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Function & Expression : gene expression data

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Gene Expression Experiments
Based on the large amount of sequence data that has become available for the first time in many nematodes, we and our collaborators have started to investigate gene expression profiles in various species using RNAseq and microarray technology. This section of Nematode.net hosts the results of various RNAseq and microarray experiments, with the goal of meeting MIAME standards where possible.

NOTE: This page only hosts datafiles for select gene expression experiments. If you are looking for gene expression data based on RNAseq mapping to predicted genes, that data is available for select species within NemaGene. Species labeled in red in the species selection list are annotated with stage/tissue specific FPKM values per gene. If you are looking for putative transcripts based on cDNA assemblies, we have Sanger EST based assembly contigs available for download from our Cluster Data FTP page, and we also have 454 cDNA isotigs available on our cDNA Assemblies page.



Available experimental data:
(last updated 04-30-13)
Species Project Publication Data type Raw data Processed data Sample annotations Experimental design Array annotation Methods Other information
Ascaris suum Ascaris suum microarray data PMID:23572074 Microarray compressed tarfile compressed textfile compressed xls file compressed xls file compressed textfile compressed textfile *note: Available in NCBI GEO: GSE36690
Ascaris suum Ascaris suum RNAseq-based expression data under review RNAseq NA compressed textfile NA NA NA compressed textfile NA
Brugia malayi Brugia malayi annotation v2 PMID:15992941 Microarray Zip file NA NA NA Excel spreadsheet NA Bmalayi gene fasta

Bmalayi gene GO assignments

*note: Available in NCBI GEO: GPL1483
Brugia malayi Brugia malayi lifecycle stage microarray PMID:19527522 Microarray compressed tarfile compressed file NA NA compressed file NA Bmalayi interproscan results
Heterodera glycines Affymetrix Soybean Genome Array GeneChip PMID:19183474 Microarray compressed tarfile compressed tarfile compressed tarfile compressed tarfile compressed tarfile compressed tarfile Hglycines contig fasta
Necator americanus Necator americanus RNAseq-based expression data accepted RNAseq NA excel spreadsheet NA NA NA NA NA
                     


 
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