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| Status |
Public on Apr 19, 2024 |
| Title |
SAC-seq for transcriptome-wide quantitative sequencing of mRNA m6A at base resolution |
| Organism |
Oryza sativa Japonica Group |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Here, we reported transcriptome-wide m6A modification maps within single-base resolution using m6A-SAC-seq in rice and Arabidopsis. Our analysis uncovered a total of 205,691 m6A sites distributed across 22,574 genes in rice, and 188,282 m6A sites across 19,984 genes in Arabidopsis.
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| Overall design |
To establish a comprehensive atlas to investigate the tissue specificity and evolutionary conservation of poly(A) RNA m6A regulation in plants, we first extracted the total RNA of nine Arabidopsis tissues (seedling, shoot, root, rosetta leaf, cauline leaf, stem, flower, silique and seed) as well as eight rice tissues (plumule dark, plumule light, Seedling at 8 days, Seedling at 2 weeks, panicle, flag leaf at 10 days after anthesis, endosperm at 10 days after anthesis, and embryo at 10 days after anthesis with two biological replicates for each sample (Fig. 1b, c ). poly(A) RNA of each biological replicate was captured first for LC-MS/MS to measure the m6A/A ration in the whole transcriptome.
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| Citation(s) |
38849358 |
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| Submission date |
Sep 21, 2023 |
| Last update date |
Jun 28, 2024 |
| Contact name |
CHUAN HE |
| E-mail(s) |
chuanhe@uchicago.edu
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| Organization name |
University of Chicago
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| Street address |
929 East 57th Street, GCIS E313
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| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platforms (1) |
| GPL27860 |
Illumina NovaSeq 6000 (Oryza sativa Japonica Group) |
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| Samples (32)
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| GSM7794752 |
Nip_seedling, polyA RNA, treated, rep1 |
| GSM7794753 |
Nip_seedling, polyA RNA, treated, rep2 |
| GSM7794754 |
Nip_seedling, polyA RNA, untreated, rep1 |
| GSM7794755 |
Nip_seedling, polyA RNA, untreated, rep2 |
| GSM7794756 |
Nip_flagleaf, polyA RNA, treated, rep1 |
| GSM7794757 |
Nip_flagleaf, polyA RNA, treated, rep2 |
| GSM7794758 |
Nip_flagleaf, polyA RNA, untreated, rep1 |
| GSM7794759 |
Nip_flagleaf, polyA RNA, untreated, rep2 |
| GSM7794760 |
Nip_plumule_light, polyA RNA, treated, rep1 |
| GSM7794761 |
Nip_plumule_light, polyA RNA, treated, rep2 |
| GSM7794762 |
Nip_plumule_light, polyA RNA, untreated, rep1 |
| GSM7794763 |
Nip_plumule_light, polyA RNA, untreated, rep2 |
| GSM7794764 |
Nip_plumule_dark, polyA RNA, treated, rep1 |
| GSM7794765 |
Nip_plumule_dark, polyA RNA, treated, rep2 |
| GSM7794766 |
Nip_plumule_dark, polyA RNA, untreated, rep1 |
| GSM7794767 |
Nip_plumule_dark, polyA RNA, untreated, rep2 |
| GSM7794768 |
Nip_panicle, polyA RNA, treated, rep1 |
| GSM7794769 |
Nip_panicle, polyA RNA, treated, rep2 |
| GSM7794770 |
Nip_panicle, polyA RNA, untreated, rep1 |
| GSM7794771 |
Nip_panicle, polyA RNA, untreated, rep2 |
| GSM7794772 |
Nip_seedling_2Week, polyA RNA, treated, rep1 |
| GSM7794773 |
Nip_seedling_2Week, polyA RNA, treated, rep2 |
| GSM7794774 |
Nip_seedling_2Week, polyA RNA, untreated, rep1 |
| GSM7794775 |
Nip_seedling_2Week, polyA RNA, untreated, rep2 |
| GSM7794776 |
Nip_embryo, polyA RNA, treated, rep1 |
| GSM7794777 |
Nip_embryo, polyA RNA, treated, rep2 |
| GSM7794778 |
Nip_embryo, polyA RNA, untreated, rep1 |
| GSM7794779 |
Nip_embryo, polyA RNA, untreated, rep2 |
| GSM7794780 |
Nip_endosperm, polyA RNA, treated, rep1 |
| GSM7794781 |
Nip_endosperm, polyA RNA, treated, rep2 |
| GSM7794782 |
Nip_endosperm, polyA RNA, untreated, rep1 |
| GSM7794783 |
Nip_endosperm, polyA RNA, untreated, rep2 |
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| Relations |
| BioProject |
PRJNA1019705 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE243722_rice_gene_expression.txt.gz |
2.2 Mb |
(ftp)(http) |
TXT |
| GSE243722_rice_m6A_modification.tsv.gz |
12.4 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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