Additional file 8: of Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

Balasubramanian, Mukundh N.
Panserat, Stephane
Dupont-Nivet, Mathilde
Quillet, Edwige
Montfort, Jerome
Le Cam, Aurelie
Medale, Francoise
Kaushik, Sadasivam J.
Geurden, Inge

June 2016

Background: The achievement of sustainable feeding practices in aquaculture by reducing the reliance...

Additional file 8: of Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients

Roy Danzmann (3501500)
Andrea Kocmarek (3501506)
Joseph Norman (3501497)
Caird Rexroad (3501503)
Yniv Palti (166374)

January 2016

Contigs with higher expression in September fish. FDR significant genes used for the GSEA are highli...

Additional file 4: of RNA-Seq analysis of differentially expressed genes relevant to innate and adaptive immunity in cecropin P1 transgenic rainbow trout (Oncorhynchus mykiss)

Yueh-Chiang Han (5874644)
Chun-Mean Lin (5874647)
Thomas Chen (247817)

October 2018

Supplement figures from KEGG database and sprayed by the DEGs expression profiles. (PDF 240 kb

Additional file 6: of Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

Mukundh Balasubramanian (3564614)
Stephane Panserat (3564623)
Mathilde Dupont-Nivet (143686)
Edwige Quillet (22709)
Jerome Montfort (3564617)
Aurelie Le Cam (3497714)
Francoise Medale (3564620)
Sadasivam Kaushik (421073)
Inge Geurden (326970)

June 2016

List of probes in pathways significantly enriched based on early nutritional history in the liver. T...

Additional file 7: of Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

Mukundh Balasubramanian (3564614)
Stephane Panserat (3564623)
Mathilde Dupont-Nivet (143686)
Edwige Quillet (22709)
Jerome Montfort (3564617)
Aurelie Le Cam (3497714)
Francoise Medale (3564620)
Sadasivam Kaushik (421073)
Inge Geurden (326970)

June 2016

Confirmation by real-time RT-PCR of selected genes differentially expressed in trout swim-up fry (a)...

Additional file 2: of Changes in the liver transcriptome of farmed Atlantic salmon (Salmo salar) fed experimental diets based on terrestrial alternatives to fish meal and fish oil

Albert Caballero-Solares (4424959)
Xi Xue (3489176)
Christopher Parrish (161575)
Maryam Foroutani (5926820)
Richard Taylor (34490)
Matthew Rise (3489173)

November 2018

Table S2. Complete list of microarray probes identified as diet-responsive. The results from the gen...

Additional file 6: of Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients

Roy Danzmann (3501500)
Andrea Kocmarek (3501506)
Joseph Norman (3501497)
Caird Rexroad (3501503)
Yniv Palti (166374)

January 2016

Results from the Broad Institute gene set enrichment analysis (GSEA) highlighting significant pathwa...

Additional file 1: of RNA-Seq analysis of differentially expressed genes relevant to innate and adaptive immunity in cecropin P1 transgenic rainbow trout (Oncorhynchus mykiss)

Yueh-Chiang Han (5874644)
Chun-Mean Lin (5874647)
Thomas Chen (247817)

October 2018

Supplemental figures for pie charts of qualities of clean reads and results of sequencing saturation...

Additional file 14: of Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients

Roy Danzmann (3501500)
Andrea Kocmarek (3501506)
Joseph Norman (3501497)
Caird Rexroad (3501503)
Yniv Palti (166374)

January 2016

Results from the Broad Institute gene set enrichment analysis (GSEA) highlighting significant pathwa...

Additional file 5: of Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients

Roy Danzmann (3501500)
Andrea Kocmarek (3501506)
Joseph Norman (3501497)
Caird Rexroad (3501503)
Yniv Palti (166374)

January 2016

Results from the Broad Institute gene set enrichment analysis (GSEA) highlighting significant pathwa...

Additional file 15: of Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients

Roy Danzmann (3501500)
Andrea Kocmarek (3501506)
Joseph Norman (3501497)
Caird Rexroad (3501503)
Yniv Palti (166374)

January 2016

Results from the Broad Institute gene set enrichment analysis (GSEA) highlighting significant pathwa...

