Additional file 4: of Long-term health and germline transmission in transgenic cattle following transposon-mediated gene transfer

Additional file 4: of In vivo competition and horizontal gene transfer among distinct Staphylococcus aureus lineages as major drivers for adaptational changes during long-term persistence in humans

Lars Langhanki (3369824)
Petya Berger (5881013)
Janina Treffon (3369830)
Francesco Catania (375780)
Barbara Kahl (374193)
Alexander Mellmann (72273)

October 2018

Gene names, locus tags and position information characterizing the 14.2Â kb DNA transposon and the 2...

Additional file 3: of Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle

Majid Khansefid (3398150)
Jennie Pryce (241354)
Sunduimijid Bolormaa (543860)
Yizhou Chen (532732)
Catriona Millen (3398147)
Amanda Chamberlain (817482)
Christy Vander Jagt (817483)
Michael Goddard (3398153)

November 2018

Table S12. GWAS using SNP-chip data. The detailed results of p-values for each SNP in GWA studies fo...

Additional file 1: of Genome-wide association between single nucleotide polymorphisms with beef fatty acid profile in Nellore cattle using the single step procedure

Marcos Lemos (3577223)
Hermenegildo Chiaia (3508658)
Mariana Berton (3508631)
Fabieli Feitosa (3508652)
Carolyn Aboujaoud (3577217)
GregĂłrio Camargo (3577229)
AngĂŠlica Pereira (3508661)
Lucia Albuquerque (3577211)
Adrielle Ferrinho (3508619)
Lenise Mueller (3508643)
Monica Mazalli (3577214)
Joyce Furlan (3577220)
Roberto Carvalheiro (523642)
Daniel Gordo (3508613)
Rafael Tonussi (3508604)
Rafael Espigolan (3160104)
Rafael Silva (1872808)
Henrique de Oliveira (3508649)
Susan Duckett (3508607)
Ignacio Aguilar (3577208)
Fernando Baldi (2833280)

March 2016

Manhattan plot of the genome-wide association study for fatty acids in Nellore. The X-axis represent...

Additional file 2: of Long-term health and germline transmission in transgenic cattle following transposon-mediated gene transfer

Soo-Young Yum (805553)
Song-Jeon Lee (5269664)
Sin-Gi Park (647380)
In-Gang Shin (5269667)
Sang-Eun Hahn (5269643)
Woo-Jae Choi (5269649)
Hee-Soo Kim (1831327)
Hyeong-Jong Kim (5269658)
Seong-Hun Bae (5269646)
Je-Hyeong Lee (5269640)
Joo-Yeong Moon (5269661)
Woo-Sung Lee (5269655)
Ji-Hyun Lee (145976)
Choong-Il Lee (5269652)
Seong-Jin Kim (179277)
Goo Jang (311299)

May 2018

Figure S1. SNU-F1–1 lacks the YFP transgene, as demonstrated by PCR analysis of genomic DNA from SNU...

Additional file 5: of Long-term health and germline transmission in transgenic cattle following transposon-mediated gene transfer

Soo-Young Yum (805553)
Song-Jeon Lee (5269664)
Sin-Gi Park (647380)
In-Gang Shin (5269667)
Sang-Eun Hahn (5269643)
Woo-Jae Choi (5269649)
Hee-Soo Kim (1831327)
Hyeong-Jong Kim (5269658)
Seong-Hun Bae (5269646)
Je-Hyeong Lee (5269640)
Joo-Yeong Moon (5269661)
Woo-Sung Lee (5269655)
Ji-Hyun Lee (145976)
Choong-Il Lee (5269652)
Seong-Jin Kim (179277)
Goo Jang (311299)

May 2018

Figure S4. Germline transmission of GFP expression in uterus, ovary and oocytes from SNU-PB-2. Fluor...

