Additional file 2: of Whole exome sequencing in the rat

Additional file 1: of Exonic duplication of the OTC gene by a complex rearrangement that likely occurred via a replication-based mechanism: a case report

Katsuyuki Yokoi (6080771)
Yoko Nakajima (6080777)
Hidehito Inagaki (560626)
Makiko Tsutsumi (177321)
Tetsuya Ito (667382)
Hiroki Kurahashi (560630)

December 2018

PCR primers and genomic coordinates. (a) Primers for Sanger sequences of OTC exons. (b) Primers for ...

Additional file 1: of The oncoprotein TBX3 is controlling severity in experimental arthritis

Samra Sardar (6197525)
Alish Kerr (6197528)
DaniĂŤlle Vaartjes (6197531)
Emilie Moltved (6197534)
Edita Karosiene (5392358)
Ramneek Gupta (437350)
Ăsa Andersson (6197537)

January 2019

Table S1. List of primers used for genotyping of mice. Table S2. List of primers for Tbx3 and Tbx5 s...

Additional file 1: Table S1. of Somatic loss of function mutations in neurofibromin 1 and MYC associated factor X genes identified by exome-wide sequencing in a wild-type GIST case

Martin Belinsky (3554900)
Lori Rink (277122)
Kathy Cai (3554894)
Stephen Capuzzi (3554897)
Yen Hoang (3554903)
Jeremy Chien (185202)
Andrew Godwin (811543)
Margaret Mehren (3554906)

November 2015

Primers for Sanger sequencing. Nucleotide sequences are listed for primers used for exon-based valid...

Additional file 1: of Whole exome sequencing in the rat

Julie Foley (340580)
Dhiral Phadke (200474)
Owen Hardy (5431265)
Sara Hardy (72527)
Victor Miller (5431283)
Anup Madan (250323)
Kellie Howard (3586490)
Kimberly Kruse (5431271)
Cara Lord (5431277)
Sreenivasa Ramaiahgari (4343395)
Gregory Solomon (55846)
Ruchir Shah (3467510)
Arun Pandiri (5431280)
Ronald Herbert (5431274)
Robert Sills (5431268)
B. Merrick (5479904)

June 2018

Table S1. Rat exome-seq 500 flanking bp primer design for validation. (XLSX 20 kb

Additional file 3: of Whole exome sequencing in the rat

Julie Foley (340580)
Dhiral Phadke (200474)
Owen Hardy (5431265)
Sara Hardy (72527)
Victor Miller (5431283)
Anup Madan (250323)
Kellie Howard (3586490)
Kimberly Kruse (5431271)
Cara Lord (5431277)
Sreenivasa Ramaiahgari (4343395)
Gregory Solomon (55846)
Ruchir Shah (3467510)
Arun Pandiri (5431280)
Ronald Herbert (5431274)
Robert Sills (5431268)
B. Merrick (5479904)

June 2018

Figure S1. Exonic Variant Read Distribution. The distribution of all exonic variant reads across all...

Additional file 1: of Persistent accumulation of unrepaired DNA damage in rat cortical neurons: nuclear organization and ChIP-seq analysis of damaged DNA

Jorge Mata-Garrido (5563985)
Olga Tapia (705967)
Iñigo Casafont (5563988)
Maria Berciano (5563991)
Ana Cuadrado (5563994)
Miguel Lafarga (261451)

July 2018

Table S1. Primers used for ChIP-qPCR in different rat genomic regions. (XLSX 62 kb

Additional file 1: of Design and application of a target capture sequencing of exons and conserved non-coding sequences for the rat

Minako Yoshihara (3416264)
Daisuke Saito (575812)
Tetsuya Sato (2359468)
Osamu Ohara (3060)
Takashi Kuramoto (115452)
Mikita Suyama (17958)

August 2016

Table S1. Summary statistics for SNV and INDEL in various depths. Figure S1. Sequence coverage of th...

Additional file 1: Table S1. of Tracking the origin of simultaneous endometrial and ovarian cancer by next-generation sequencing â a case report

Nadejda Valtcheva (3682978)
Franziska Lang (3682987)
Aurelia Noske (321353)
Eleftherios Samartzis (3682981)
Anna-Maria Schmidt (3682990)
Elisa Bellini (758376)
Daniel Fink (337132)
Holger Moch (159876)
Markus Rechsteiner (802404)
Konstantin Dedes (3682984)
Peter Wild (18726)

January 2017

Sequences of the primers used for Sanger sequencing. Table S2. Comprehensive list of variants from t...

Whole exome sequencing in the rat

Julie F. Foley
Dhiral P. Phadke
Owen Hardy
Sara Hardy
Victor Miller
Anup Madan
Kellie Howard
Kimberly Kruse
Cara Lord
Sreenivasa Ramaiahgari
Gregory G. Solomon
Ruchir R. Shah
Arun R. Pandiri
Ronald A. Herbert
Robert C. Sills
B. Alex Merrick

June 2018

Abstract Background The rat genome was sequenced in 2004 with the aim to improve human health altere...

