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RNASeq Steinernema carpocapsae

Steinernema carpocapsae - public RNASeq studies

Analysed

SRP084244: Comparative transcriptomics of Steinernema and Caenorhabditis single embryos reveals gene expression divergence during early embryogenesis

University of California, Irvine

Downloads

  • Characteristics and conditions per run

  • Counts of aligned reads per run (HTSeq2)

  • Gene expression (TPM) per run

  • Gene expression (TPM) per condition as median across runs

  • Differential expression

Design: 11 conditions

Condition num. replicates Developmental stage Organism part
1.5-fold 4 1.5-fold whole organism
2-cell 4 2-cell whole organism
2-fold 4 2-fold whole organism
24-44-cell 4 24-44-cell whole organism
4-cell 4 4-cell whole organism
64-78-cell 4 64-78-cell whole organism
8-cell 4 8-cell whole organism
L1 4 L1 whole organism
comma 4 comma whole organism
moving 4 moving whole organism
zygote 4 zygote whole organism

SRP093685: Activated entomopathogenic nematode infective juveniles release lethal venom proteins

University of California, Irvine


Downloads

  • Characteristics and conditions per run

  • Counts of aligned reads per run (HTSeq2)

  • Gene expression (TPM) per run

  • Gene expression (TPM) per condition as median across runs

Design: 5 conditions

Condition num. replicates Timepoint Treatment Developmental stage Organism part Strain
whole individual worm, infective juvenile, in vitro activated, 12h 3 12h in vitro activated infective juvenile (IJ) whole organism ALL
whole individual worm, infective juvenile, in vivo activated, 12h 3 12h in vivo activated infective juvenile (IJ) whole organism ALL
whole individual worm, infective juvenile, in vivo activated, 15h 3 15h in vivo activated infective juvenile (IJ) whole organism ALL
whole individual worm, infective juvenile, in vivo activated, 9h 3 9h in vivo activated infective juvenile (IJ) whole organism ALL
whole individual worm, infective juvenile, nonactivated 3 0h nonactivated infective juvenile (IJ) whole organism ALL

SRP133740: Small RNA and transcriptomic profiles of three isolates (All, Breton, UK1) of Steinernema carpocapsae Infective Juveniles. Warnock et al.

Queens University Belfast

Downloads

  • Characteristics and conditions per run

  • Counts of aligned reads per run (HTSeq2)

  • Gene expression (TPM) per run

  • Gene expression (TPM) per condition as median across runs

  • Differential expression

Design: 3 conditions

Condition num. replicates Geographic location Isolate Developmental stage Host Organism part
All 6 USA All Infective Juvenile Various larvae whole organism
Breton 6 Portugal Breton Infective Juvenile Various larvae whole organism
UK1 6 United Kingdom UK1 Infective Juvenile Various larvae whole organism

SRP277817: Comparative Transcriptomics of heads and tails between Steinernema carpocapsae and Caenorhabditis elegans

Mortazavi, Developmental and cell biology, University of California, Irvine

Downloads

Design: 9 conditions

Condition num. replicates Developmental stage Genotype Organism part Source name Strain Title
sc_female_head 3 young adult wild type head activated in lawn of Xenorhabdus nematophila ALL sc_female_head
sc_female_tail 3 young adult wild type tail activated in lawn of Xenorhabdus nematophila ALL sc_female_tail
sc_female_whole 3 young adult wild type whole organism activated in lawn of Xenorhabdus nematophila ALL sc_female_whole
sc_male_head 3 young adult wild type head activated in lawn of Xenorhabdus nematophila ALL sc_male_head
sc_male_tail 3 young adult wild type tail activated in lawn of Xenorhabdus nematophila ALL sc_male_tail
sc_male_whole 3 young adult wild type whole organism activated in lawn of Xenorhabdus nematophila ALL sc_male_whole
sc_nave_head 3 Infective Juvenile (IJ) wild type head not activated Infective Juvenile(IJ) ALL sc_nave_head
sc_nave_tail 3 Infective Juvenile (IJ) wild type tail not activated Infective Juvenile(IJ) ALL sc_nave_tail
sc_nave_whole 3 Infective Juvenile (IJ) wild type whole organism not activated Infective Juvenile(IJ) ALL sc_nave_whole

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.

SRP058023: Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks

University of California, Irvine

8 runs in ENA

SRP187486: Hybrid assembly of the genome of the entomopathogenic nematode Steinernema carpocapsae identifies the X-chromosome.

University of California Irvine

1 run in ENA