Additional file 3: of Long-term health and germline transmission in transgenic cattle following transposon-mediated gene transfer

Soo-Young Yum (805553)
Song-Jeon Lee (5269664)
Sin-Gi Park (647380)
In-Gang Shin (5269667)
Sang-Eun Hahn (5269643)
Woo-Jae Choi (5269649)
Hee-Soo Kim (1831327)
Hyeong-Jong Kim (5269658)
Seong-Hun Bae (5269646)
Je-Hyeong Lee (5269640)
Joo-Yeong Moon (5269661)
Woo-Sung Lee (5269655)
Ji-Hyun Lee (145976)
Choong-Il Lee (5269652)
Seong-Jin Kim (179277)
Goo Jang (311299)

May 2018

Figure S2. Detection of the expression of YFP in milk from SNU-SB-1 by confocal microscopy. Images o...

Additional file 3: of Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle

Prerna Vohra (3610208)
Roy Chaudhuri (480357)
Matthew Mayho (22198)
Christina Vrettou (6188414)
Cosmin Chintoan-Uta (6188417)
Nicholas Thomson (190404)
Jayne Hope (3571163)
John Hopkins (79788)
Mark Stevens (8903)

January 2019

Figure S2. Circular diagrams of the S. Typhimurium chromosome and plasmids showing the distribution ...

Additional file 1: of Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle

Prerna Vohra (3610208)
Roy Chaudhuri (480357)
Matthew Mayho (22198)
Christina Vrettou (6188414)
Cosmin Chintoan-Uta (6188417)
Nicholas Thomson (190404)
Jayne Hope (3571163)
John Hopkins (79788)
Mark Stevens (8903)

January 2019

Figure S1. Experimental strategy to screen TraDIS mutants in vivo. An input pool of random transposo...

Additional file 4: Fig. S1. of Candidate genes for male and female reproductive traits in Canchim beef cattle

Marcos Buzanskas (3407801)
Daniela Grossi (3688171)
Ricardo Ventura (3407792)
Flavio Schenkel (598286)
Tatiane Chud (3407807)
Nedenia Stafuzza (3462848)
Luciana Rola (4387648)
Sarah Meirelles (4387639)
Fabiana Mokry (3407816)
Maurício Mudadu (3407822)
Roberto Higa (3462839)
Marcos Silva (4387645)
Maurício Alencar (4387642)
Luciana Regitano (3407810)
Danísio Munari (3407825)

August 2017

Linkage disequilibrium for scrotal circumference at 420 d of age on chromosome 5. Fig. S2. Linkage d...

Additional file 2: of Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle

Prerna Vohra (3610208)
Roy Chaudhuri (480357)
Matthew Mayho (22198)
Christina Vrettou (6188414)
Cosmin Chintoan-Uta (6188417)
Nicholas Thomson (190404)
Jayne Hope (3571163)
John Hopkins (79788)
Mark Stevens (8903)

January 2019

Table S1. The complete TraDIS dataset showing the positions of all transposon insertions in the geno...

Additional file 3: of In vivo competition and horizontal gene transfer among distinct Staphylococcus aureus lineages as major drivers for adaptational changes during long-term persistence in humans

Lars Langhanki (3369824)
Petya Berger (5881013)
Janina Treffon (3369830)
Francesco Catania (375780)
Barbara Kahl (374193)
Alexander Mellmann (72273)

October 2018

Genomic organization of the 25.7Â kb transposon. Genes on the forward strand are depicted as right-s...

Additional file 3: of Genome changes due to artificial selection in U.S. Holstein cattle

Li Ma (46633)
Tad Sonstegard (392288)
John Cole (392281)
Curtis VanTassell (6323411)
George Wiggans (392282)
Brian Crooker (3529250)
Cheng Tan (293674)
Dzianis Prakapenka (3142692)
George Liu (122581)
Yang Da (89805)

February 2019

Figure S3. Overview of allele frequency differences (AFD) and extended haplotype homozygosity (EHH)....

Additional file 2: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Figure S1. Gene coverage uniformity plots for each tissue type for a) all genes, b) 500 highest expr...

Additional file 1: of Characterization of recombination features and the genetic basis in multiple cattle breeds

Botong Shen (822728)
Jicai Jiang (122571)
Eyal Seroussi (31976)
George Liu (122581)
Li Ma (46633)

April 2018

Eight breed- and sex-specific recombination maps for Holstein, Jersey, Brown Swiss, and Ayrshire in ...

