|
| Status |
Public on Dec 11, 2017 |
| Title |
Col-0, 4h, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis leaves
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: leaves
genotype: Col-0 WT
time: 4 h
|
| Treatment protocol |
Plants were shifted from 28°C to 19°C for 4 and 8h before collecting and freezing the samples. T0 samples were not shifted.
|
| Growth protocol |
Plants were grown for 3,5 weeks at 28°C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA were extracted using the Qiagen Rneasy kit. RNA were DNaseI-treated and a purification was done using the Qiagen Rneasy MinElute kit. Ribosomal RNAs were depleted from 2.5 µg RNA using the RiboMinus Plant Kit for RNA-seq (Life Technologies).
For library preparation, oligodT-primed cDNA synthesis was done using the TruSeq RNA preparation kit (Life Technologies). All proceadures were performed according to the manufacturer's instructions.
paired-end RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
polyA-enriched and rRNA-depleted RNA
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequencing read quality control was performed using FastQC version 0.11.2
Sequenced reads were mapped to the genome of Arabidopsis thaliana (TAIR10) using tophat v2.0.10 with parameters -a 10 -g 10 - r 160 --mate-std-dev 160 --library-type fr-unstranded
Read counts per gene per sample were obtained using the htseq-count script in the HTSeq Python package with options -s reverse -t exon
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample
|
| |
|
| Submission date |
Apr 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Barbara Kracher |
| E-mail(s) |
kracher@mpipz.mpg.de
|
| Organization name |
Max Planck Institute for Plant Breeding Research
|
| Department |
Plant-Microbe Interactions
|
| Street address |
Carl-von-Linné-Weg 10
|
| City |
Cologne |
| ZIP/Postal code |
50829 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE80448 |
Study of expression changes during RPS4-mediated resistance in Arabidopsis using a temperature-inducible system which mirrors NLR activation II |
|
| Relations |
| BioSample |
SAMN04870193 |
| SRA |
SRX1714288 |
