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RNASeq Globodera rostochiensis

Globodera rostochiensis - public RNASeq studies

Analysed

SRP055923: Globodera rostochiensis transcriptome evolution during hatching.

Agriculture and Agri-Food Canada

Design: 9 conditions

Condition num. replicates Depth Geographic location Host Strain Treatment
dry cysts 2 0-20cm Canada: St-Amable, QC potato Ro1 dry cysts
hatched J2 larvae 2 0-20cm Canada: St-Amable, QC potato Ro1 hatched J2 larvae
hydrated cysts 2 0-20cm Canada: St-Amable, QC potato Ro1 hydrated cysts
hydrated cysts soaked 15m in PRD 2 0-20cm Canada: St-Amable, QC potato Ro1 hydrated cysts soaked 15m in PRD
hydrated cysts soaked 1h in PRD 2 0-20cm Canada: St-Amable, QC potato Ro1 hydrated cysts soaked 1h in PRD
hydrated cysts soaked 24h in PRD 2 0-20cm Canada: St-Amable, QC potato Ro1 hydrated cysts soaked 24h in PRD
hydrated cysts soaked 48h in PRD 2 0-20cm Canada: St-Amable, QC potato Ro1 hydrated cysts soaked 48h in PRD
hydrated cysts soaked 7d in PRD 2 0-20cm Canada: St-Amable, QC potato Ro1 hydrated cysts soaked 7d in PRD
hydrated cysts soaked 8h in PRD 2 0-20cm Canada: St-Amable, QC potato Ro1 hydrated cysts soaked 8h in PRD

Other

These studies are available in ENA, and the reads successfully align to our genomes.
We have decided not to include them in our analysis.
Either they failed to meet minimal criteria for inclusion, we've been asked to exclude them for data quality reasons, or we were unable to interpret the metadata.

ERP001236: Globodera pallida transcriptomics

Wellcome Sanger Institute

As part of the Globodera pallida (potato cyst nematode) genome project we are profiling the transcriptome of the parasite across its life cycle using RNA-Seq. .

4 runs in ENA

ERP013515: 100 bp paired-end Illumina Hiseq RNAseq of G. rostochiensis females 14 days post infection.

University of Dundee

100 bp paired-end Illumina Hiseq RNAseq of G. rostochiensis females 14 days post infection each in biological duplicate. Pathotype Ro1 infecting potato.

2 runs in ENA

SRP146253: Globodera spp. host specificity

Agriculture and Agri-Food Canada

2 runs in ENA