Additional file 2: of Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction

Additional file 2: of Progesterone signalling in broiler skeletal muscle is associated with divergent feed efficiency

Walter Bottje (658238)
Byung-Whi Kong (77322)
Antonio Reverter (61185)
Ashley Waardenberg (3795016)
Kentu Lassiter (658235)
Nicholas Hudson (3577538)

February 2017

The qPCR primers used to validate the DE of a subset of genes prioritised by RNAseq. (DOCX 12Â kb

Additional file 2: of Multi-tissue transcriptomic study reveals the main role of liver in the chicken adaptive response to a switch in dietary energy source through the transcriptional regulation of lipogenesis

C. Desert (4920955)
E. BaĂŠza (4920979)
M. Aite (4921006)
M. Boutin (4920970)
A. Le Cam (4920964)
J. Montfort (4921003)
M. Houee-Bigot (4920994)
Y. Blum (4920967)
P. Roux (4920988)
C. Hennequet-Antier (4920997)
C. Berri (4921000)
S. Metayer-Coustard (4920982)
A. Collin (4920976)
S. Allais (4920985)
E. Le Bihan (4920961)
D. Causeur (4920958)
F. Gondret (4920991)
M. Duclos (4371508)
S. Lagarrigue (4920973)

March 2018

Exploration by Principal Component Analysis (PCA) of transcriptomic data (all expressed genes) for e...

Additional file 3: Table S2. of Proteomics reveals changes in hepatic proteins during chicken embryonic development: an alternative model to study human obesity

Mengling Peng (4744806)
Shengnan Li (345816)
Qianian He (4744809)
Jinlong Zhao (552117)
Longlong Li (790974)
Haitian Ma (737252)

January 2018

Differentially expressed proteins at H1d when compared to E19d in chicken embryos. (DOCX 68 kb

Additional file 1: of Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction

Susanne Bornelöv (189128)
Eyal Seroussi (31976)
Sara Yosefi (165264)
Sharon Benjamini (5144234)
Shoval Miyara (4346146)
Mark Ruzal (5144231)
Manfred Grabherr (2576317)
Nima Rafati (3292704)
Anna-Maja Molin (190648)
Ken Pendavis (4110652)
Shane Burgess (3505550)
Leif Andersson (42573)
Miriam Friedman-Einat (165278)

April 2018

RNA-seq. Data. Table S1. Information about the RNA sequencing. Table S2: Transcripts identified by R...

Additional file 5: of Transcriptional analysis of abdominal fat in chickens divergently selected on bodyweight at two ages reveals novel mechanisms controlling adiposity: validating visceral adipose tissue as a dynamic endocrine and metabolic organ

C. Resnyk (4371526)
W. CarrĂŠ (4371559)
X. Wang (770484)
T. Porter (4371517)
J. Simon (4371529)
E. Le Bihan-Duval (4371523)
M. Duclos (4371508)
S. Aggrey (4371514)
L. Cogburn (4371520)

August 2017

Differentially expressed (DE) (FDR â¤0.05) identified by RNA-Seq analysis of abdominal fat in HG an...

Additional file 1: of Transcriptional analysis of abdominal fat in chickens divergently selected on bodyweight at two ages reveals novel mechanisms controlling adiposity: validating visceral adipose tissue as a dynamic endocrine and metabolic organ

C. Resnyk (4371526)
W. Carré (4371511)
X. Wang (770484)
T. Porter (4371517)
J. Simon (4371529)
E. Le Bihan-Duval (4371523)
M. Duclos (4371508)
S. Aggrey (4371514)
L. Cogburn (4371520)

August 2017

Microarray experimental design. A Microsoft Excel file containing a single work sheet “Array Hybridi...

Additional file 2: of Transcriptional profiling of liver during the critical embryo-to-hatchling transition period in the chicken (Gallus gallus)

Larry Cogburn (3468785)
Nares Trakooljul (723346)
Chuming Chen (223254)
Hongzhan Huang (14342)
Cathy Wu (216122)
Wilfrid Carré (86460)
Xiaofei Wang (135107)
Harold White (4913224)

September 2018

Primers used for qRT-PCR analysis. A Microsoft Excel file containing a single work sheet “qRT-PCR Pr...

Additional file 4: of Transcriptional profiling and pathway analysis reveal differences in pituitary gland function, morphology, and vascularization in chickens genetically selected for high or low body weight

Laura Ellestad (6637436)
Larry Cogburn (3468785)
Jean Simon (802790)
Elisabeth Bihan-Duval (3578903)
Samuel Aggrey (4949878)
Mardi Byerly (6637445)
Michel Duclos (3550625)
Tom Porter (4411789)

April 2019

Primer sequences. A Microsoft excel file containing a single worksheet (âRT-qPCR primersâ) listi...

