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RNASeq Caenorhabditis remanei

Caenorhabditis remanei - public RNASeq studies

Analysed

SRP016006: Caenorhabditis sex-specific RNAseq

Haag Lab, Department of Biology, University of Maryland

Simplification and desexualization of gene expression in self-fertile nematodes. (Thomas .. Haag, 2012)

Design: 2 conditions

Condition num. replicates Developmental stage Rna Strain
L4 & adult females 3 L4 & adult females poly-A RNA PB4641 (WT)
L4 & adult males 3 L4 & adult males poly-A RNA PB4641 (WT)

SRP040962: Rapid evolution of phenotypic plasticity and shifting thresholds of genetic assimilation in the nematode Caenorhabditis remanei

Institute of Ecology and Evolution, University of Oregon

Rapid evolution of phenotypic plasticity and shifting thresholds of genetic assimilation in the nematode Caenorhabditis remanei. (Sikkink .. Phillips, 2014)

Design: 6 conditions

Condition num. replicates Developmental stage Strain Temperature
Control selected, derived from PX443, 20°C 6 L1 Control selected, derived from PX443 20°C
Control selected, derived from PX443, 30°C 6 L1 Control selected, derived from PX443 30°C
Heat-selected, derived from PX443, 20°C 6 L1 Heat-selected, derived from PX443 20°C
Heat-selected, derived from PX443, 30°C 6 L1 Heat-selected, derived from PX443 30°C
PX443, 20°C 6 L1 PX443 20°C
PX443, 30°C 6 L1 PX443 30°C

SRP049403: Evolution of phenotypic plasticity and transgenerational effects of heat stress in the nematode Caenorhabditis remanei

Institute of Ecology and Evolution, University of Oregon

The transgenerational effects of heat stress in the nematode Caenorhabditis remanei are negative and rapidly eliminated under direct selection for increased stress resistance in larvae. (Sikkink .. Phillips, 2014)

Design: 6 conditions

Condition num. replicates Developmental stage Larval rearing temperature Parental temperature Strain
20°C, Control-selected, derived from PX443 2 L1 20°C 30°C Control-selected, derived from PX443
20°C, Heat-selected, derived from PX443 2 L1 20°C 30°C Heat-selected, derived from PX443
20°C, PX443 2 L1 20°C 30°C PX443
30°C, Control-selected, derived from PX443 2 L1 30°C 30°C Control-selected, derived from PX443
30°C, Heat-selected, derived from PX443 2 L1 30°C 30°C Heat-selected, derived from PX443
30°C, PX443 2 L1 30°C 30°C PX443

SRP126964: Dissecting the genetic basis of an evolved acute heat stress and oxidative stress resistance in the nematode Caenorhabditis remanei reveals a complex and unique genetic architecture

Biology, University of Oregon

Design: 4 conditions

Condition num. replicates Developmental stage Strain
Control selected, derived from PX443 8 L1 Control selected, derived from PX443
Heat-selected, derived from PX443 8 L1 Heat-selected, derived from PX443
Oxidative-selected, derived from PX443 6 L1 Oxidative-selected, derived from PX443
PX443 6 L1 PX443

SRP150050: Environmental and evolutionary drivers of the modular gene regulatory network underlying phenotypic plasticity for stress resistance in the nematode Caenorhabditis remanei

Emilie Snell-Rood, Ecology, Evolution, and Behavior, University of Minnesota

Environmental and Evolutionary Drivers of the Modular Gene Regulatory Network Underlying Phenotypic Plasticity for Stress Resistance in the Nematode Caenorhabditis remanei. (Sikkink .. Phillips, 2019)

