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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

Other

These studies are available in ENA, and the reads successfully align to our genomes.
They have not been included in our analysis for one of the following reasons:
Failed to meet minimal criteria for differential expression analysis, failure to pass data quality filters, or we were unable to interpret accompanying 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

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

Queens University Belfast

12 runs in ENA