Additional file 1: of Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content

Wei Na (2618470)
Yuan-Yuan Wu (5269484)
Peng-Fei Gong (5269487)
Chun-Yan Wu (1818925)
Bo-Han Cheng (5269481)
Yu-Xiang Wang (32380)
Ning Wang (108353)
Zhi-Qiang Du (229183)
Hui Li (32376)

May 2018

Figure S1. Number of genes expressed and novel transcripts. L and F represent the lean and fat chick...

Additional file 2: of Transcriptional profiling of liver in riboflavin-deficient chicken embryos explains impaired lipid utilization, energy depletion, massive hemorrhaging, and delayed feathering

Larry Cogburn (3468785)
Danielle Smarsh (4913221)
Xiaofei Wang (135107)
Nares Trakooljul (723346)
Wilfrid Carré (86460)
Harold White (4913224)

March 2018

Primers used for qRT-PCR analysis. A Microsoft Excel file containing a single work sheet “qRT-PCR Pr...

Additional file 2: Table S2. of Probiotic (Enterococcus faecium) induced responses of the hepatic proteome improves metabolic efficiency of broiler chickens (Gallus gallus)

Aijuan Zheng (219579)
Jianjie Luo (3469967)
Kun Meng (141278)
Jianke Li (219587)
Wayne Bryden (3469970)
Wenhuan Chang (3163065)
Shu Zhang (22238)
L. Wang (2327974)
Guohua Liu (506590)
Bin Yao (4375)

February 2016

The primer sequences used for qPCR analysis of the differentially expressed proteins of the liver of...

Additional file 2: of A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Gabriel Moreira (4799577)
Clarissa Boschiero (4799571)
Aline Cesar (3508628)
James Reecy (3561878)
Thaís Godoy (4799562)
Priscila Trevisoli (5245721)
Maurício Cantão (5245718)
Mônica Ledur (4799565)
Adriana Ibelli (5245727)
Jane de Oliveira Peixoto (790338)
Ana Moura (5245724)
Dorian Garrick (3572441)
Luiz Coutinho (3508640)

May 2018

An excel file with the characterization of all the SNP windows analyzed including the proportion of ...

Additional file 9: of Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content

Wei Na (2618470)
Yuan-Yuan Wu (5269484)
Peng-Fei Gong (5269487)
Chun-Yan Wu (1818925)
Bo-Han Cheng (5269481)
Yu-Xiang Wang (32380)
Ning Wang (108353)
Zhi-Qiang Du (229183)
Hui Li (32376)

May 2018

Figure S4. Proportion of clean tag numbers (>â96%). L and F represent the lean and fat chicken lin...

Additional file 7: of Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content

Wei Na (2618470)
Yuan-Yuan Wu (5269484)
Peng-Fei Gong (5269487)
Chun-Yan Wu (1818925)
Bo-Han Cheng (5269481)
Yu-Xiang Wang (32380)
Ning Wang (108353)
Zhi-Qiang Du (229183)
Hui Li (32376)

May 2018

Figure S2. Protein profiling on liver tissues of chicken embryos. A total of 15 gels were assayed, a...

Additional file 2: of Biological mechanisms discriminating growth rate and adult body weight phenotypes in two Chinese indigenous chicken breeds

Tengfei Dou (4163974)
Sumei Zhao (4163986)
Hua Rong (4163989)
Dahai Gu (4163980)
Qihua Li (4163977)
Ying Huang (53474)
Zhiqiang Xu (103072)
Xiaohui Chu (4163968)
Linli Tao (4163992)
Lixian Liu (4163995)
Changrong Ge (213754)
Marinus Pas (4163983)
Junjing Jia (4163971)

June 2017

The microarray hybridization data for the liver tissue. The file shows the liver tissue microarray d...

Additional file 2: of Progesterone signalling in broiler skeletal muscle is associated with divergent feed efficiency

Walter Bottje (658238)
Byung-Whi Kong (77322)
Antonio Reverter (61185)
Ashley Waardenberg (3795016)
Kentu Lassiter (658235)
Nicholas Hudson (3577538)

February 2017

The qPCR primers used to validate the DE of a subset of genes prioritised by RNAseq. (DOCX 12Â kb

Additional file 2: of Multi-tissue transcriptomic study reveals the main role of liver in the chicken adaptive response to a switch in dietary energy source through the transcriptional regulation of lipogenesis

C. Desert (4920955)
E. BaĂŠza (4920979)
M. Aite (4921006)
M. Boutin (4920970)
A. Le Cam (4920964)
J. Montfort (4921003)
M. Houee-Bigot (4920994)
Y. Blum (4920967)
P. Roux (4920988)
C. Hennequet-Antier (4920997)
C. Berri (4921000)
S. Metayer-Coustard (4920982)
A. Collin (4920976)
S. Allais (4920985)
E. Le Bihan (4920961)
D. Causeur (4920958)
F. Gondret (4920991)
M. Duclos (4371508)
S. Lagarrigue (4920973)

March 2018

Exploration by Principal Component Analysis (PCA) of transcriptomic data (all expressed genes) for e...