Additional file 4: of Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle

Prerna Vohra (3610208)
Roy Chaudhuri (480357)
Matthew Mayho (22198)
Christina Vrettou (6188414)
Cosmin Chintoan-Uta (6188417)
Nicholas Thomson (190404)
Jayne Hope (3571163)
John Hopkins (79788)
Mark Stevens (8903)

January 2019

Table S2. All newly identified transposon-insertion mutants and mutants with newly resolved fitness ...

Additional file 4: of In vivo competition and horizontal gene transfer among distinct Staphylococcus aureus lineages as major drivers for adaptational changes during long-term persistence in humans

Lars Langhanki (3369824)
Petya Berger (5881013)
Janina Treffon (3369830)
Francesco Catania (375780)
Barbara Kahl (374193)
Alexander Mellmann (72273)

October 2018

Gene names, locus tags and position information characterizing the 14.2Â kb DNA transposon and the 2...

Additional file 3: of Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle

Majid Khansefid (3398150)
Jennie Pryce (241354)
Sunduimijid Bolormaa (543860)
Yizhou Chen (532732)
Catriona Millen (3398147)
Amanda Chamberlain (817482)
Christy Vander Jagt (817483)
Michael Goddard (3398153)

November 2018

Table S12. GWAS using SNP-chip data. The detailed results of p-values for each SNP in GWA studies fo...

Additional file 1: of Genome-wide association between single nucleotide polymorphisms with beef fatty acid profile in Nellore cattle using the single step procedure

Marcos Lemos (3577223)
Hermenegildo Chiaia (3508658)
Mariana Berton (3508631)
Fabieli Feitosa (3508652)
Carolyn Aboujaoud (3577217)
GregĂłrio Camargo (3577229)
AngĂŠlica Pereira (3508661)
Lucia Albuquerque (3577211)
Adrielle Ferrinho (3508619)
Lenise Mueller (3508643)
Monica Mazalli (3577214)
Joyce Furlan (3577220)
Roberto Carvalheiro (523642)
Daniel Gordo (3508613)
Rafael Tonussi (3508604)
Rafael Espigolan (3160104)
Rafael Silva (1872808)
Henrique de Oliveira (3508649)
Susan Duckett (3508607)
Ignacio Aguilar (3577208)
Fernando Baldi (2833280)

March 2016

Manhattan plot of the genome-wide association study for fatty acids in Nellore. The X-axis represent...

Additional file 2: of Long-term health and germline transmission in transgenic cattle following transposon-mediated gene transfer

Soo-Young Yum (805553)
Song-Jeon Lee (5269664)
Sin-Gi Park (647380)
In-Gang Shin (5269667)
Sang-Eun Hahn (5269643)
Woo-Jae Choi (5269649)
Hee-Soo Kim (1831327)
Hyeong-Jong Kim (5269658)
Seong-Hun Bae (5269646)
Je-Hyeong Lee (5269640)
Joo-Yeong Moon (5269661)
Woo-Sung Lee (5269655)
Ji-Hyun Lee (145976)
Choong-Il Lee (5269652)
Seong-Jin Kim (179277)
Goo Jang (311299)

May 2018

Figure S1. SNU-F1–1 lacks the YFP transgene, as demonstrated by PCR analysis of genomic DNA from SNU...

Additional file 5: of Long-term health and germline transmission in transgenic cattle following transposon-mediated gene transfer

Soo-Young Yum (805553)
Song-Jeon Lee (5269664)
Sin-Gi Park (647380)
In-Gang Shin (5269667)
Sang-Eun Hahn (5269643)
Woo-Jae Choi (5269649)
Hee-Soo Kim (1831327)
Hyeong-Jong Kim (5269658)
Seong-Hun Bae (5269646)
Je-Hyeong Lee (5269640)
Joo-Yeong Moon (5269661)
Woo-Sung Lee (5269655)
Ji-Hyun Lee (145976)
Choong-Il Lee (5269652)
Seong-Jin Kim (179277)
Goo Jang (311299)

May 2018

Figure S4. Germline transmission of GFP expression in uterus, ovary and oocytes from SNU-PB-2. Fluor...