Design: 48 conditions

Condition num. replicates Batch Description title Strain Developmental stage Source name
SAMN09381546 1 C CTRL_m20h30-1 Control selected, derived from PX443 L1 pooled L1 tissue
SAMN09381552 1 C CTRL_m20h20-2 Control selected, derived from PX443 L1 pooled L1 tissue
SAMN09381553 1 C CTRL_m20h20-1 Control selected, derived from PX443 L1 pooled L1 tissue
SAMN09381581 1 E HEAT_m20h30-2 Heat selected, derived from PX443 L1 pooled L1 tissue
SAMN09381582 1 E HEAT_m20h30-1 Heat selected, derived from PX443 L1 pooled L1 tissue
SAMN09381587 1 E HEAT_m20h20-2 Heat selected, derived from PX443 L1 pooled L1 tissue
SAMN09381588 1 E HEAT_m20h20-1 Heat selected, derived from PX443 L1 pooled L1 tissue
SAMN09381593 1 C CTRL_m20h30-2 Control selected, derived from PX443 L1 pooled L1 tissue
SRR7280017 1 A ANC_m20h20-1 PX443 L1 pooled L1 tissue
SRR7280018 1 A ANC_m20h20-2 PX443 L1 pooled L1 tissue
SRR7280019 1 B ANC_m20h20-3 PX443 L1 pooled L1 tissue
SRR7280020 1 B ANC_m20h20-4 PX443 L1 pooled L1 tissue
SRR7280021 1 B ANC_m20h20-5 PX443 L1 pooled L1 tissue
SRR7280022 1 B ANC_m20h20-6 PX443 L1 pooled L1 tissue
SRR7280023 1 A ANC_m20h30-1 PX443 L1 pooled L1 tissue
SRR7280024 1 A ANC_m20h30-2 PX443 L1 pooled L1 tissue
SRR7280025 1 B ANC_m20h30-3 PX443 L1 pooled L1 tissue
SRR7280026 1 B ANC_m20h30-4 PX443 L1 pooled L1 tissue
SRR7280027 1 A ANC_m20h30-5 PX443 L1 pooled L1 tissue
SRR7280028 1 A ANC_m20h30-6 PX443 L1 pooled L1 tissue
SRR7280033 1 D CTRL_m20h20-3 Control selected, derived from PX443 L1 pooled L1 tissue
SRR7280034 1 D CTRL_m20h20-4 Control selected, derived from PX443 L1 pooled L1 tissue
SRR7280035 1 D CTRL_m20h20-5 Control selected, derived from PX443 L1 pooled L1 tissue
SRR7280036 1 D CTRL_m20h20-6 Control selected, derived from PX443 L1 pooled L1 tissue
SRR7280041 1 D CTRL_m20h30-3 Control selected, derived from PX443 L1 pooled L1 tissue
SRR7280042 1 D CTRL_m20h30-4 Control selected, derived from PX443 L1 pooled L1 tissue
SRR7280043 1 D CTRL_m20h30-5 Control selected, derived from PX443 L1 pooled L1 tissue
SRR7280044 1 D CTRL_m20h30-6 Control selected, derived from PX443 L1 pooled L1 tissue
SRR7280049 1 F HEAT_m20h20-3 Heat selected, derived from PX443 L1 pooled L1 tissue
SRR7280050 1 F HEAT_m20h20-4 Heat selected, derived from PX443 L1 pooled L1 tissue
SRR7280051 1 F HEAT_m20h20-5 Heat selected, derived from PX443 L1 pooled L1 tissue
SRR7280052 1 F HEAT_m20h20-6 Heat selected, derived from PX443 L1 pooled L1 tissue
SRR7280057 1 F HEAT_m20h30-3 Heat selected, derived from PX443 L1 pooled L1 tissue
SRR7280058 1 F HEAT_m20h30-4 Heat selected, derived from PX443 L1 pooled L1 tissue
SRR7280059 1 F HEAT_m20h30-5 Heat selected, derived from PX443 L1 pooled L1 tissue
SRR7280060 1 F HEAT_m20h30-6 Heat selected, derived from PX443 L1 pooled L1 tissue
SRR7280061 1 G OXID_m20h20-1 Oxidative stress selected, derived from PX443 L1 pooled L1 tissue
SRR7280062 1 G OXID_m20h20-2 Oxidative stress selected, derived from PX443 L1 pooled L1 tissue
SRR7280063 1 G OXID_m20h20-3 Oxidative stress selected, derived from PX443 L1 pooled L1 tissue
SRR7280064 1 G OXID_m20h20-4 Oxidative stress selected, derived from PX443 L1 pooled L1 tissue
SRR7280065 1 G OXID_m20h20-5 Oxidative stress selected, derived from PX443 L1 pooled L1 tissue
SRR7280066 1 G OXID_m20h20-6 Oxidative stress selected, derived from PX443 L1 pooled L1 tissue
SRR7280067 1 G OXID_m20h30-1 Oxidative stress selected, derived from PX443 L1 pooled L1 tissue
SRR7280068 1 G OXID_m20h30-2 Oxidative stress selected, derived from PX443 L1 pooled L1 tissue
SRR7280069 1 G OXID_m20h30-3 Oxidative stress selected, derived from PX443 L1 pooled L1 tissue
SRR7280070 1 G OXID_m20h30-4 Oxidative stress selected, derived from PX443 L1 pooled L1 tissue
SRR7280071 1 G OXID_m20h30-5 Oxidative stress selected, derived from PX443 L1 pooled L1 tissue
SRR7280072 1 G OXID_m20h30-6 Oxidative stress selected, derived from PX443 L1 pooled L1 tissue

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.

SRP112745: Caenorhabditis remanei PX439 Genome sequencing

University of Oregon

1 run in ENA