|
| Status |
Public on Dec 11, 2017 |
| Title |
Rpm1_camta3D_2 |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis leaves
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
treatment: Pst DC3000 AvrRpm1 OD600=0.001
genotype: camta3-D (sr1-4d)
time: 4h
|
| Treatment protocol |
Leaves were syringe-infiltrated with the indicated solution. For each sample, six leaf discs were taken at the specified time point from six independent plants and used for RNA extraction.
|
| Growth protocol |
The plants were initially grown on MS-agar plates for 2 weeks under sterile conditions and subsequently transferred to Jiffy pots supplemented with a fertilizer, Wuxal TopN (Aglukon Spezialdünger), and grown for an additional 2 weeks under short day conditions. Four week-old plants were used for the PAMP and bacterial treatments.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extraction was performed using the RNeasy Plant Mini Kit (Qiagen) according to the manufacurer's instruction, including an on-column DNA digestion.
RNA-seq libraries were prepared from total RNA by the Max Planck Genome Center Cologne (http://mpgc.mpipz.mpg.de) according to the TruSeq RNA sample preparation v2 guide (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
polyA-enriched 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 --library-type fr-firststrand
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 (Arabidopsis)
Supplementary_files_format_and_content: tab-delimited text files including read counts per gene per sample
|
| |
|
| Submission date |
Dec 21, 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 |
GPL17639 |
| Series (1) |
| GSE92702 |
Early ETI and PTI responses in Arabidopsis thaliana camta3-D (sr1-4d) mutant |
|
| Relations |
| BioSample |
SAMN06172627 |
| SRA |
SRX2438618 |