Additional file 3: of Long-term health and germline transmission in transgenic cattle following transposon-mediated gene transfer

Soo-Young Yum (805553)
Song-Jeon Lee (5269664)
Sin-Gi Park (647380)
In-Gang Shin (5269667)
Sang-Eun Hahn (5269643)
Woo-Jae Choi (5269649)
Hee-Soo Kim (1831327)
Hyeong-Jong Kim (5269658)
Seong-Hun Bae (5269646)
Je-Hyeong Lee (5269640)
Joo-Yeong Moon (5269661)
Woo-Sung Lee (5269655)
Ji-Hyun Lee (145976)
Choong-Il Lee (5269652)
Seong-Jin Kim (179277)
Goo Jang (311299)

May 2018

Figure S2. Detection of the expression of YFP in milk from SNU-SB-1 by confocal microscopy. Images o...

Additional file 3: of Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle

Prerna Vohra (3610208)
Roy Chaudhuri (480357)
Matthew Mayho (22198)
Christina Vrettou (6188414)
Cosmin Chintoan-Uta (6188417)
Nicholas Thomson (190404)
Jayne Hope (3571163)
John Hopkins (79788)
Mark Stevens (8903)

January 2019

Figure S2. Circular diagrams of the S. Typhimurium chromosome and plasmids showing the distribution ...

Additional file 1: of Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle

Prerna Vohra (3610208)
Roy Chaudhuri (480357)
Matthew Mayho (22198)
Christina Vrettou (6188414)
Cosmin Chintoan-Uta (6188417)
Nicholas Thomson (190404)
Jayne Hope (3571163)
John Hopkins (79788)
Mark Stevens (8903)

January 2019

Figure S1. Experimental strategy to screen TraDIS mutants in vivo. An input pool of random transposo...

Additional file 4: Fig. S1. of Candidate genes for male and female reproductive traits in Canchim beef cattle

Marcos Buzanskas (3407801)
Daniela Grossi (3688171)
Ricardo Ventura (3407792)
Flavio Schenkel (598286)
Tatiane Chud (3407807)
Nedenia Stafuzza (3462848)
Luciana Rola (4387648)
Sarah Meirelles (4387639)
Fabiana Mokry (3407816)
Maurício Mudadu (3407822)
Roberto Higa (3462839)
Marcos Silva (4387645)
Maurício Alencar (4387642)
Luciana Regitano (3407810)
Danísio Munari (3407825)

August 2017

Linkage disequilibrium for scrotal circumference at 420 d of age on chromosome 5. Fig. S2. Linkage d...

Additional file 2: of Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle

Prerna Vohra (3610208)
Roy Chaudhuri (480357)
Matthew Mayho (22198)
Christina Vrettou (6188414)
Cosmin Chintoan-Uta (6188417)
Nicholas Thomson (190404)
Jayne Hope (3571163)
John Hopkins (79788)
Mark Stevens (8903)

January 2019

Table S1. The complete TraDIS dataset showing the positions of all transposon insertions in the geno...

Additional file 3: of In vivo competition and horizontal gene transfer among distinct Staphylococcus aureus lineages as major drivers for adaptational changes during long-term persistence in humans

Lars Langhanki (3369824)
Petya Berger (5881013)
Janina Treffon (3369830)
Francesco Catania (375780)
Barbara Kahl (374193)
Alexander Mellmann (72273)

October 2018

Genomic organization of the 25.7Â kb transposon. Genes on the forward strand are depicted as right-s...

Additional file 3: of Genome changes due to artificial selection in U.S. Holstein cattle

Li Ma (46633)
Tad Sonstegard (392288)
John Cole (392281)
Curtis VanTassell (6323411)
George Wiggans (392282)
Brian Crooker (3529250)
Cheng Tan (293674)
Dzianis Prakapenka (3142692)
George Liu (122581)
Yang Da (89805)

February 2019

Figure S3. Overview of allele frequency differences (AFD) and extended haplotype homozygosity (EHH)....

