|
| Status |
Public on May 30, 2018 |
| Title |
Overexpressor HSFA1b-RFP Heat stress rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Leaves
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia 0
age: 5 weeks
genotype: wild type
treatment: heat stress
|
| Treatment protocol |
Plants were subjected to heat stress treatment at 37°C for 30 minutes with relative humidity of 86% to maintain the vapour pressure deficit at 1 kPa.
|
| Growth protocol |
Arabidopsis thaliana Col-0 ecotype was obtained from the European Arabidopsis Stock Centre and 35S:HSFA1b-RFP/Col-0 plants have been described previously (Bechtold et al 2013 J. Exp. Bot. 64: 3467). Plants were grown in a controlled environment chamber under the following conditions: 8/16 hours light/dark cycles, temperature 23°C, relative humidity 60% (growth vapour pressure deficit was 1kPa), light intensity of 120 µmols m-2 s-1. Three Arabidopsis seed was sown onto a wetted soil mix (Scotts Levingtons F2+S compost) in pots (5.5 cm diameter x 5.5 cm deep) and stratifed for 2 days at 4°C before transfer to the growth conditions. Seedlings were thinned to one per pot and grown until 5 weeks after germination.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Plants were harvested immedaitely at the end of the stress and snap frozen in liquid nitrogen. Plant material was ground in liquid nitrogen to a fine powder uisng a mortar and pestle. RNA extraction was carried out using TRI-reagent (Life Technologies Inc.) according to the manufacturer's instructions, with the following modifications: Each sample was homogenised in 1ml of TRI-reagent, vortexed for 2 min and 200 µl chlorofrom added, vortexed and the phases separated by centrifugation (18,400 x g for 20 min). Nucleic acid was precipitated from the aqueous phase (500 µl) by adition of an equal volume of isopropanol. The nucleic acid pellet was dissovled in 30 µl sterile water and genomic DNA was removed using the DNA-free kit (Ambion Inc.) according to the manufacturer's instructions.
Libraries were constructed using Illumina TruSeq RNA library preparation kit at The Genome Analysis Centre (TGAC, Norwich, UK)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample_720_LIB5042_LDI3994
|
| Data processing |
Raw short reads files were obtained in fastq format
Illumina adapters and low quality as well as overrepresented Illumina TruSeq primer sequences were trimmed from fastq files using in-house made programs
Quality-trimmed RNA-seq reads were aligned to the Arabidopsis thaliana genome (TAIR10) using the aligner GSNAP with the known splices options for RNA-seq (5 mismatches allowed).
Transcript assembly, absolute expression analysis (Fragments per kilobase exon model; FPKM) and differential expression analysis were carried out using Cufflinks and Cuffdiff (Trapnel et al 2008) using the geometric library normalization method with threshold q ≤ 0.05.
Genome_build: TAIR10
Supplementary_files_format_and_content: text files containing FPKM s with p-values, q-values, and fold changes and separate text file containing normalized FPKM values from each replicate
|
| |
|
| Submission date |
Aug 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Philip M Mullineaux |
| E-mail(s) |
mullin@essex.ac.uk
|
| Phone |
+44 (0) 1206 872118
|
| Organization name |
University of Essex
|
| Department |
Environmental and Plant Bioscience Research Group
|
| Lab |
5.36
|
| Street address |
Wivenhoe Park
|
| City |
Colchester |
| State/province |
Essex |
| ZIP/Postal code |
CO4 3SQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE85653 |
Genome-wide mapping of the Arabidopsis thaliana heat shock transcription factor A1b binding sites under non-stress and heat stress conditions [RNA-seq] |
| GSE85655 |
Genome-wide mapping of the Arabidopsis thaliana heat shock transcription factor A1b binding sites under non-stress and heat stress conditions |
|
| Relations |
| BioSample |
SAMN05578498 |
| SRA |
SRX2024362 |