Additional file 6: of RNA-Seq analysis of differentially expressed genes relevant to innate and adaptive immunity in cecropin P1 transgenic rainbow trout (Oncorhynchus mykiss)

Yueh-Chiang Han (5874644)
Chun-Mean Lin (5874647)
Thomas Chen (247817)

October 2018

Summarizing of software versions, databases and parameters for Bioinformatics analyses. (XLSX 9 kb

Additional file 1: of Transcriptome analysis of egg viability in rainbow trout, Oncorhynchus mykiss

Hao Ma (114667)
Kyle Martin (3711160)
Doug Dixon (6643148)
Alvaro Hernandez (260919)
Gregory Weber (1828339)

April 2019

Table S1. Differentially expressed transcripts among low-, medium- and high-quality eggs identified ...

Additional file 2: of RNA-Seq analysis of differentially expressed genes relevant to innate and adaptive immunity in cecropin P1 transgenic rainbow trout (Oncorhynchus mykiss)

Yueh-Chiang Han (5874644)
Chun-Mean Lin (5874647)
Thomas Chen (247817)

October 2018

Singular enrichment analyses among three tissues, grouped by both GOSlim biological process and KEGG...

Additional file 6: of Early nutritional programming affects liver transcriptome in diploid and triploid Atlantic salmon, Salmo salar

L. Vera (4601566)
C. Metochis (4601575)
J. Taylor (4601572)
M. Clarkson (4601563)
K. SkjĂŚrven (4601569)
H. Migaud (4111705)
D. Tocher (4601560)

November 2017

Pathways significantly enriched based on diet x ploidy, as indicated by two-way ANOVA (pÂ <Â 0.05). ...

Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

Balasubramanian, Mukundh N.
Panserat, Stephane
Dupont-Nivet, Mathilde
Quillet, Edwige
Montfort, Jerome
Le Cam, Aurelie
Medale, Francoise
Kaushik, Sadasivam J.
Geurden, Inge

June 2016

Background: The achievement of sustainable feeding practices in aquaculture by reducing the reliance...

Additional file 8: of Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients

Roy Danzmann (3501500)
Andrea Kocmarek (3501506)
Joseph Norman (3501497)
Caird Rexroad (3501503)
Yniv Palti (166374)

January 2016

Contigs with higher expression in September fish. FDR significant genes used for the GSEA are highli...

Additional file 4: of RNA-Seq analysis of differentially expressed genes relevant to innate and adaptive immunity in cecropin P1 transgenic rainbow trout (Oncorhynchus mykiss)

Yueh-Chiang Han (5874644)
Chun-Mean Lin (5874647)
Thomas Chen (247817)

October 2018

Supplement figures from KEGG database and sprayed by the DEGs expression profiles. (PDF 240 kb

Additional file 6: of Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

Mukundh Balasubramanian (3564614)
Stephane Panserat (3564623)
Mathilde Dupont-Nivet (143686)
Edwige Quillet (22709)
Jerome Montfort (3564617)
Aurelie Le Cam (3497714)
Francoise Medale (3564620)
Sadasivam Kaushik (421073)
Inge Geurden (326970)

June 2016

List of probes in pathways significantly enriched based on early nutritional history in the liver. T...

Additional file 7: of Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

Mukundh Balasubramanian (3564614)
Stephane Panserat (3564623)
Mathilde Dupont-Nivet (143686)
Edwige Quillet (22709)
Jerome Montfort (3564617)
Aurelie Le Cam (3497714)
Francoise Medale (3564620)
Sadasivam Kaushik (421073)
Inge Geurden (326970)

June 2016

Confirmation by real-time RT-PCR of selected genes differentially expressed in trout swim-up fry (a)...

Additional file 2: of Changes in the liver transcriptome of farmed Atlantic salmon (Salmo salar) fed experimental diets based on terrestrial alternatives to fish meal and fish oil

Albert Caballero-Solares (4424959)
Xi Xue (3489176)
Christopher Parrish (161575)
Maryam Foroutani (5926820)
Richard Taylor (34490)
Matthew Rise (3489173)

November 2018

Table S2. Complete list of microarray probes identified as diet-responsive. The results from the gen...

Additional file 6: of Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients

Roy Danzmann (3501500)
Andrea Kocmarek (3501506)
Joseph Norman (3501497)
Caird Rexroad (3501503)
Yniv Palti (166374)

January 2016

Results from the Broad Institute gene set enrichment analysis (GSEA) highlighting significant pathwa...

