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| Status |
Public on Apr 19, 2024 |
| Title |
Nip_seedling, polyA RNA, untreated, rep1 |
| Sample type |
SRA |
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| Source name |
Nip_seedling
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| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: Nip_seedling
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
A total of 50 ug total RNA for each of the two biological replicates was used for mRNA capture (Dynabeads mRNA DIRECT Purification Kit (Invitrogen)) following the manufacturer′ s instructions with modification. Briefly, 50 ug total RNA was diluted with H2O in 100ul volume and then denatured under 65°C for 2 min, and immediately put on the ice for exactly 2 min. Next, a total of 100ul Dynabeads were washed twice with 200ul lysis/binding buffer provided in the above kit. The washed beads were then eluted in 100ul lysis/binding buffer, which further mixed with the denatured total RNA. Then, the sample was put on the rotor to binding for 15 min at room temperature. After binding, wash buffer B was used to wash the beads for twice. 30ul H2O was used to elute the beads and immediately put on the 75°C for 2min. The eluted mRNA was collected after magnetic separation. The mRNA capture process was repeated as described above to obtain the more purified mRNA.
50ng mRNAs of each replicate were used for the library construction. All these libraries were constructed exactly following the previously published protocols
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
m6A sites were detected using the method previously published (https://github.com/y9c/m6A-SACseq) 18. The analysis utilized the reference genome downloaded from the Ensembl database, with assembly versions TAIR10 and IRGSP-1.0 employed for Arabidopsis and rice respectively.
Assembly: IRGSP-1.0
Supplementary files format and content: TSV
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| Submission date |
Sep 21, 2023 |
| Last update date |
Apr 19, 2024 |
| Contact name |
CHUAN HE |
| E-mail(s) |
[email protected]
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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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| Platform ID |
GPL27860 |
| Series (1) |
| GSE243722 |
SAC-seq for transcriptome-wide quantitative sequencing of mRNA m6A at base resolution |
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| Relations |
| BioSample |
SAMN37494789 |
| SRA |
SRX21849380 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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