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De novo transcriptome assembly of Schizaphis gramium Biotype I feeding on wheat
Transcriptome was generated from pooled adult aphids that were fed on wheat plants containing the Dn4 and DN7 resistance gene as well as Yuma plants containing no resistant genes (Dn0). The assembly was generated using Trinity. All assembled transcripts, including those that were not predicted to encode ORFs, are included along with their corresponding functional annotations from Trinotate. Resources in this dataset:Resource Title: De novo transcriptome assembly of Schizaphis graminum Biotype I. File Name: Trinity.fasta_.txtResource Description: Reads were assembled using Trinity version 2.3.2. All transcripts greater than 200 nt were retained in this version of the assembly. Resource Software Recommended: Notepad++,url: https://notepad-plus-plus.org/ Resource Title: Filtered Transcriptome Assembly of Schizaphis graminum. File Name: GreenbugFilteredTrinity.transdecoder.mRNA.fasta_.txtResource Description: Only transcripts with transcripts per million mapped reads values (TPM) >=0.05 and transcripts whose expression levels represented >=10% of their dominant isoform were retained for differential expression. Resource Software Recommended: Notepad++,url: https://notepad-plus-plus.org/ Resource Title: Trinotate results for Schizaphis graminum transcriptome assembly. File Name: Greenbug_trinotate_annotation_report.xlsResource Description: Trinotate was used to obtain highest scoring blastp matches to annotated proteins curated in the swiss-prot, detect Pfam domains, obtain gene ontology annotations, and obtain KEGG annotations. Resource Software Recommended: Microsoft Excel,url: https://products.office.com/en-us/excel Resource Title: Protein coding translations of Schizaphis graminum assembly. File Name: Greenbug_FilteredTrinityfastafromTrial6.sh.o2516954.fasta.transdecoder.pep.txtResource Description: TransDecoder was used to predict open reading frames in the final transcriptome assembly. Resource Software Recommended: Notepad++,url: https://notepad-plus-plus.org/
Resources
4 resources available
-
Trinity.fasta__0.txt
TXT -
Greenbug_FilteredTrinity.transdecoder.mRNA_.fasta_.txt
TXT -
Greenbug_trinotate_annotation_report.xls
XLS -
Greenbug_FilteredTrinityfasta_fromTrial6.sh_.o2516954.fasta_.transdecoder.pep_.txt
TXT
Complete Metadata
| @type | dcat:Dataset |
|---|---|
| accessLevel | public |
| bureauCode |
[
"005:18"
]
|
| contactPoint |
{
"fn": "Scully, Erin",
"hasEmail": "mailto:Erin.Scully@ars.usda.gov"
}
|
| description | <p>Transcriptome was generated from pooled adult aphids that were fed on wheat plants containing the Dn4 and DN7 resistance gene as well as Yuma plants containing no resistant genes (Dn0). The assembly was generated using Trinity. All assembled transcripts, including those that were not predicted to encode ORFs, are included along with their corresponding functional annotations from Trinotate. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: De novo transcriptome assembly of Schizaphis graminum Biotype I.</p> <p>File Name: Trinity.fasta_.txt</p><p>Resource Description: Reads were assembled using Trinity version 2.3.2. All transcripts greater than 200 nt were retained in this version of the assembly. </p><p>Resource Software Recommended: Notepad++,url: <a href="https://notepad-plus-plus.org/">https://notepad-plus-plus.org/</a> </p></li><br><li><p>Resource Title: Filtered Transcriptome Assembly of Schizaphis graminum.</p> <p>File Name: Greenbug<em>FilteredTrinity.transdecoder.mRNA</em>.fasta_.txt</p><p>Resource Description: Only transcripts with transcripts per million mapped reads values (TPM) >=0.05 and transcripts whose expression levels represented >=10% of their dominant isoform were retained for differential expression. </p><p>Resource Software Recommended: Notepad++,url: <a href="https://notepad-plus-plus.org/">https://notepad-plus-plus.org/</a> </p></li><br><li><p>Resource Title: Trinotate results for Schizaphis graminum transcriptome assembly.</p> <p>File Name: Greenbug_trinotate_annotation_report.xls</p><p>Resource Description: Trinotate was used to obtain highest scoring blastp matches to annotated proteins curated in the swiss-prot, detect Pfam domains, obtain gene ontology annotations, and obtain KEGG annotations. </p><p>Resource Software Recommended: Microsoft Excel,url: <a href="https://products.office.com/en-us/excel">https://products.office.com/en-us/excel</a> </p></li><br><li><p>Resource Title: Protein coding translations of Schizaphis graminum assembly.</p> <p>File Name: Greenbug_FilteredTrinityfasta<em>fromTrial6.sh</em>.o2516954.fasta<em>.transdecoder.pep</em>.txt</p><p>Resource Description: TransDecoder was used to predict open reading frames in the final transcriptome assembly. </p><p>Resource Software Recommended: Notepad++,url: <a href="https://notepad-plus-plus.org/">https://notepad-plus-plus.org/</a> </p></li></ul><p></p> |
| distribution |
[
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{
"@type": "dcat:Distribution",
"title": "Greenbug_FilteredTrinity.transdecoder.mRNA_.fasta_.txt",
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"title": "Greenbug_FilteredTrinityfasta_fromTrial6.sh_.o2516954.fasta_.transdecoder.pep_.txt",
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|
| identifier | 10.15482/USDA.ADC/1517669 |
| keyword |
[
"ARS",
"RNA de novo assembly",
"RNA-Seq",
"data.gov",
"de novo transcriptome"
]
|
| license | https://www.usa.gov/publicdomain/label/1.0/ |
| modified | 2025-11-21 |
| programCode |
[
"005:040"
]
|
| publisher |
{
"name": "Agricultural Research Service",
"@type": "org:Organization"
}
|
| spatial |
"{"type": "Point", "coordinates": [-96.580518186092, 39.19235913618]}"
|
| title | De novo transcriptome assembly of Schizaphis gramium Biotype I feeding on wheat |