Additional file 2: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang (103347)
Ben Hayes (90023)
Christy Vander Jagt (817483)
Iona MacLeod (3770932)
Majid Khansefid (3398150)
Phil Bowman (3550763)
Zehu Yuan (3144171)
Claire Prowse-Wilkins (5482388)
Coralie Reich (3695740)
Brett Mason (5482391)
Josie Garner (5482394)
Leah Marett (1986853)
Yizhou Chen (532732)
Sunduimijid Bolormaa (543860)
Hans Daetwyler (3525329)
Amanda Chamberlain (817482)
Michael Goddard (3398153)

July 2018

Figure S1. Gene coverage uniformity plots for each tissue type for a) all genes, b) 500 highest expr...

Additional file 1: of Characterization of recombination features and the genetic basis in multiple cattle breeds

Botong Shen (822728)
Jicai Jiang (122571)
Eyal Seroussi (31976)
George Liu (122581)
Li Ma (46633)

April 2018

Eight breed- and sex-specific recombination maps for Holstein, Jersey, Brown Swiss, and Ayrshire in ...

Additional file 4: of Retrospective application of transposon-directed insertion-site sequencing to investigate niche-specific virulence of Salmonella Typhimurium in cattle

Prerna Vohra (3610208)
Roy Chaudhuri (480357)
Matthew Mayho (22198)
Christina Vrettou (6188414)
Cosmin Chintoan-Uta (6188417)
Nicholas Thomson (190404)
Jayne Hope (3571163)
John Hopkins (79788)
Mark Stevens (8903)

January 2019

Table S2. All newly identified transposon-insertion mutants and mutants with newly resolved fitness ...

Additional file 4: of In vivo competition and horizontal gene transfer among distinct Staphylococcus aureus lineages as major drivers for adaptational changes during long-term persistence in humans

Lars Langhanki (3369824)
Petya Berger (5881013)
Janina Treffon (3369830)
Francesco Catania (375780)
Barbara Kahl (374193)
Alexander Mellmann (72273)

October 2018

Gene names, locus tags and position information characterizing the 14.2Â kb DNA transposon and the 2...

Additional file 3: of Comparing allele specific expression and local expression quantitative trait loci and the influence of gene expression on complex trait variation in cattle

Majid Khansefid (3398150)
Jennie Pryce (241354)
Sunduimijid Bolormaa (543860)
Yizhou Chen (532732)
Catriona Millen (3398147)
Amanda Chamberlain (817482)
Christy Vander Jagt (817483)
Michael Goddard (3398153)

November 2018

Table S12. GWAS using SNP-chip data. The detailed results of p-values for each SNP in GWA studies fo...

Additional file 1: of Genome-wide association between single nucleotide polymorphisms with beef fatty acid profile in Nellore cattle using the single step procedure

Marcos Lemos (3577223)
Hermenegildo Chiaia (3508658)
Mariana Berton (3508631)
Fabieli Feitosa (3508652)
Carolyn Aboujaoud (3577217)
GregĂłrio Camargo (3577229)
AngĂŠlica Pereira (3508661)
Lucia Albuquerque (3577211)
Adrielle Ferrinho (3508619)
Lenise Mueller (3508643)
Monica Mazalli (3577214)
Joyce Furlan (3577220)
Roberto Carvalheiro (523642)
Daniel Gordo (3508613)
Rafael Tonussi (3508604)
Rafael Espigolan (3160104)
Rafael Silva (1872808)
Henrique de Oliveira (3508649)
Susan Duckett (3508607)
Ignacio Aguilar (3577208)
Fernando Baldi (2833280)

March 2016

Manhattan plot of the genome-wide association study for fatty acids in Nellore. The X-axis represent...

Additional file 4: of Long-term health and germline transmission in transgenic cattle following transposon-mediated gene transfer

Abstract

Extracted data

Additional file 4: of Long-term health and germline transmission in transgenic cattle following transposon-mediated gene transfer

Abstract

Extracted data

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