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RNASeq Meloidogyne incognita

Meloidogyne incognita - public RNASeq studies

Analysed

ERP009887: Meloidogyne incognita transcriptomes

Genoscope

As part of the Meloidogyne incognita (root-knot nematode) genome sequencing project we have profiled the transcriptome of this plant parasite across its life cycle using RNA-Seq. The ensemble of transcriptomic data has been used to provide evidence for gene prediction. Genome assembly and accompanying transcriptome data is available at http://meloidogyne.inra.fr
Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. (Blanc-Mathieu .. Danchin, 2017)

Design: 7 conditions

Condition num. replicates Developmental stage
adult female 1 adult female
adult male 1 adult male
egg 1 egg
juvenile 2 juvenile
juvenile J3-J4 1 juvenile J3-J4
preparasitic J2.1 1 preparasitic J2.1
preparasitic J2.2 1 preparasitic J2.2

SRP109232: RNA-Seq analysis at various developmental stages of the Meloidogyne incognita life cycle

Rural Development Administration

RNA-Seq of Plant-Parasitic Nematode Meloidogyne incognita at Various Stages of Its Development. (Choi .. Hahn, 2017)

Design: 5 conditions

Condition num. replicates Depth Developmental stage Geographic location Host Isolation source Temperature
Egg 3 15 cm Egg South Korea Solanum lycopersicum Infected roots 25 C
J2 juveniles 3 15 cm J2 juveniles South Korea Solanum lycopersicum Infected roots 25 C
J3 3 15 cm J3 South Korea Solanum lycopersicum Infected roots 25 C
J4 3 15 cm J4 South Korea Solanum lycopersicum Infected roots 25 C
adult female 3 15 cm adult female South Korea Solanum lycopersicum Infected roots 25 C

SRP152065: Meloidogyne incognita Transcriptome or Gene expression

ICAR-IARI, New Delhi, INDIA

A transcriptomic snapshot of early molecular communication between Pasteuria penetrans and Meloidogyne incognita. (Phani .. Rao, 2018)

Design: 2 conditions

Condition num. replicates Developmental stage Infection
Pasteuria penetrans 2 second stage juvenile Pasteuria penetrans
Uninfected juveniles 2 second stage juvenile

SRP155330: A transcriptomic comparison of fed and starved Meloidogyne incognita J2 larvae to fresh J2s

ICAR-IARI, New Delhi, INDIA

Design: 3 conditions

Condition num. replicates Developmental stage Treatment
Fresh juveniles 2 second stage juvenile
Mi-sbp-1 ds-RNA 2 second stage juvenile Mi-sbp-1 ds-RNA
starvation, 6 days 2 second stage juvenile starvation, 6 days

SRP155472: Meloidogyne incognita strain:New Delhi | isolate:IARI Transcriptome or Gene expression

ICAR-IARI, New Delhi, INDIA

Design: 4 conditions

Condition num. replicates Developmental stage Treatment
Control (GFP) 2 second stage juvenile Control (GFP)
Control (Untreated) 2 second stage juvenile
msp-1 silenced 2 second stage juvenile msp-1 silenced
msp-20 silenced 2 second stage juvenile msp-20 silenced

SRP187776: Transcriptional signatures of invasiveness in Meloidogyne incognita populations from sub-Saharan Africa

Queens University Belfast

Design: 3 conditions

Condition num. replicates Isolate Isolation source Host Organism part
Kenya 3 Kenya Amaranthus viridae Tomato j2
Nigeria 1 3 Nigeria 1 Celosia Tomato j2
Nigeria 2 3 Nigeria 2 Not available Tomato j2

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.

ERP010859: Meloidogyne incognita transcriptomes

Genoscope

As part of the Meloidogyne incognita (root-knot nematode) genome sequencing project we have profiled the transcriptome of this plant parasite across its life cycle using RNA-Seq. The ensemble of transcriptomic data has been used to provide evidence for gene prediction. Genome assembly and accompanying transcriptome data is available at http://meloidogyne.inra.fr

1 run in ENA

SRP003867: Identification of Novel and Conserved MicroRNAs of Root-knot Nematode Using a Deep-sequencing Approach

SRP019992: Meloidogyne incognita Variation

Hunan Agricultural University

2 runs in ENA

SRP068483: Transcriptome of early-infected root-knot nematodes by the bacterial pathogen Pasteuria penetrans

Chinese Academy of Tropical Agricultural Sciences

2 runs in ENA