line rep1 F |
| GSM6640527 |
N cell line rep1 H |
| GSM6640528 |
N cell line rep2 B |
| GSM6640529 |
N cell line rep2 F |
| GSM6640530 |
N cell line rep2 H |
| GSM6640531 |
B cell line rep1 B |
| GSM6640532 |
B cell line rep1 F |
| GSM6640533 |
B cell line rep1 H |
| GSM6640534 |
B cell line rep2 B |
| GSM6640535 |
B cell line rep2 F |
| GSM6640536 |
B cell line rep2 H |
| GSM7669523 |
E.coli WGA rep1 B |
| GSM7669524 |
E.coli WGA rep1 F |
| GSM7669525 |
E.coli WGA rep1 H |
| GSM7669526 |
E.coli WGA rep2 B |
| GSM7669527 |
E.coli WGA rep2 F |
| GSM7669528 |
E.coli WGA rep2 H |
| GSM7669529 |
E.coli WGA rep3 B |
| GSM7669530 |
E.coli WGA rep3 F |
| GSM7669531 |
E.coli WGA rep3 H |
| GSM7669532 |
Oligo 5% B |
| GSM7669533 |
Oligo 5% F |
| GSM7669534 |
Oligo 5% H |
| GSM7669535 |
Oligo 10% B |
| GSM7669536 |
Oligo 10% F |
| GSM7669537 |
Oligo 10% H |
| GSM7669538 |
Oligo 15% B |
| GSM7669539 |
Oligo 15% F |
| GSM7669540 |
Oligo 15% H |
| GSM7669541 |
Oligo 20% B |
| GSM7669542 |
Oligo 20% F |
| GSM7669543 |
Oligo 20% H |
| GSM7669544 |
Oligo 25% B |
| GSM7669545 |
Oligo 25% F |
| GSM7669546 |
Oligo 25% H |
| GSM7908628 |
H3K27me3 IP rep1, NIH/3T3 |
| GSM7908629 |
H3K27me3 IP rep2, NIH/3T3 |
| GSM7908630 |
H3K9me3 IP rep1, NIH/3T3 |
| GSM7908631 |
H3K9me3 IP rep2, NIH/3T3 |
| GSM7908632 |
H3K4me3 IP rep1, NIH/3T3 |
| GSM7908633 |
H3K4me3 IP rep2, NIH/3T3 |
| GSM7908634 |
H3K27me3 IP rep1, B104-1-1 |
| GSM7908635 |
H3K27me3 IP rep2, B104-1-1 |
| GSM7908636 |
H3K9me3 IP rep1, B104-1-1 |
| GSM7908637 |
H3K9me3 IP rep2, B104-1-1 |
| GSM7908638 |
H3K4me3 IP rep1, B104-1-1 |
| GSM7908639 |
H3K4me3 IP rep2, B104-1-1 |
| GSM7908640 |
Input rep1, NIH/3T3 |
| GSM7908641 |
Input rep2, NIH/3T3 |
| GSM7908642 |
Input rep1, B104-1-1 |
| GSM7908643 |
Input rep2, B104-1-1 |
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| Relations |
| BioProject |
PRJNA882844 |
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