Annotations of Unigenes Assembled from Schizaphis graminum and Sipha flava
<p>Transcriptomes were assembled de novo from pools of adult aphids that were feeding on sorghum and switchgrass. Reads from all replicates were pooled, normalized in silico to 25X coverage, and assembled using Trinity. Only the most abundant isoform for each unigene was retained for annotation and unigenes with transcripts per million mapped reads (TPM) less than 0.5 were removed from the dataset. The remaining unigenes were annotated using Trinotate with BLASTP comparisons against the Swiss-Prot/UniProt database. In addition, Pfam-A assignments were computed using hmmer, signal peptide predictions were performed using SignalP, and transmembrane domain predictions were performed using tmHMM. Gene ontology (GO assignments) were retrieved from Trinotate using the highest scoring BLASTp matches as queries.</p> <p>[Note: Supplemental files 1-6 added 2/5/2019] </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Trinotate annotations for unigenes assembled from Schizaphis graminum (greenbug).</p> <p>File Name: GB_annotation_trinotate<em>final</em>.xls</p><p>Resource Description: ::Note:: Data file is large and may take time to load.</p> <p></p><p>Resource Software Recommended: 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: Trinotate annotations of unigenes assembled from Sipha flava (yellow sugarcane aphid).</p> <p>File Name: YSA_annotation_trinotate<em>final</em>.xls</p><p>Resource Description: ::Note:: Data file is large and may take time to load. </p><p>Resource Software Recommended: 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: Supplemental Data 1: Differential expression analysis of starvation and BCK60 sorghum treatments in S. graminum at 12 and 24 hours.</p> <p>File Name: Supplemental Data 1.xlsx</p><p>Resource Description: Reads were mapped back to the transcriptome assembly using bowtie2 and RSEM and differential expression analysis was performed using edgeR as described in the Materials and Methods. Unigenes with log fold-change values > 0 are upregulated in the BCK60 treatment relative to the starvation treatment while unigenes with log fold-change values < 0 are downregulated in this comparison. Log fold-change and FDR corrected-p-value thresholds were set at 0.25 and 0.05, respectively. Tab labeled 12 represents 12 hr post infestation and tab labeled 24 represents 24 hr post infestation. </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: Supplemental Data 2. Differential expression analysis of starvation and BCK60 sorghum treatments in S. flava at 12 and 24 hours.</p> <p>File Name: Supplemental Data 2.xlsx</p><p>Resource Description: Reads were mapped back to the transcriptome assembly using bowtie2 and RSEM and differential expression analysis was performed using edgeR as described in the Materials and Methods. Unigenes with log fold-change values < 0 are downregulated in the BCK60 treatment relative to the starvation treatment while unigenes with log fold-change values < 0 are downregulated in this comparison. Log fold-change and FDR corrected-p-value thresholds were set at 0.25 and 0.05, respectively. Tab labeled 12 represents 12 hr post infestation and tab labeled 24 represents 24 hr post infestation. </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: Supplemental Data 3. Differential expression analysis of Summer switchgrass and BCK60 sorghum treatments in S. graminum at 12 and 24 hours.</p> <p>File Name: Supplemental Data 3.xlsx</p><p>Resource Description: Reads were mapped back to the transcriptome assembly using bowtie2 and RSEM and differential expression analysis was performed using edgeR as described in the Materials and Methods. Unigenes with log fold-change values > 0 are upregulated in the Summer treatment relative to the BCK60 treatment while unigenes with log fold-change values < 0 are downregulated in this comparison. Log fold-change and FDR corrected-p-value thresholds were set at 0.25 and 0.05, respectively. Tab labeled 12 represents 12 hr post infestation and tab labeled 24 represents 24 hr post infestation. </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: Supplemental Data 4. Differential expression analysis of Summer switchgrass and BCK60 sorghum treatments in S. flava at 12 and 24 hours.</p> <p>File Name: Supplemental Data 4.xlsx</p><p>Resource Description: Reads were mapped back to the transcriptome assembly using bowtie2 and RSEM and differential expression analysis was performed using edgeR as described in the Materials and Methods. Unigenes with log fold-change values > 0 are upregulated in the Summer treatment relative to the BCK60 treatment while unigenes with log fold-change values < 0 are downregulated in this comparison. Log fold-change and FDR corrected-p-value thresholds were set at 0.25 and 0.05, respectively. Tab labeled 12 represents 12 hr post infestation and tab labeled 24 represents 24 hr post infestation. </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: Supplemental Data 5. Differential expression analysis of Kanlow switchgrass and BCK60 sorghum treatments in S. graminum t 12 and 24 hours.</p> <p>File Name: Supplemental Data 5.xlsx</p><p>Resource Description: Reads were mapped back to the transcriptome assembly using bowtie2 and RSEM and differential expression analysis was performed using edgeR as described in the Materials and Methods. Unigenes with log fold-change values > 0 are upregulated in the Kanlow treatment relative to the BCK60 treatment while unigenes with log fold-change values < 0 are downregulated in this comparison. Log fold-change and FDR corrected-p-value thresholds were set at 0.25 and 0.05, respectively. Tab labeled 12 represents 12 hr post infestation and tab labeled 24 represents 24 hr post infestation. </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: Supplemental Data 6. Differential expression analysis of Kanlow switchgrass and BCK60 sorghum treatments in S. flava t 12 and 24 hours.</p> <p>File Name: Supplemental Data 6.xlsx</p><p>Resource Description: Reads were mapped back to the transcriptome assembly using bowtie2 and RSEM and differential expression analysis was performed using edgeR as described in the Materials and Methods. Unigenes with log fold-change values > 0 are upregulated in the Kanlow treatment relative to the BCK60 treatment while unigenes with log fold-change values < 0 are downregulated in this comparison. Log fold-change and FDR corrected-p-value thresholds were set at 0.25 and 0.05, respectively.<br> Tab labeled 12 represents 12 hr post infestation and tab labeled 24 represents 24 hr post infestation.<br> </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></ul><p></p>
| Main Authors: | , , , , , , |
|---|---|
| Format: | Dataset biblioteca |
| Published: |
2018
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| Subjects: | Genomics and transcriptomics, Genetics, switchgrass, Kanlow, summer, de novo transcriptome, RNA-Seq, Sorghum bicolor, Panicum virgatum, BCK60, biotic stress, abiotic stress, NP215, NP304, |
| Online Access: | https://figshare.com/articles/dataset/Annotations_of_Unigenes_Assembled_from_Schizaphis_graminum_and_Sipha_flava/24852930 |
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