Ryan Ghan
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View article: Incorporation of automated buffer exchange empowers high-throughput protein and plasmid purification for downstream uses
Incorporation of automated buffer exchange empowers high-throughput protein and plasmid purification for downstream uses Open
The continued acceleration of time-to-market product development and rising demand for biotherapeutics have hastened the need for higher throughput within the biopharmaceutical industry. Automated liquid handlers (ALH) are increasingly pop…
View article: Is foliar Cl- concentration the cause of photosynthetic decline in grapevine during mild salinity?
Is foliar Cl- concentration the cause of photosynthetic decline in grapevine during mild salinity? Open
Moderate levels of Cl- have been associated with grapevine salt tolerance. The hypothesis to be tested in this work is: photosynthesis in grapevine is negatively correlated with foliar Cl- concentration. To further test this hypothesis, mu…
View article: A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening.
A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening. Open
Background Grape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition. Results To be…
View article: A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening.
A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening. Open
Background Grape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition. Results To be…
View article: Additional file 6 of A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening
Additional file 6 of A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening Open
Additional file 6. Module membership (MM) of all filtered transcripts as defined by WGCNA. Values are the kME (module eigengene connectivity).
View article: Additional file 9 of A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening
Additional file 9 of A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening Open
Additional file 9. topGO analysis of the top 400 genes with the greatest differential expression between high and low °Brix samples in BOD berry skins.
View article: Additional file 13 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling
Additional file 13 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling Open
Gene module membership in the root samples. (XLSX 45939 kb)
View article: Additional file 5 of A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening
Additional file 5 of A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening Open
Additional file 5. Common genes between BOD and RNO from transcriptomic approaches 2 and 3.
View article: Additional file 14 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling
Additional file 14 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling Open
Summary of the WGCNA modules in the roots. (XLSX 36 kb)
View article: Additional file 10 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling
Additional file 10 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling Open
DEA and TPM values for the ABA related genes from comparison results between drought treated and control vines for each organ x week x genotype combination. (XLSX 97 kb)
View article: Additional file 8 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling
Additional file 8 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling Open
Gene Ontology enrichment analysis of Biological Process category on Venn gene lists. (XLSX 307 kb)
View article: Additional file 1 of A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening
Additional file 1 of A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening Open
Additional file 1. Log2 transcripts per million (TPM) to genes uniquely mapped to the V1 Cabernet Sauvignon genome.
View article: Additional file 18 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling
Additional file 18 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling Open
Genes strongly induced by the WD in the roots and the shoot of RM. (XLSX 30 kb)
View article: Additional file 7 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling
Additional file 7 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling Open
Functional categories representative of a response to WD. (XLSX 10 kb)
View article: Additional file 2 of A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening
Additional file 2 of A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening Open
Additional file 2. Differentially expresses genes (DEGs) determined by DESeq2 for berry skin samples at 22°Brix from BOD and RNO.
View article: Additional file 3 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling
Additional file 3 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling Open
Statistics for the long-term WD experiment from day 12 to day 20. (XLSX 22 kb)
View article: Additional file 10 of A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening
Additional file 10 of A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening Open
Additional file 10. topGO analysis of the top 400 genes with the greatest differential expression between high and low °Brix samples in RNO berry skins.
View article: Additional file 8 of A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening
Additional file 8 of A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening Open
Additional file 8. topGO analysis of all modules with genes having a kME > 0.80. The results for each module are on a separate tab within the file.
View article: Additional file 12 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling
Additional file 12 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling Open
DEA and TPM values for the MIP family genes from comparison results between drought treated and control vines for each organ x week x genotype combinations. (XLSX 62 kb)
View article: Additional file 2 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling
Additional file 2 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling Open
Statistics for the WD recovery experiment at day 6 and 8. (XLSX 13 kb)
View article: Additional file 16 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling
Additional file 16 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling Open
Gene module membership in the leaf samples. (XLSX 34506 kb)
View article: Additional file 17 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling
Additional file 17 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling Open
Summary of the WGCNA modules in the leaves. (XLSX 29 kb)
View article: Additional file 9 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling
Additional file 9 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling Open
BIN code enrichment analysis on Venn gene lists. (XLSX 99 kb)
View article: Additional file 19 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling
Additional file 19 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling Open
Primer list. (XLSX 9 kb)
View article: Additional file 3 of A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening
Additional file 3 of A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening Open
Additional file 3. Statistical results from gene set enrichment analysis of the DEGs using topGO.
View article: Additional file 6 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling
Additional file 6 of Drought tolerance of the grapevine, Vitis champinii cv. Ramsey, is associated with higher photosynthesis and greater transcriptomic responsiveness of abscisic acid biosynthesis and signaling Open
Differential expression analysis results per genotype, organ and week. (XLSX 27292 kb)
View article: A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening.
A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening. Open
Background Grape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition. Results To be…
View article: A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening.
A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening. Open
Background Grape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition. Results To be…