Caenorhabditis briggsae - public RNASeq studies
Table of Contents
- Caenorhabditis sex-specific RNAseq
- Conservation of mRNA and protein expression during development of C. elegans
- Caenorhabditis briggsae transcriptome and genome sequencing
- Genome-wide expression analysis of Caenorhabditis briggsae SPR-4/IVP-1 and HTZ-1/IVP-2 mutants
- Transcriptional profiling of Caenorhabditis elegans and Caenorhabditis briggsae before and after heat shock
- 5 other studies
Analysed
SRP016006: Caenorhabditis sex-specific RNAseq
Haag Lab, Department of Biology, University of Maryland
Design: 2 conditions
| Condition | num. replicates | Developmental stage | Sex | Strain |
|---|---|---|---|---|
| male - XO | 3 | L4 & adult | male - XO | AF16 (WT) |
| pseudofemale - XX | 3 | L4 & adult | pseudofemale - XX | she-1(v47) |
SRP034522: Conservation of mRNA and protein expression during development of C. elegans
Max Planck Institute of Immunobiology and Epigenetics
Design: 4 conditions
| Condition | num. replicates | Developmental stage | Strain | Temperature |
|---|---|---|---|---|
| L1 larvae | 2 | L1 larvae | AF16 | 20C |
| mixed embryos | 2 | mixed embryos | AF16 | 20C |
| mixed stages reference | 1 | mixed stages reference | AF16 | 20C |
| young adults | 1 | young adults | AF16 | 20C |
SRP173664: Caenorhabditis briggsae transcriptome and genome sequencing
University of Toronto
Design: 6 conditions
| Condition | num. replicates | Strain | Developmental stage |
|---|---|---|---|
| AF14 | 3 | AF14 | young adult |
| AF20 | 3 | AF20 | young adult |
| AF30 | 3 | AF30 | young adult |
| HK14 | 3 | HK14 | young adult |
| HK20 | 3 | HK20 | young adult |
| HK30 | 3 | HK30 | young adult |
SRP212884: Genome-wide expression analysis of Caenorhabditis briggsae SPR-4/IVP-1 and HTZ-1/IVP-2 mutants
LSB322, Biology, McMaster University
Design: 3 conditions
| Condition | num. replicates | Strain | Developental stage | Source name |
|---|---|---|---|---|
| AF16 wild-type isolate | 3 | AF16 wild-type isolate | L3 | Whole animal |
| Cbr-htz-1(gu167)/Cbr-ivp-2(gu167) | 3 | Cbr-htz-1(gu167)/Cbr-ivp-2(gu167) | L3 | Whole animal |
| Cbr-spr-4(gu163)/Cbr-ivp-1(gu163) | 3 | Cbr-spr-4(gu163)/Cbr-ivp-1(gu163) | L3 | Whole animal |
SRP218832: Transcriptional profiling of Caenorhabditis elegans and Caenorhabditis briggsae before and after heat shock
University of California, San Diego
HASH(0x4bdbb28) (Garrigues .. Pasquinelli, 2019)
Design: 2 conditions
| Condition | num. replicates | Strain | Treatment | Developmental stage | Organism part |
|---|---|---|---|---|---|
| Control | 3 | AF16 | control (NHS) | L2 | whole organism |
| Heat-shocked | 3 | AF16 | heat-shocked (HS) | L2 | whole organism |
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.
SRP011366: Caenorhabditis briggsae strain:AF16 Transcriptome or Gene expression
Simon Fraser University
2 runs in ENA
SRP019476: Caenorhabditis briggsae strain:AF16 Transcriptome or Gene expression
University of Toronto
2 runs in ENA
SRP067756: Analysis of Hybrid Incompatability between C nigoni and C briggsae by mRNA sequencing
Hong Kong Baptist University
4 runs in ENA
SRP100798: Transcriptional response to viral infection in Caenorhabditis nematodes
Washington University in St. Louis
6 runs in ENA
SRP159488: Illumina sequencing of 4 Caenorhabditis species L4-early adult polyA+ 50bp PE RNAseq
Centre for Genomic Regulation (CRG)
1 run in ENA
Release 15 - October 2020
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