WormBase ParaSite HomeVersion: WBPS15 (WS276)
RNASeq Caenorhabditis briggsae

Caenorhabditis briggsae - 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 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

Conservation of mRNA and protein expression during development of C. elegans. (GrĂ¼n .. Rajewsky, 2014)

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

Evolution of Transcriptional Repressors Impacts Caenorhabditis Vulval Development. (Chamberlin .. Gupta, 2020)

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

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