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Status |
Public on Aug 07, 2023 |
Title |
Wild-type inflorescence RNA, CMC-treated, replicate 5 |
Sample type |
SRA |
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Source name |
inflorescence
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Organism |
Arabidopsis thaliana |
Characteristics |
tissue: inflorescence genotype: Col-0 treatment: CMC
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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 |
SAMN34276901 |
SRA |
SRX20032306 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7207852_WT_inf_CMC+_rep5_counts.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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