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Series GSE243722 Query DataSets for GSE243722
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
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.
 
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.
 
Citation(s) 38849358
Submission date Sep 21, 2023
Last update date Jun 28, 2024
Contact name CHUAN HE
E-mail(s) chuanhe@uchicago.edu
Organization name University of Chicago
Street address 929 East 57th Street, GCIS E313
City Chicago
State/province Illinois
ZIP/Postal code 60637
Country USA
 
Platforms (1)
GPL27860 Illumina NovaSeq 6000 (Oryza sativa Japonica Group)
Samples (32)
GSM7794752 Nip_seedling, polyA RNA, treated, rep1
GSM7794753 Nip_seedling, polyA RNA, treated, rep2
GSM7794754 Nip_seedling, polyA RNA, untreated, rep1
Relations
BioProject PRJNA1019705

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Series Matrix File(s) TXTHelp

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
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