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| Status |
Public on Aug 07, 2023 |
| Title |
Pseudouridine in small RNAs |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Pseudouridine is an isomer of uridine and is the most common RNA modification in both procaryotes and eucaryotes. It is found in ribosomal, transfer, and other structural RNA as well as in some mRNA and non-coding RNA. We have found abundant pseudouridine in small RNA and their precursors in Arabidopsis.
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| Overall design |
Identification of pseudouridylated small RNAs and their precursors in Arabidopsis thaliana
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| Contributor(s) |
Herridge RP, Martienssen RA, Dolata J, de Santis Alves C |
| Citation(s) |
37398006 |
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| Submission date |
Apr 21, 2023 |
| Last update date |
Aug 08, 2023 |
| Contact name |
Rowan Paul Herridge |
| E-mail(s) |
rowan.herridge@otago.ac.nz
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| Organization name |
University of Otago
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| Department |
Biochemistry
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| Street address |
710 Cumberland Street
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| City |
Dunedin |
| ZIP/Postal code |
9016 |
| Country |
New Zealand |
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| Platforms (2) |
| GPL17970 |
Illumina MiSeq (Arabidopsis thaliana) |
| GPL19580 |
Illumina NextSeq 500 (Arabidopsis thaliana) |
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| Samples (70)
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| GSM7207813 |
Col-0 pollen RNA, IP fraction, replicate 1 |
| GSM7207814 |
Col-0 pollen RNA, IP fraction, replicate 2 |
| GSM7207815 |
Col-0 pollen RNA, IP fraction, replicate 3 |
| GSM7207816 |
Col-0 pollen RNA, unbound fraction, replicate 1 |
| GSM7207817 |
Col-0 pollen RNA, unbound fraction, replicate 2 |
| GSM7207818 |
Col-0 pollen RNA, unbound fraction, replicate 3 |
| GSM7207819 |
psd-13 inflorescence RNA, IP fraction, replicate 1 |
| GSM7207820 |
psd-13 inflorescence RNA, IP fraction, replicate 2 |
| GSM7207821 |
psd-13 inflorescence RNA, unbound fraction, replicate 1 |
| GSM7207822 |
psd-13 inflorescence RNA, unbound fraction, replicate 2 |
| GSM7207823 |
psd-13 pollen, input RNA, replicate 1 |
| GSM7207824 |
psd-13 pollen, input RNA, replicate 2 |
| GSM7207825 |
psd-13 pollen, input RNA, replicate 3 |
| GSM7207826 |
psd-13 pollen RNA, IP fraction, replicate 1 |
| GSM7207827 |
psd-13 pollen RNA, IP fraction, replicate 2 |
| GSM7207828 |
psd-13 pollen RNA, IP fraction, replicate 3 |
| GSM7207829 |
psd-13 pollen RNA, unbound fraction, replicate 1 |
| GSM7207830 |
psd-13 pollen RNA, unbound fraction, replicate 2 |
| GSM7207831 |
psd-13 pollen RNA, unbound fraction, replicate 3 |
| GSM7207832 |
pus10 inflorescence RNA, mock-treated, replicate1 |
| GSM7207833 |
pus10 inflorescence RNA, mock-treated, replicate2 |
| GSM7207834 |
pus10 inflorescence RNA, CMC-treated, replicate1 |
| GSM7207835 |
pus10 inflorescence RNA, CMC-treated, replicate2 |
| GSM7207836 |
pus7 inflorescence RNA, mock-treated, replicate1 |
| GSM7207837 |
pus7 inflorescence RNA, mock-treated, replicate2 |
| GSM7207838 |
pus7 inflorescence RNA, CMC-treated, replicate1 |
| GSM7207839 |
pus7 inflorescence RNA, CMC-treated, replicate2 |
| GSM7207840 |
Wild-type inflorescence RNA, mock-treated, replicate 1 |
| GSM7207841 |
Wild-type inflorescence RNA, mock-treated, replicate 2 |
| GSM7207842 |
Wild-type inflorescence RNA, mock-treated, replicate 3 |
| GSM7207843 |
Wild-type inflorescence RNA, mock-treated, replicate 4 |
| GSM7207844 |
Wild-type inflorescence RNA, mock-treated, replicate 5 |
| GSM7207845 |
Wild-type inflorescence RNA, mock-treated, replicate 6 |
| GSM7207846 |
Wild-type inflorescence RNA, mock-treated, replicate 7 |
| GSM7207847 |
Wild-type inflorescence RNA, mock-treated, replicate 8 |
| GSM7207848 |
Wild-type inflorescence RNA, CMC-treated, replicate 1 |
| GSM7207849 |
Wild-type inflorescence RNA, CMC-treated, replicate 2 |
| GSM7207850 |
Wild-type inflorescence RNA, CMC-treated, replicate 3 |
| GSM7207851 |
Wild-type inflorescence RNA, CMC-treated, replicate 4 |
| GSM7207852 |
Wild-type inflorescence RNA, CMC-treated, replicate 5 |
| GSM7207853 |
Wild-type inflorescence RNA, CMC-treated, replicate 6 |
| GSM7207854 |
Wild-type inflorescence RNA, CMC-treated, replicate 7 |
| GSM7207855 |
Wild-type inflorescence RNA, CMC-treated, replicate 8 |
| GSM7207856 |
Wild-type inflorescence RNA, IP fraction, replicate 1 |
| GSM7207857 |
Wild-type inflorescence RNA, IP fraction, replicate 2 |
| GSM7207858 |
Wild-type inflorescence RNA, IP fraction, replicate 3 |
| GSM7207859 |
Wild-type inflorescence RNA, IP fraction, replicate 4 |
| GSM7207860 |
Wild-type inflorescence RNA, IP fraction, replicate 5 |
| GSM7207861 |
Wild-type inflorescence RNA, Unbound fraction, replicate 1 |
| GSM7207862 |
Wild-type inflorescence RNA, Unbound fraction, replicate 2 |
| GSM7207863 |
Wild-type inflorescence RNA, Unbound fraction, replicate 3 |
| GSM7207864 |
Wild-type inflorescence RNA, Unbound fraction, replicate 4 |
| GSM7207865 |
Wild-type inflorescence RNA, Unbound fraction, replicate 5 |
| GSM7207866 |
Wild-type pollen RNA, mock-treated, replicate 1 |
| GSM7207867 |
Wild-type pollen RNA, mock-treated, replicate 2 |
| GSM7207868 |
Wild-type pollen RNA, CMC-treated, replicate 1 |
| GSM7207869 |
Wild-type pollen RNA, CMC-treated, replicate 2 |
| GSM7207870 |
Wild-type pollen RNA, IP fraction, replicate 1 |
| GSM7207871 |
Wild-type pollen RNA, IP fraction, replicate 2 |
| GSM7207872 |
Wild-type pollen RNA, IP fraction, replicate 3 |
| GSM7207873 |
Wild-type pollen RNA, IP fraction, replicate 4 |
| GSM7207874 |
Wild-type pollen RNA, IP fraction, replicate 5 |
| GSM7207875 |
Wild-type pollen RNA, Unbound fraction, replicate 1 |
| GSM7207876 |
Wild-type pollen RNA, Unbound fraction, replicate 2 |
| GSM7207877 |
Wild-type pollen RNA, Unbound fraction, replicate 3 |
| GSM7207878 |
Wild-type pollen RNA, Unbound fraction, replicate 4 |
| GSM7207879 |
Wild-type pollen RNA, Unbound fraction, replicate 5 |
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| Relations |
| BioProject |
PRJNA958093 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE230228_RAW.tar |
486.6 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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