Caenorhabditis remanei - public RNASeq studies
Table of Contents
- Caenorhabditis sex-specific RNAseq
- Rapid evolution of phenotypic plasticity and shifting thresholds of genetic assimilation in the nematode Caenorhabditis remanei
- Evolution of phenotypic plasticity and transgenerational effects of heat stress in the nematode Caenorhabditis remanei
- 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
- Environmental and evolutionary drivers of the modular gene regulatory network underlying phenotypic plasticity for stress resistance in the nematode Caenorhabditis remanei
- 2 other studies
Analysed
SRP016006: Caenorhabditis sex-specific RNAseq
Haag Lab, Department of Biology, University of Maryland
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
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
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
Design: 4 conditions
| Condition | num. replicates | Strain | Developmental stage | Source name |
|---|---|---|---|---|
| Control selected, derived from PX443 | 16 | Control selected, derived from PX443 | L1 | pooled L1 tissue |
| Heat selected, derived from PX443 | 16 | Heat selected, derived from PX443 | L1 | pooled L1 tissue |
| Oxidative stress selected, derived from PX443 | 12 | Oxidative stress selected, derived from PX443 | L1 | pooled L1 tissue |
| PX443 | 12 | PX443 | L1 | pooled L1 tissue |
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.
SRP026198: mRNA and Ribosome Profiling in Four Nematode Species Traversing a Shared Developmental Transition
Fire, Pathology, Stanford University
3 runs in ENA
SRP112745: Caenorhabditis remanei PX439 Genome sequencing
University of Oregon
1 run in ENA
Release 18 - April 2023
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