Additional file 3: Table S2. of Proteomics reveals changes in hepatic proteins during chicken embryonic development: an alternative model to study human obesity

Mengling Peng (4744806)
Shengnan Li (345816)
Qianian He (4744809)
Jinlong Zhao (552117)
Longlong Li (790974)
Haitian Ma (737252)

January 2018

Differentially expressed proteins at H1d when compared to E19d in chicken embryos. (DOCX 68 kb

Additional file 1: of Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction

Susanne Bornelöv (189128)
Eyal Seroussi (31976)
Sara Yosefi (165264)
Sharon Benjamini (5144234)
Shoval Miyara (4346146)
Mark Ruzal (5144231)
Manfred Grabherr (2576317)
Nima Rafati (3292704)
Anna-Maja Molin (190648)
Ken Pendavis (4110652)
Shane Burgess (3505550)
Leif Andersson (42573)
Miriam Friedman-Einat (165278)

April 2018

RNA-seq. Data. Table S1. Information about the RNA sequencing. Table S2: Transcripts identified by R...

Additional file 5: of Transcriptional analysis of abdominal fat in chickens divergently selected on bodyweight at two ages reveals novel mechanisms controlling adiposity: validating visceral adipose tissue as a dynamic endocrine and metabolic organ

C. Resnyk (4371526)
W. CarrĂŠ (4371559)
X. Wang (770484)
T. Porter (4371517)
J. Simon (4371529)
E. Le Bihan-Duval (4371523)
M. Duclos (4371508)
S. Aggrey (4371514)
L. Cogburn (4371520)

August 2017

Differentially expressed (DE) (FDR â¤0.05) identified by RNA-Seq analysis of abdominal fat in HG an...

Additional file 1: of Transcriptional analysis of abdominal fat in chickens divergently selected on bodyweight at two ages reveals novel mechanisms controlling adiposity: validating visceral adipose tissue as a dynamic endocrine and metabolic organ

C. Resnyk (4371526)
W. Carré (4371511)
X. Wang (770484)
T. Porter (4371517)
J. Simon (4371529)
E. Le Bihan-Duval (4371523)
M. Duclos (4371508)
S. Aggrey (4371514)
L. Cogburn (4371520)

August 2017

Microarray experimental design. A Microsoft Excel file containing a single work sheet “Array Hybridi...

Additional file 2: of Transcriptional profiling of liver during the critical embryo-to-hatchling transition period in the chicken (Gallus gallus)

Larry Cogburn (3468785)
Nares Trakooljul (723346)
Chuming Chen (223254)
Hongzhan Huang (14342)
Cathy Wu (216122)
Wilfrid Carré (86460)
Xiaofei Wang (135107)
Harold White (4913224)

September 2018

Primers used for qRT-PCR analysis. A Microsoft Excel file containing a single work sheet “qRT-PCR Pr...

Additional file 4: of Transcriptional profiling and pathway analysis reveal differences in pituitary gland function, morphology, and vascularization in chickens genetically selected for high or low body weight

Laura Ellestad (6637436)
Larry Cogburn (3468785)
Jean Simon (802790)
Elisabeth Bihan-Duval (3578903)
Samuel Aggrey (4949878)
Mardi Byerly (6637445)
Michel Duclos (3550625)
Tom Porter (4411789)

April 2019

Primer sequences. A Microsoft excel file containing a single worksheet (âRT-qPCR primersâ) listi...

Additional file 1: of Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content

Wei Na (2618470)
Yuan-Yuan Wu (5269484)
Peng-Fei Gong (5269487)
Chun-Yan Wu (1818925)
Bo-Han Cheng (5269481)
Yu-Xiang Wang (32380)
Ning Wang (108353)
Zhi-Qiang Du (229183)
Hui Li (32376)

May 2018

Figure S1. Number of genes expressed and novel transcripts. L and F represent the lean and fat chick...

Additional file 2: of Transcriptional profiling of liver in riboflavin-deficient chicken embryos explains impaired lipid utilization, energy depletion, massive hemorrhaging, and delayed feathering

Larry Cogburn (3468785)
Danielle Smarsh (4913221)
Xiaofei Wang (135107)
Nares Trakooljul (723346)
Wilfrid Carré (86460)
Harold White (4913224)

March 2018

Primers used for qRT-PCR analysis. A Microsoft Excel file containing a single work sheet “qRT-PCR Pr...

