Additional file 7: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Structural variants and short tandem repeats impact gene expression and splicing in bovine testis tissue

Bhati, Meenu
Mapel, Xena
Lloret-Villas, Audald
Pausch, Hubert

August 2023

The files are output data of the research article “Structural variants and short tandem repeats impa...

Additional file 8: 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

Table S1. Genome regions with signature of selection detected by long-range frequency differences in...

Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang
Ben J. Hayes
Christy J. Vander Jagt
Iona M. MacLeod
Majid Khansefid
Phil J. Bowman
Zehu Yuan
Claire P. Prowse-Wilkins
Coralie M. Reich
Brett A. Mason
Josie B. Garner
Leah C. Marett
Yizhou Chen
Sunduimijid Bolormaa
Hans D. Daetwyler
Amanda J. Chamberlain
Michael E. Goddard

July 2018

Abstract Background Mammalian phenotypes are shaped by numerous genome variants, many of which may r...

Additional file 6: 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

Table S4. Genes that display significant differential splicing cross tissues. (XLSX 18699 kb

Additional file 8: 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

Table S6. Summary of significant cis splicing sQTLs (within 1Â Mb distance to the exon). (XLSX 14902...

Additional file 5: 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

Table S3. 2âĂâ2 tables for the overlap between exon and intron analyses. (XLSX 15 kb

Additional file 9: 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

Table S7. Summary table for count values of sQTLs and eeQTLs in white blood and milk cells. (XLSX 9 ...

Additional file 4: 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

Table S2. Splicing junction annotation analysis using BAM files generated by different alignment sof...

Additional file 10: 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

Table S8. SNP overlap between expression QTLs and SNPs with pleiotropic effects on conventional trai...

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 7: of A splice donor variant in CCDC189 is associated with asthenospermia in Nordic Red dairy cattle

Terhi Iso-Touru (505133)
Christine Wurmser (151766)
Heli Venhoranta (236269)
Maya Hiltpold (6581882)
Tujia Savolainen (6581885)
Anu Sironen (403686)
Konrad Fischer (6581888)
Krzysztof Flisikowski (133283)
Ruedi Fries (151786)
Alejandro Vicente-Carrillo (3119754)
Manuel Alvarez-Rodriguez (3665020)
Szabolcs Nagy (2231290)
Mervi Mutikainen (6581891)
Jaana Peippo (4805769)
Juhani Taponen (236295)
Goutam Sahana (126076)
Bernt Guldbrandtsen (340532)
Henri Simonen (6581894)
Heriberto Rodriguez-Martinez (3119748)
Magnus Andersson (236322)
Hubert Pausch (151770)

April 2019

Sequencing depth along chromosome 25 in two asthenospermic bulls. The depth of sequencing coverage i...

Genome variants associated with RNA splicing variations in bovine are extensive shared between tissues

Xiang, R
Hayes, BJ
Vander Jagt, CJ
MacLeod, IM
Khansefid, M
Bowman, PJ
Yuan, Z
Prowse-Wilkins, CP
Reich, CM
Mason, BA
Garner, JB
Marett, LC
Chen, Y
Bolormaa, S
Daetwyler, HD
Chamberlain, AJ
Goddard, ME

July 2018

BACKGROUND: Mammalian phenotypes are shaped by numerous genome variants, many of which may regulate ...

Additional file 9: of Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits

Joaquim da Silva (3455798)
Poliana Giachetto (3455801)
Luiz da Silva (3455792)
Leandro Cintra (3455804)
Samuel Paiva (184995)
Michel Yamagishi (3455795)
Alexandre Caetano (3455789)

June 2016

CNVRs overlapping with previously detected QTLs from the Bovine QTL Database. (XLSX 2973 kb

Additional file 4: 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 S13. GWAS using imputed whole genome sequence data. The detailed results of p-values for each ...

Additional file 5: Table S4. of Meta-analysis of sequence-based association studies across three cattle breeds reveals 25 QTL for fat and protein percentages in milk at nucleotide resolution

Hubert Pausch (151770)
Reiner Emmerling (167481)
Birgit Gredler-Grandl (4584202)
Ruedi Fries (151786)
Hans Daetwyler (3525329)
Michael Goddard (3398153)

November 2017

Characteristics of 25 QTL in three breeds analysed. Frequency of 25 QTL in the BV, FV and HOL cattle...

Structural variants and short tandem repeats impact gene expression and splicing in bovine testis tissue

Bhati, Meenu
Mapel, Xena
Lloret-Villas, Audald
Pausch, Hubert

August 2023

The files are output data of the research article “Structural variants and short tandem repeats impa...

Additional file 8: 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

Table S1. Genome regions with signature of selection detected by long-range frequency differences in...

Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang
Ben J. Hayes
Christy J. Vander Jagt
Iona M. MacLeod
Majid Khansefid
Phil J. Bowman
Zehu Yuan
Claire P. Prowse-Wilkins
Coralie M. Reich
Brett A. Mason
Josie B. Garner
Leah C. Marett
Yizhou Chen
Sunduimijid Bolormaa
Hans D. Daetwyler
Amanda J. Chamberlain
Michael E. Goddard

July 2018

Abstract Background Mammalian phenotypes are shaped by numerous genome variants, many of which may r...

Additional file 6: 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

Table S4. Genes that display significant differential splicing cross tissues. (XLSX 18699 kb

Additional file 8: 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

Table S6. Summary of significant cis splicing sQTLs (within 1Â Mb distance to the exon). (XLSX 14902...

Additional file 5: 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

Table S3. 2âĂâ2 tables for the overlap between exon and intron analyses. (XLSX 15 kb

Additional file 9: 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

Table S7. Summary table for count values of sQTLs and eeQTLs in white blood and milk cells. (XLSX 9 ...

Additional file 4: 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

Table S2. Splicing junction annotation analysis using BAM files generated by different alignment sof...

Additional file 10: 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

Table S8. SNP overlap between expression QTLs and SNPs with pleiotropic effects on conventional trai...

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 7: of A splice donor variant in CCDC189 is associated with asthenospermia in Nordic Red dairy cattle

Terhi Iso-Touru (505133)
Christine Wurmser (151766)
Heli Venhoranta (236269)
Maya Hiltpold (6581882)
Tujia Savolainen (6581885)
Anu Sironen (403686)
Konrad Fischer (6581888)
Krzysztof Flisikowski (133283)
Ruedi Fries (151786)
Alejandro Vicente-Carrillo (3119754)
Manuel Alvarez-Rodriguez (3665020)
Szabolcs Nagy (2231290)
Mervi Mutikainen (6581891)
Jaana Peippo (4805769)
Juhani Taponen (236295)
Goutam Sahana (126076)
Bernt Guldbrandtsen (340532)
Henri Simonen (6581894)
Heriberto Rodriguez-Martinez (3119748)
Magnus Andersson (236322)
Hubert Pausch (151770)

April 2019

Sequencing depth along chromosome 25 in two asthenospermic bulls. The depth of sequencing coverage i...

Genome variants associated with RNA splicing variations in bovine are extensive shared between tissues

Xiang, R
Hayes, BJ
Vander Jagt, CJ
MacLeod, IM
Khansefid, M
Bowman, PJ
Yuan, Z
Prowse-Wilkins, CP
Reich, CM
Mason, BA
Garner, JB
Marett, LC
Chen, Y
Bolormaa, S
Daetwyler, HD
Chamberlain, AJ
Goddard, ME

July 2018

BACKGROUND: Mammalian phenotypes are shaped by numerous genome variants, many of which may regulate ...

Additional file 9: of Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits

Joaquim da Silva (3455798)
Poliana Giachetto (3455801)
Luiz da Silva (3455792)
Leandro Cintra (3455804)
Samuel Paiva (184995)
Michel Yamagishi (3455795)
Alexandre Caetano (3455789)

June 2016

CNVRs overlapping with previously detected QTLs from the Bovine QTL Database. (XLSX 2973 kb

Additional file 4: 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 S13. GWAS using imputed whole genome sequence data. The detailed results of p-values for each ...

Additional file 5: Table S4. of Meta-analysis of sequence-based association studies across three cattle breeds reveals 25 QTL for fat and protein percentages in milk at nucleotide resolution

Hubert Pausch (151770)
Reiner Emmerling (167481)
Birgit Gredler-Grandl (4584202)
Ruedi Fries (151786)
Hans Daetwyler (3525329)
Michael Goddard (3398153)

November 2017

Characteristics of 25 QTL in three breeds analysed. Frequency of 25 QTL in the BV, FV and HOL cattle...

Structural variants and short tandem repeats impact gene expression and splicing in bovine testis tissue

Bhati, Meenu
Mapel, Xena
Lloret-Villas, Audald
Pausch, Hubert

August 2023

The files are output data of the research article “Structural variants and short tandem repeats impa...

Additional file 8: 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

Table S1. Genome regions with signature of selection detected by long-range frequency differences in...

Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Ruidong Xiang
Ben J. Hayes
Christy J. Vander Jagt
Iona M. MacLeod
Majid Khansefid
Phil J. Bowman
Zehu Yuan
Claire P. Prowse-Wilkins
Coralie M. Reich
Brett A. Mason
Josie B. Garner
Leah C. Marett
Yizhou Chen
Sunduimijid Bolormaa
Hans D. Daetwyler
Amanda J. Chamberlain
Michael E. Goddard

July 2018

Abstract Background Mammalian phenotypes are shaped by numerous genome variants, many of which may r...

Additional file 7: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Abstract

Extracted data

Additional file 7: of Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

Abstract

Extracted data

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