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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 07, 2023 |
| Title |
Wild-type pollen RNA, Unbound fraction, replicate 5 |
| Sample type |
SRA |
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| Source name |
pollen
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: pollen
genotype: Col-0
treatment: unbound (IP)
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| Treatment protocol |
N-cyclohexyl-N′-β-(4-methylmorpholinium) ethylcarbodiimide (CMC); pseudouridine antibody (D347-3, MBL)
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| Extracted molecule |
total RNA |
| Extraction protocol |
tissue ground in liquid nitrogen, Trizol total RNA extraction, 15% urea PAGE fractionation, 17-40nt cut and eluted ON
NEBNext small RNA sequencing kit (CMC samples); Perkin Elmer Nextflex v3 (IP samples)
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Adapter trimming (Fastx clipper, v0.0.14)
De-multiplexing (Fastx collapser v0.0.14)
Mapping (Bowtie2 v2.3.4.1)
feature counts (bedtools v2.29.0)
Assembly: TAIR10
Supplementary files format and content: Gene/TE name, sequence length, and RPM
Supplementary files format and content: Sequence, readcount (for pus7 and pus10 samples)
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| Submission date |
Apr 21, 2023 |
| Last update date |
Aug 07, 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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| Platform ID |
GPL19580 |
| Series (1) |
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| Relations |
| BioSample |
SAMN34276874 |
| SRA |
SRX20032333 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7207879_WT_pollen_UB_rep5_counts.txt.gz |
770.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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