|
| Status |
Public on Apr 11, 2013 |
| Title |
wt Col total small RNA |
| Sample type |
SRA |
| |
|
| Source name |
Inflorescence tissue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
background strain: Col-0
tissue: unopened flower buds
growth conditions: 18 hour light, 23C
|
| Growth protocol |
Plants were grown on soil in 18 hour per day light at 23C. All plants used in this study were grown side-by-side.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent, and small RNAs were purified using mirVana microRNA isloation kit.
Cloning of small RNAs was performed using the Illumina TruSeq Small RNA Sample Preparation Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
library strategy: small-RNA-seq
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads de-multiplexed and were trimmed for adaptor sequence
Sequences were masked for low-complexity or low-quality sequence, filtered for reads 18-28 nt in size, then mapped to the genome using bowtie with parameters --best --strata -M1
tRNA and rRNA-matching reads were removed
Genome_build: TAIR10
Supplementary_files_format_and_content: small RNA sequence and the number of times they were sequenced
|
| |
|
| Submission date |
Oct 22, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard Keith Slotkin |
| E-mail(s) |
slotkin.2@osu.edu
|
| Organization name |
The Ohio State University
|
| Department |
Molecular Genetics
|
| Lab |
Slotkin Laboratory
|
| Street address |
318 West 12th Ave.
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL11221 |
| Series (1) |
| GSE41755 |
Arabidopsis small RNAs associated with RDR6-dependent RNA-directed DNA Methylation |
|
| Relations |
| Reanalyzed by |
GSM2102962 |
| Reanalyzed by |
GSM3336846 |
| SRA |
SRX199954 |
| BioSample |
SAMN01774218 |
