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| Status |
Public on Aug 05, 2024 |
| Title |
Cicer arietinum roots inoculated with Phytophthora medicaginis_60hpi_rep1 |
| Sample type |
SRA |
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| Source name |
Cicer arietinum variety 'Sonali' and Phytophthora medicaginis isolate 7831
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| Organisms |
Cicer arietinum; Phytophthora medicaginis |
| Characteristics |
tissue: Root and mycellium
treatment: 60 hours post inoculation
diseased state: diseased
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| Treatment protocol |
Roots were inoculated with P. medicaginis mycellial agar blocks 1 cm from the root tip and harvested at 8, 16, 20, 28, 32, 36, 40, 44, 48, 60, 84, 96, 108, 120, 132 and 144 hpi.
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| Growth protocol |
Chickpea var. 'Sonali' seeds were surface sterilised (4% NaOCl solution for 15 min, 70% EtOH for ten minutes and sterile ddH2O rinse three times) before sowing on modified full strength Murashige and Skoog agar plates (4.4% MS; 3% CaCO3, pH 7, 1.1% bacto agar) supplemented with Gamborg’s vitamins. Seedlings were grown in controlled growth chambers with 15 h light/ 9 h dark cycle at 18˚C, 70% relative humidity and 500 μmol m-2 s-1 light intensity. Fifteen-day old seedlings were used for inoculation. P. medicaginis isolate TR7831 was maintained on V8 juice agar plates (containing 200 mL L-1 V8TM bottled juice; 3.0 g L-1 CaCO3, 15.0 g L-1 agar) supplemented with ampicillin (100 μg mL-1) at 25˚C in the dark. Prior to inoculations, P. medicaginis was passaged through the host to ensure pathogenicity, and after reisolating on V8 juice agar plates supplemented with ampicillin (100 ug mL-1), the 2rd generation of P. medicaginis was used to prepare inoculum. P. medicaginis inoculum (3rd generation) was prepared one day before inoculations by aseptically transferring mycelial agar blocks taken from the edge of an actively growing culture onto 0.5 x 0.5 mm2 sterile membranes overlaid on V8 juice agar plates.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Root samples flash frozen with liquen nitrogen; RNA was extracted using the Bioline Plant II RNA extraction kit according to the manufacturer’s guidelines.
Poly-A RNA libraries were prepared and sequenced using Illumina HiSeq platform with a 150bp paired-end configuration
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Cicer arietinum roots inoculated with Phytophthora medicaginis mycellium
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| Data processing |
Raw RNA-seq data from one replicate each for the 19 hpi timepoints, and a control sample were mapped to the coding genes of Phytophthora medicaginis and primary transcripts of the Cicer arietinum Desi genome (Jain et al., 2013) using CLC Genomics Workbench 10. The alignment stringency included a minimum length fraction of 0.8, minimum similarity fraction of 0.9 and maximum number of hits per read of 10 while all other parameters were set to default.
Unique gene reads were calculated using CLC Genomics Workbench 10.
Genome_build: Phytophthora medicaginis isolate 7831 genome primary transcripts or Cicer arietinum Desi genome primary transcripts (Jain, M., Misra, G., Patel, R. K., Priya, P., Jhanwar, S., Khan, A. W., Shah, N., Singh, V. K., Garg, R., Jeena, G., Yadav, M., Kant, C., Sharma, P., Yadav, G., Bhatia, S., Tyagi, A. K. & Chattopadhyay, D. 2013. A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). The Plant Journal, 74, 715-729.)
Supplementary_files_format_and_content: One matrix table of the raw gene counts for every Phytophthora medicaginis gene and every sample (processed data_1.txt). A second matrix table of the raw gene counts for every Cicer arietinum gene and every sample (processed data_2.txt).
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| Submission date |
Sep 07, 2021 |
| Last update date |
Aug 05, 2024 |
| Contact name |
Jonathan Michael Plett |
| E-mail(s) |
J.Plett@westernsydney.edu.au
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| Phone |
+61 422535833
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| Organization name |
Western Sydney University
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| Department |
Soil Biology and Genomics
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| Lab |
Plett laboratory
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| Street address |
50 Bourke street
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| City |
Sydney |
| State/province |
New South Wales |
| ZIP/Postal code |
2753 |
| Country |
Australia |
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| Platform ID |
GPL30598 |
| Series (1) |
| GSE183604 |
Functional genomics identifies a small secreted protein that plays a role during the biotrophic to necrotrophic shift in the root rot pathogen Phytophthora medicaginis |
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| Relations |
| BioSample |
SAMN21322326 |
| SRA |
SRX12035627 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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