|
| Status |
Public on Oct 24, 2022 |
| Title |
Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination [eTAM-seq] |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Other
|
| Summary |
We report evolved TadA-assisted N6-methyladenosine sequencing (eTAM-seq), an enzyme-assisted sequencing technology for quantitative, base-resolution profiling of m6A. eTAM-seq functions by global adenosine deamination, enabling detection of m6A as persistent A. We demonstrate adenosine-to-inosine (I) conversion rates up to 99% using a hyperactive TadA variant. With eTAM-seq, we profile and quantify m6A in the whole transcriptomes of HeLa cells and mouse embryonic stem cells (mESCs), with simultaneous deconvolution of the transcriptome and epitranscriptome. Further, we showcase deep sequencing-free, site-specific m6A quantification with as few as 10 cells, an input demand that is at least 4 orders of magnitude lower than existing methods. Collectively, eTAM-seq enables sensitive detection and faithful quantification of m6A with limited RNA input, representing a novel solution to deciphering the epitranscriptome.
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| |
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| Overall design |
Nine HeLa wild type (3 FTO-, 3 FTO+ and 3 IVT), six mESC wild type (2 FTO-, 2 FTO+ and 2 IVT), two mESC Mettl3 cko ctrl (1 FTO- and 1 FTO+) and two mESC Mettl3 cko (1 FTO- and 1 FTO+) polyA samples were collected for high-throughput sequencing.
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| |
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| Contributor(s) |
Xiao Y, Liu S, Ge R, Wu Y, He C, Chen M, Tang W |
| Citation(s) |
36593412 |
| |
| Submission date |
Aug 15, 2022 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Shun Liu |
| Organization name |
University of Chicago
|
| Department |
Chemistry
|
| Lab |
Chuan He Lab
|
| Street address |
929 E. 57th. Street
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (19)
|
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| This SubSeries is part of SuperSeries: |
| GSE201064 |
Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination |
|
| Relations |
| BioProject |
PRJNA869740 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE211303_hela.polya.wt.ftom.ftop.rep1.deep.hits.txt.gz |
715.4 Kb |
(ftp)(http) |
TXT |
| GSE211303_hela.polya.wt.ftom.ftop.rep1.hits.txt.gz |
386.0 Kb |
(ftp)(http) |
TXT |
| GSE211303_hela.polya.wt.ftom.ftop.rep2.hits.txt.gz |
352.4 Kb |
(ftp)(http) |
TXT |
| GSE211303_hela.polya.wt.ftom.ftop.rep3.hits.txt.gz |
281.4 Kb |
(ftp)(http) |
TXT |
| GSE211303_hela.polya.wt.ftom.ivt.rep1.deep.hits.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
| GSE211303_hela.polya.wt.ftom.ivt.rep1.hits.txt.gz |
362.1 Kb |
(ftp)(http) |
TXT |
| GSE211303_hela.polya.wt.ftom.ivt.rep2.hits.txt.gz |
374.5 Kb |
(ftp)(http) |
TXT |
| GSE211303_hela.polya.wt.ftom.ivt.rep3.hits.txt.gz |
288.9 Kb |
(ftp)(http) |
TXT |
| GSE211303_mesc.polya.m3cko.ftom.ftop.rep1.hits.txt.gz |
49.2 Kb |
(ftp)(http) |
TXT |
| GSE211303_mesc.polya.m3ckoctrl.ftom.ftop.rep1.hits.txt.gz |
175.5 Kb |
(ftp)(http) |
TXT |
| GSE211303_mesc.polya.wt.ftom.ftop.rep1.deep.hits.txt.gz |
851.5 Kb |
(ftp)(http) |
TXT |
| GSE211303_mesc.polya.wt.ftom.ftop.rep1.hits.txt.gz |
522.0 Kb |
(ftp)(http) |
TXT |
| GSE211303_mesc.polya.wt.ftom.ftop.rep2.hits.txt.gz |
332.6 Kb |
(ftp)(http) |
TXT |
| GSE211303_mesc.polya.wt.ftom.ivt.rep1.deep.hits.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
| GSE211303_mesc.polya.wt.ftom.ivt.rep1.hits.txt.gz |
469.3 Kb |
(ftp)(http) |
TXT |
| GSE211303_mesc.polya.wt.ftom.ivt.rep2.hits.txt.gz |
518.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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