Additional file 1: of RNA-Seq analysis of differentially expressed genes relevant to innate and adaptive immunity in cecropin P1 transgenic rainbow trout (Oncorhynchus mykiss)

Yueh-Chiang Han (5874644)
Chun-Mean Lin (5874647)
Thomas Chen (247817)

October 2018

Supplemental figures for pie charts of qualities of clean reads and results of sequencing saturation...

Additional file 14: of Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients

Roy Danzmann (3501500)
Andrea Kocmarek (3501506)
Joseph Norman (3501497)
Caird Rexroad (3501503)
Yniv Palti (166374)

January 2016

Results from the Broad Institute gene set enrichment analysis (GSEA) highlighting significant pathwa...

Additional file 5: of Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients

Roy Danzmann (3501500)
Andrea Kocmarek (3501506)
Joseph Norman (3501497)
Caird Rexroad (3501503)
Yniv Palti (166374)

January 2016

Results from the Broad Institute gene set enrichment analysis (GSEA) highlighting significant pathwa...

Additional file 15: of Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients

Roy Danzmann (3501500)
Andrea Kocmarek (3501506)
Joseph Norman (3501497)
Caird Rexroad (3501503)
Yniv Palti (166374)

January 2016

Results from the Broad Institute gene set enrichment analysis (GSEA) highlighting significant pathwa...

Additional file 6: of RNA-Seq analysis of differentially expressed genes relevant to innate and adaptive immunity in cecropin P1 transgenic rainbow trout (Oncorhynchus mykiss)

Yueh-Chiang Han (5874644)
Chun-Mean Lin (5874647)
Thomas Chen (247817)

October 2018

Summarizing of software versions, databases and parameters for Bioinformatics analyses. (XLSX 9 kb

Additional file 1: of Transcriptome analysis of egg viability in rainbow trout, Oncorhynchus mykiss

Hao Ma (114667)
Kyle Martin (3711160)
Doug Dixon (6643148)
Alvaro Hernandez (260919)
Gregory Weber (1828339)

April 2019

Table S1. Differentially expressed transcripts among low-, medium- and high-quality eggs identified ...

Additional file 2: of RNA-Seq analysis of differentially expressed genes relevant to innate and adaptive immunity in cecropin P1 transgenic rainbow trout (Oncorhynchus mykiss)

Yueh-Chiang Han (5874644)
Chun-Mean Lin (5874647)
Thomas Chen (247817)

October 2018

Singular enrichment analyses among three tissues, grouped by both GOSlim biological process and KEGG...

Additional file 6: of Early nutritional programming affects liver transcriptome in diploid and triploid Atlantic salmon, Salmo salar

L. Vera (4601566)
C. Metochis (4601575)
J. Taylor (4601572)
M. Clarkson (4601563)
K. SkjĂŚrven (4601569)
H. Migaud (4111705)
D. Tocher (4601560)

November 2017

Pathways significantly enriched based on diet x ploidy, as indicated by two-way ANOVA (pÂ <Â 0.05). ...

Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

Balasubramanian, Mukundh N.
Panserat, Stephane
Dupont-Nivet, Mathilde
Quillet, Edwige
Montfort, Jerome
Le Cam, Aurelie
Medale, Francoise
Kaushik, Sadasivam J.
Geurden, Inge

June 2016

Background: The achievement of sustainable feeding practices in aquaculture by reducing the reliance...

Additional file 8: of Transcriptome profiling in fast versus slow-growing rainbow trout across seasonal gradients

Roy Danzmann (3501500)
Andrea Kocmarek (3501506)
Joseph Norman (3501497)
Caird Rexroad (3501503)
Yniv Palti (166374)

January 2016

Contigs with higher expression in September fish. FDR significant genes used for the GSEA are highli...

Additional file 4: of RNA-Seq analysis of differentially expressed genes relevant to innate and adaptive immunity in cecropin P1 transgenic rainbow trout (Oncorhynchus mykiss)

Yueh-Chiang Han (5874644)
Chun-Mean Lin (5874647)
Thomas Chen (247817)

October 2018

Supplement figures from KEGG database and sprayed by the DEGs expression profiles. (PDF 240 kb

Additional file 8: of Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

Abstract

Extracted data

Additional file 8: of Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

Abstract

Extracted data

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