|
| Status |
Public on Jul 01, 2012 |
| Title |
Endogenous small RNAs from wild-type Col, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Col rep2
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genetic background: Col-0
genotype: wt
tissue: inflorescences
|
| Growth protocol |
Plants were grown under long day (16 h light/ 8 h darkness) conditions at 22°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNAs of a desired size range (15–40 nt) were fractionated from 25ug total RNAs by 15% polyacrylamide gel electrophoresis. These small RNAs were sequentially ligated with the 3' and 5' adapters using the Small RNA Sample Preparation Kit (Illumina) according to the manufacturer’s instructions. A reverse transcription reaction followed by a low cycle PCR was performed to obtain sufficient amounts of products for deep sequencing. The wild type, heso1-1, hen1-8, and hen1-8 heso1-1 libraries were barcoded and sequenced in one channel on an Illumina Hiseq2000. Two biological replicates were performed.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The raw sequences were filtered to remove low quality reads and the ones that passed the quality filter were trimmed to remove the adaptor sequences. Reads that matched to tRNAs and rRNAs were removed.
|
| |
|
| Submission date |
Feb 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Lei Gao |
| E-mail(s) |
leigao@szu.edu.cn
|
| Organization name |
shenzhen university
|
| Department |
College of Life Sciences
|
| Street address |
Nanhai Ave 3688
|
| City |
shenzhen |
| State/province |
guangdong |
| ZIP/Postal code |
518060 |
| Country |
China |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE35479 |
Nucleotidyltransferase gene HESO1 |
|
| Relations |
| SRA |
SRX118311 |
| BioSample |
SAMN00780040 |
