|
| Status |
Public on Mar 01, 2012 |
| Title |
Small RNA population (wt) |
| Sample type |
SRA |
| |
|
| Source name |
immature flowers
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col0
developmental stage: inflorescences stages 1-12
genotype/variation: WT
|
| Growth protocol |
Plant seeds were stratified for two days at 4°C before growth in chambers on soil at 23°C under a 16h-light/8h-dark cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted as described in Pelissier et al. (2004) NAR 32:3957-3966) using immature floral inflorescences (stages 1-12). 12 to 18ug of total RNA samples were heat-treated in 1.5 volume of standard formamide buffer and loaded on 15% polyacrylamide (19 :1 acrylamide :bis-acrylamide) – 8.3M urea - 0.5X TBE gel and separated by electrophoresis. Small RNAs (18 to 36 nucleotides) were cut out of the gels, used to construct libraries according to the manufacturer protocol (Illumina Small RNA Sample Prep Kits) and sequenced on a HiSeq 2000 system (Illumina) at the MGX platform (http://www.mgx.cnrs.fr/)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
21 to 24-nt
|
| Data processing |
Small read counts were normalized by taking highly expressed conserved miRNAs that were shown by northern hybridization to be invariant in Col0, and calculating normalization factors for each condition. The normalized data was cross-confirmed by calculating the normalization factor for all significantly expressed 36-nt (that represent general breakdown RNA products), which yielded similar values. Only small RNAs having 10 or more read counts in at least one condition were considered
|
| |
|
| Submission date |
Feb 24, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Jean-Marc Deragon |
| E-mail(s) |
jean-marc.deragon@univ-perp.fr
|
| Phone |
33468662119
|
| Organization name |
Université de Perpignan, CNRS
|
| Department |
Biology
|
| Lab |
LGDP
|
| Street address |
58 avenue Paul Alduy
|
| City |
Perpignan |
| ZIP/Postal code |
66860 |
| Country |
France |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE27517 |
Analysis of small RNA population in Arabidopsis drb2 and drb4 mutants |
|
| Relations |
| SRA |
SRX054619 |
| BioSample |
SAMN00254203 |
