|
| Status |
Public on Jan 01, 2014 |
| Title |
ATH1_WS_water_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
rosette leaves
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
tissue: rosette leaves
genotype: WS
stress: Watered condition (control)
|
| Treatment protocol |
Repeated dehydration stresses were performed by air-drying for 2 h followed by a 22 h period of full re-hydration recovery. S1 sample taken at first dehydration, S3 at third dehydration.
|
| Growth protocol |
Arabidopsis thaliana (Col-0) plants were grown in potting soil in growth rooms at 22 °C with a 12-h light photoperiod and light intensity of 180 μmol m− 2 s−1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from materials by using TRIzol Reagent (Invitrogen cat#: P/N 15596-018), followed by further purification by Qiagen RNeasy Mini Kit (P/N 74104). RNA qualities were assessed using an Agilent BioAnalyzer 2100 system (Agilent Technologies).
RNA libraries were prepared from 4ug total RNA using the Illumina TruSeq RNA Sample Prep Kit-V2 set A (RS-122-2002 ) according to the manufacturer’s instructions. Libraries were analyzed and measured by gel electrophoresis and Nanodrop 1000 Spectrophotometer to a concentration of 10nM each.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Replicate 1 of 2
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
RNA-Seq reads were aligned to the Arabidopsis thaliana genome assembly (TAIR10) using tophat version 0.12.8 with default parameters.
Digital gene expression files were generated using cuffdiff version v2.0.2 (3522) with default parameters, and results were further annotated and summarised via in-house perl scripts.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab delimited file containing FPKM gene-level values (abundance counts) for each sample, as well as a cuffdiff generated, merged, and further annotated tab-delimited file containing fold-changes and q-values of S1 versus water and S3 versus S1 (see GeneExpression.txt, linked as a supplementary file on the Series record).
|
| |
|
| Submission date |
Jun 24, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jean-Jack M. Riethoven |
| E-mail(s) |
jeanjack@unl.edu
|
| Organization name |
University of Nebraska-Lincoln
|
| Department |
Beadle Center for Biotechnology
|
| Lab |
Bioinformatics Core Research Facility
|
| Street address |
1901 Vine Street
|
| City |
Lincoln |
| State/province |
NE |
| ZIP/Postal code |
68588-0665 |
| Country |
USA |
| |
|
| Platform ID |
GPL9302 |
| Series (1) |
| GSE48235 |
Four distinct types of dehydration stress memory genes in Arabidopsis thaliana |
|
| Relations |
| BioSample |
SAMN02212497 |
| SRA |
SRX314612 |
