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Protocols specifications


Unique identifier OMICS_03135
Restrictions to use None
Maintained Yes

Publication for citations


The Role of DAF 21/Hsp90 in Mouth Form Plasticity in Pristionchus pacificus

Mol Biol Evol
PMCID: 5455966
PMID: 28333289
DOI: 10.1093/molbev/msx106
call_split See protocol

[…] As a first step, we searched for homologs of Hsp90 in P. pacificus genome. Protein sequences were retrieved from Genbank and the databases. Alignment was done using MUSCLE (). Conserved sites were manually selected using SeaView (). Phylogenetic trees were inferred using PhyML () with the LG + G substitution mo […]


Life History Responses and Gene Expression Profiles of the Nematode Pristionchus pacificus Cultured on Cryptococcus Yeasts

PLoS One
PMCID: 5065204
PMID: 27741297
DOI: 10.1371/journal.pone.0164881

[…] Raw reads were aligned to the P. pacificus reference genome (version Hybrid1) using TopHat (version 2.0.14) []. We downloaded the TAU2011 annotation of P. pacificus genes from and estimated expression levels for each data set separately using cufflinks (version 2.0.1) []. Principal component analysis was done using R. Differential expression analysis was do […]


Chromatin remodelling and antisense mediated up regulation of the developmental switch gene eud 1 control predatory feeding plasticity

Nat Commun
PMCID: 4976200
PMID: 27487725
DOI: 10.1038/ncomms12337
call_split See protocol

[…] s on an Illumina HiSeq 2000, yielding 30.6 million reads for the wild type and 31.6 million reads for the lsy-12 sample. Raw reads were aligned to the reference genomes of P. pacificus (Hybrid1) (, using the software Tophat v.2.0.3 (ref. ). Expression levels were estimated and tested for differential expression using the programs Cufflinks and Cuffdiff v.2.0.1 (ref. ) resultin […]


DAF 16/FoxO Directly Regulates an Atypical AMP Activated Protein Kinase Gamma Isoform to Mediate the Effects of Insulin/IGF 1 Signaling on Aging in Caenorhabditis elegans

PLoS Genet
PMCID: 3916255
PMID: 24516399
DOI: 10.1371/journal.pgen.1004109
call_split See protocol

[…] further analysis the ones with protein sequences that showed high similarity to the C. elegans aakg genes. Finally, orthologs of P. pacificus were derived from the gene predictions available from sequence alignments of the protein sequences were done using MUSCLE . Trees were constructed with ClustalW2 Phylogeny using the Neighbour-joining method. The species tree wa […]


A host beetle pheromone regulates development and behavior in the nematode Pristionchus pacificus

PMCID: 4270288
PMID: 25317948
DOI: 10.7554/eLife.03229.018
call_split See protocol

[…] ll lanes with 2 × 76 bp that yielded 61 million and 65 million reads after preprocessing (quality control, adapter removal). More than 90% of all reads could be mapped to the P. pacificus genome ( with BWA (version 0.5.9) for each library. We then employed ACCUSA for SNP detection (). Briefly, we performed a head-to-head comparison of the mutant Ppa-obi-1 and wild-type PS312 m […]


Discovery of Anthelmintic Drug Targets and Drugs Using Chokepoints in Nematode Metabolic Pathways

PLoS Pathog
PMCID: 3731235
PMID: 23935495
DOI: 10.1371/journal.ppat.1003505

[…]; ), Meloidogyne incognita ( enomic_resources/downloads; ), Pristionchus pacificus (; ) and Trichinella spiralis . The Homo sapiens genome was downloaded from Ensembl (Homo_sapiens.GRCh37.57.pep.all.fa) and Drosophilia melanogaster were downloaded from Flybase 5.26 (h […]


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Department of Evolutionary Biology, Max-Planck-Institute for Developmental Biology, Tübingen, Germany reviews

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