|
| Status |
Public on Jun 01, 2021 |
| Title |
ark2_mutant_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
whole root
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cultivar: Nipponbare
inoculum: R. irregularis (DAOM197198)
genotype: ark2 mutant
tissue: whole root
|
| Treatment protocol |
The AM fungal model species R. irregularis (DAOM197198) was employed for all inoculation assays. Spores extracted from Agrobacterium rhizogenes transformed carrot hairy root cultures (Bécard and Fortin, 1988) were used. Aliquoted inoculum was applied onto the substrate of half-filled cones (12 cm depth, 2.5 cm diameter), after which sand substrate was replenished and germinated seedlings transferred to the containers.
|
| Growth protocol |
Plants were watered every second day, the first two weeks with reverse osmosis water (R-O H2O) followed by low Pi fertilization every other watering day with half-strength Hoagland solution containing 25 μM KH2PO4.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the TRIzol method
1 μg RNA per sample was used for library preparation generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, Hitchin, United Kingdom) following manufacturer’s instructions. Library quality was monitored on the Agilent Bioanalyzer 2100 system
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ark2_4
|
| Data processing |
RNAseq reads of FASTQ format were processed to remove low quality reads and reads containing adapter and poly-N sequences. Q20, Q30 and GC content of the clean data were calculated
The quality of the FASTQ files were validated with FastQC (v0.11.8)
The resulting reads from the raw fastq data were quality controlled and and mapped to the O. sativa reference genome Os-Nipponbare-Reference-IRGSP-1.0 using STAR (2.7.3a)
The raw counts and FPKM (Fragments per kilobase per million mapped reads) values were calculated with featureCounts in R package Rsubread (2.0.0)
The TPM (Transcripts per million) values were calculated by custom python script using the raw counts file
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary_files_format_and_content: tab separated files with the corresponding expression values
|
| |
|
| Submission date |
Mar 03, 2021 |
| Last update date |
Jun 01, 2021 |
| Contact name |
Tak Lee |
| E-mail(s) |
[email protected]
|
| Organization name |
Max Planck Institute for Plant Breeding Research
|
| Street address |
Carl-von-Linne weg 10
|
| City |
Cologne |
| ZIP/Postal code |
50829 |
| Country |
Germany |
| |
|
| Platform ID |
GPL27860 |
| Series (1) |
| GSE168162 |
A mycorrhiza-associated receptor-like kinase with an ancient origin in the green lineage |
|
| Relations |
| BioSample |
SAMN18128377 |
| SRA |
SRX10228883 |
