|
| Status |
Public on May 01, 2023 |
| Title |
amiRCWC15 Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
inflorescence
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: inflorescence
genotype: amiRCWC15
molecule subtype: small RNA
|
| Treatment protocol |
none
|
| Growth protocol |
16 hour light; 8 hour dark; at 22 oC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Flower inflorescences were collected and total RNA was extracted by Trizol. Illumina TruSeq Small RNA Sample Prep Kits was used with 1 ug of total RNA for the construction of sequencing libraries.
Illumina small RNA library protocol
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to TAIR10 whole genome with miRNA annotation using bowtie bowtie -v 0 -S -a --best --strata
Reads counts for each miRNA with htseq-count
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample
|
| |
|
| Submission date |
Mar 29, 2023 |
| Last update date |
May 02, 2023 |
| Contact name |
Chi Zhang |
| E-mail(s) |
czhang5@unl.edu
|
| Organization name |
University of Nebraska - Lincoln
|
| Street address |
1901 Vine Street
|
| City |
Lincoln |
| State/province |
NE |
| ZIP/Postal code |
68588 |
| Country |
USA |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE228510 |
CWC15 is required for miRNA accumulation |
|
| Relations |
| BioSample |
SAMN33971481 |
| SRA |
SRX19811437 |
