|
| Status |
Public on Aug 19, 2015 |
| Title |
hen1-8 urt1-1 smallRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
hen1-8 urt1-1
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
tissue: inflorescences
genotype: hen1-8 urt1-1
|
| 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.
Library was constructed with the Illumina TruSeq-small RNA sample preparation kit per manufacturer’s instructions (Illumina). In brief, gel-purified small RNAs were ligated sequentially to 3’ and 5’ adaptors. Following reverse transcription, PCR amplification of the cDNA resulted in the small RNA library, which was gel-purified and subjected to high throughput sequencing
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava software used for basecalling.
The raw reads of small RNAs were processed by PERL scripts built in house. Briefly, the raw reads were screened with Illumina’s quality control filter. The reads that passed the filter were separated into different bins according to their barcodes (indexes). The adaptor was trimmed for each read. Reads that match known rRNAs, tRNAs, snRNAs, and snoRNAs were removed. Reads of 20–24 nt were selected as the raw small RNA sequences.
small RNA reads were then mapped to the TAIR10 Arabidopsis genome using Bowtie.any small RNA read that could not be perfectly mapped back to the genome was trimmed one nucleotide at a time from the 3’ end until the remaining sequence was perfectly mapped to the genome. The trimmed 3’ sequence was designated as the “tail” whereas the longest 5’ genome-mapped component (the “head”) was compared to all annotated miRNAs in miRBase to ascertain from which miRNAs they were derived.
Genome_build: TAIR10
Supplementary_files_format_and_content: the first column: read sequence; the second column: read count
|
| |
|
| Submission date |
Sep 11, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Lei Gao |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE61362 |
Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis |
|
| Relations |
| BioSample |
SAMN03032180 |
| SRA |
SRX699876 |
