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
- Quantifying regulatory divergence using interspecies hybird RNA-seq assays in Caenorhabditis
- 7 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 |
SRP279004: Quantifying regulatory divergence using interspecies hybird RNA-seq assays in Caenorhabditis
University of Toronto
Design: 4 conditions
| Condition | num. replicates | Sex | Strain | Developmental stage | Organism part |
|---|---|---|---|---|---|
| Cbr_F | 1 | female | AF16 | Young adults | whole organism |
| Cbr_M | 3 | male | AF16 | Young adults | whole organism |
| F1H_F | 3 | female | JU1421 x AF16 | Young adults | whole organism |
| F1H_M | 3 | male | JU1421 x AF16 | Young adults | whole organism |
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.
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
SRP026198: mRNA and Ribosome Profiling in Four Nematode Species Traversing a Shared Developmental Transition
Fire, Pathology, Stanford University
2 runs in ENA
SRP056941: Developmental dynamics of C. elegans dosage compensation
Biology, New York University
Developmental Dynamics of X-Chromosome Dosage Compensation by the DCC and H4K20me1 in C. elegans. (Kramer .. Ercan, 2015)
Untangling the Contributions of Sex-Specific Gene Regulation and X-Chromosome Dosage to Sex-Biased Gene Expression in Caenorhabditis elegans. (Kramer .. Ercan, 2016)
6 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 18 - April 2023
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