 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 07, 2023 |
| Title |
Wild-type inflorescence RNA, IP fraction, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
inflorescence
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: inflorescence
genotype: Col-0
treatment: IP
|
| Treatment protocol |
N-cyclohexyl-N′-β-(4-methylmorpholinium) ethylcarbodiimide (CMC); pseudouridine antibody (D347-3, MBL)
|
| 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)
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| 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)
|
| |
|
| Submission date |
Apr 21, 2023 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Rowan Paul Herridge |
| E-mail(s) |
rowan.herridge@otago.ac.nz
|
| Organization name |
University of Otago
|
| Department |
Biochemistry
|
| Street address |
710 Cumberland Street
|
| City |
Dunedin |
| ZIP/Postal code |
9016 |
| Country |
New Zealand |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN34276897 |
| SRA |
SRX20032310 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7207856_WT_inf_IP_rep1_counts.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
