|
| Status |
Public on Dec 31, 2017 |
| Title |
mir845 1n rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Pollen
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
tissue: Pollen
|
| Growth protocol |
Plants were grown under long day conditions at 22 °C. Seeds were always surface sterilized with sodium hypochlorite, sowed on Murashige and Skoog (MS) medium and stratified for 3 days at 4ºC. Seedlings were transplanted to soil two weeks after germination and grown under long day conditions at 22 °C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Flowers were harvested in a beaker, covered with 9% sucrose solution and shaken vigorously for 5min to release pollen grains into the solution. The subsequent centrifugation- and filtering-steps were carried out in 9% sucrose solution. Total RNA was extracted using Trizol reagent (Ambion/ Life Technologies, USA) and glass beads (1.25-1.55 mm; Carl Roth).
10 μg of total RNA were run on a 14% TBE UREA Polyacrylamide gel for size selection. Gel slices containing RNA in the range of 17- to 25-nt were purified following the Illumina TrueSeq small RNA protocol for gel extraction. Libraries were constructed using the Illumina TruSeq Small RNA library preparation kit according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Small RNA
|
| Data processing |
Reads were pre-processed by trimming the 3’ adapter and filtering collapsed reads according to length and quality.
Filtered reads were mapped to the Arabidopsis TAIR10 genome annotation with bowtie reporting all multi-mappers.
Only perfect match reads were used for down-stream analysis, and reads mapped to multiple genomic locations where normalized by dividing non-redundant read counts by the number of genomic hits, and subsequently calculating the number of reads per million of filtered (18-30nt) and perfectly mapped reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt files with 18-30nt reads and counts, and RPM of 20-24nt reads mapped to TAIR10 features
|
| |
|
| Submission date |
Oct 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Filipe Borges |
| E-mail(s) |
filipe.borges@inrae.fr
|
| Organization name |
Institut Jean-Pierre Bourgin - INRAE
|
| Street address |
Route de St-Cyr (RD10)
|
| City |
Versailles |
| ZIP/Postal code |
78026 |
| Country |
France |
| |
|
| Platform ID |
GPL17639 |
| Series (2) |
| GSE106115 |
microRNA-triggered transposon small RNAs mediate genome dosage response (mir845 sRNA-Seq) |
| GSE106117 |
microRNA-triggered transposon small RNAs mediate genome dosage response |
|
| Relations |
| BioSample |
SAMN07830390 |
| SRA |
SRX3318201 |