Additional file 2: Table S2. of Probiotic (Enterococcus faecium) induced responses of the hepatic proteome improves metabolic efficiency of broiler chickens (Gallus gallus)

Aijuan Zheng (219579)
Jianjie Luo (3469967)
Kun Meng (141278)
Jianke Li (219587)
Wayne Bryden (3469970)
Wenhuan Chang (3163065)
Shu Zhang (22238)
L. Wang (2327974)
Guohua Liu (506590)
Bin Yao (4375)

February 2016

The primer sequences used for qPCR analysis of the differentially expressed proteins of the liver of...

Additional file 2: of A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

Gabriel Moreira (4799577)
Clarissa Boschiero (4799571)
Aline Cesar (3508628)
James Reecy (3561878)
Thaís Godoy (4799562)
Priscila Trevisoli (5245721)
Maurício Cantão (5245718)
Mônica Ledur (4799565)
Adriana Ibelli (5245727)
Jane de Oliveira Peixoto (790338)
Ana Moura (5245724)
Dorian Garrick (3572441)
Luiz Coutinho (3508640)

May 2018

An excel file with the characterization of all the SNP windows analyzed including the proportion of ...

Additional file 9: of Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content

Wei Na (2618470)
Yuan-Yuan Wu (5269484)
Peng-Fei Gong (5269487)
Chun-Yan Wu (1818925)
Bo-Han Cheng (5269481)
Yu-Xiang Wang (32380)
Ning Wang (108353)
Zhi-Qiang Du (229183)
Hui Li (32376)

May 2018

Figure S4. Proportion of clean tag numbers (>â96%). L and F represent the lean and fat chicken lin...

Additional file 7: of Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content

Wei Na (2618470)
Yuan-Yuan Wu (5269484)
Peng-Fei Gong (5269487)
Chun-Yan Wu (1818925)
Bo-Han Cheng (5269481)
Yu-Xiang Wang (32380)
Ning Wang (108353)
Zhi-Qiang Du (229183)
Hui Li (32376)

May 2018

Figure S2. Protein profiling on liver tissues of chicken embryos. A total of 15 gels were assayed, a...

Additional file 2: of Biological mechanisms discriminating growth rate and adult body weight phenotypes in two Chinese indigenous chicken breeds

Tengfei Dou (4163974)
Sumei Zhao (4163986)
Hua Rong (4163989)
Dahai Gu (4163980)
Qihua Li (4163977)
Ying Huang (53474)
Zhiqiang Xu (103072)
Xiaohui Chu (4163968)
Linli Tao (4163992)
Lixian Liu (4163995)
Changrong Ge (213754)
Marinus Pas (4163983)
Junjing Jia (4163971)

June 2017

The microarray hybridization data for the liver tissue. The file shows the liver tissue microarray d...

Additional file 2: of Progesterone signalling in broiler skeletal muscle is associated with divergent feed efficiency

Walter Bottje (658238)
Byung-Whi Kong (77322)
Antonio Reverter (61185)
Ashley Waardenberg (3795016)
Kentu Lassiter (658235)
Nicholas Hudson (3577538)

February 2017

The qPCR primers used to validate the DE of a subset of genes prioritised by RNAseq. (DOCX 12Â kb

Additional file 2: of Multi-tissue transcriptomic study reveals the main role of liver in the chicken adaptive response to a switch in dietary energy source through the transcriptional regulation of lipogenesis

C. Desert (4920955)
E. BaĂŠza (4920979)
M. Aite (4921006)
M. Boutin (4920970)
A. Le Cam (4920964)
J. Montfort (4921003)
M. Houee-Bigot (4920994)
Y. Blum (4920967)
P. Roux (4920988)
C. Hennequet-Antier (4920997)
C. Berri (4921000)
S. Metayer-Coustard (4920982)
A. Collin (4920976)
S. Allais (4920985)
E. Le Bihan (4920961)
D. Causeur (4920958)
F. Gondret (4920991)
M. Duclos (4371508)
S. Lagarrigue (4920973)

March 2018

Exploration by Principal Component Analysis (PCA) of transcriptomic data (all expressed genes) for e...

Additional file 3: Table S2. of Proteomics reveals changes in hepatic proteins during chicken embryonic development: an alternative model to study human obesity

Mengling Peng (4744806)
Shengnan Li (345816)
Qianian He (4744809)
Jinlong Zhao (552117)
Longlong Li (790974)
Haitian Ma (737252)

January 2018

Differentially expressed proteins at H1d when compared to E19d in chicken embryos. (DOCX 68 kb

Additional file 2: of Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction

Abstract

Extracted data

Additional file 2: of Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction

Abstract

Extracted data

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