Additional file 21: of Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

Lyudmila Dergunova (5722535)
Ivan Filippenkov (5722541)
Vasily Stavchansky (5722544)
Alina Denisova (5722547)
Vadim Yuzhakov (5722550)
Sergey Mozerov (5722553)
Leonid Gubsky (4524799)
Svetlana Limborska (264231)

September 2018

Table S21. The characterization of the primers for real-time RT-PCR. (XLSX 12Â kb

Additional file 2: of Application of long single-stranded DNA donors in genome editing: generation and validation of mouse mutants

Gemma Codner (3407399)
Joffrey MiannĂŠ (3407429)
Adam Caulder (3407402)
Jorik Loeffler (5431574)
Rachel Fell (5431583)
Ruairidh King (5431589)
Alasdair Allan (5431595)
Matthew Mackenzie (5431592)
Fran Pike (5431568)
Christopher McCabe (206680)
Skevoulla Christou (5431577)
Sam Joynson (5431580)
Marie Hutchison (3578627)
Michelle Stewart (618852)
Saumya Kumar (530117)
Michelle Simon (530116)
Loranne Agius (2527249)
Quentin Anstee (5431571)
Kirill Volynski (5431598)
Dimitri Kullmann (5431586)
Sara Wells (106305)
Lydia Teboul (106309)

June 2018

Figure S1. Screening by Sanger sequencing of animals for the generation of a Syt7 conditional allele...

Additional file 2: Table S2. of Replicate exome-sequencing in a multiple-generation family: improved interpretation of next-generation sequencing data

Praveen Cherukuri (3492785)
Valerie Maduro (235138)
Karin Fuentes-Fajardo (3552710)
Kevin Lam (1404526)
David Adams (202540)
Cynthia Tifft (202569)
James Mullikin (374795)
William Gahl (3492812)
Cornelius Boerkoel (137810)

November 2015

Titration of percentage target exome sequenced as a function of depth of sequencing thresholds. (XLS...

Additional file 1: Table S1 of Unexpected effects of different genetic backgrounds on identification of genomic rearrangements via whole-genome next generation sequencing

Zhangguo Chen (3421043)
Katherine Gowan (477831)
Sonia Leach (3421034)
Sawanee Viboolsittiseri (3421046)
Ameet Mishra (3421040)
Tanya Kadoishi (3421037)
Katrina Diener (3421031)
Bifeng Gao (179750)
Kenneth Jones (781854)
Jing Wang (1228470)

October 2016

The numbers of CTXs in each sample after filtering process and chromosome coordinates of all CTXs. 1...

Additional file 2: Table S2. of Transcriptome profile of rat genes in injured spinal cord at different stages by RNA-sequencing

Ling-Ling Shi (439914)
Nan Zhang (46264)
Xiu-Mei Xie (3751375)
Yue-Juan Chen (3751372)
Rui Wang (52434)
Lin Shen (507259)
Jian-Sheng Zhou (3751366)
Jian-Guo Hu (3751363)
He-Zuo LĂź (3751378)

February 2017

The list of most relevant genes that are over-expressed or under-expressed in the different injured ...

Additional file 4: Table S4. of Genome-wide segregation of single nucleotide and structural variants into single cancer cells

John Easton (4615627)
Veronica Gonzalez-Pena (4615624)
Donald Yergeau (4615630)
Xiaotu Ma (44228)
Charles Gawad (186011)

November 2017

List of Amplicon Primers used in Resequencing. This file provides a list of the primers used for int...

Additional file 1: of Exonic duplication of the OTC gene by a complex rearrangement that likely occurred via a replication-based mechanism: a case report

Katsuyuki Yokoi (6080771)
Yoko Nakajima (6080777)
Hidehito Inagaki (560626)
Makiko Tsutsumi (177321)
Tetsuya Ito (667382)
Hiroki Kurahashi (560630)

December 2018

PCR primers and genomic coordinates. (a) Primers for Sanger sequences of OTC exons. (b) Primers for ...

Additional file 1: of The oncoprotein TBX3 is controlling severity in experimental arthritis

Samra Sardar (6197525)
Alish Kerr (6197528)
DaniĂŤlle Vaartjes (6197531)
Emilie Moltved (6197534)
Edita Karosiene (5392358)
Ramneek Gupta (437350)
Ăsa Andersson (6197537)

January 2019

Table S1. List of primers used for genotyping of mice. Table S2. List of primers for Tbx3 and Tbx5 s...

Additional file 1: Table S1. of Somatic loss of function mutations in neurofibromin 1 and MYC associated factor X genes identified by exome-wide sequencing in a wild-type GIST case

Martin Belinsky (3554900)
Lori Rink (277122)
Kathy Cai (3554894)
Stephen Capuzzi (3554897)
Yen Hoang (3554903)
Jeremy Chien (185202)
Andrew Godwin (811543)
Margaret Mehren (3554906)

November 2015

Primers for Sanger sequencing. Nucleotide sequences are listed for primers used for exon-based valid...

Additional file 1: of Whole exome sequencing in the rat

Julie Foley (340580)
Dhiral Phadke (200474)
Owen Hardy (5431265)
Sara Hardy (72527)
Victor Miller (5431283)
Anup Madan (250323)
Kellie Howard (3586490)
Kimberly Kruse (5431271)
Cara Lord (5431277)
Sreenivasa Ramaiahgari (4343395)
Gregory Solomon (55846)
Ruchir Shah (3467510)
Arun Pandiri (5431280)
Ronald Herbert (5431274)
Robert Sills (5431268)
B. Merrick (5479904)

June 2018

Table S1. Rat exome-seq 500 flanking bp primer design for validation. (XLSX 20 kb

Additional file 3: of Whole exome sequencing in the rat

Julie Foley (340580)
Dhiral Phadke (200474)
Owen Hardy (5431265)
Sara Hardy (72527)
Victor Miller (5431283)
Anup Madan (250323)
Kellie Howard (3586490)
Kimberly Kruse (5431271)
Cara Lord (5431277)
Sreenivasa Ramaiahgari (4343395)
Gregory Solomon (55846)
Ruchir Shah (3467510)
Arun Pandiri (5431280)
Ronald Herbert (5431274)
Robert Sills (5431268)
B. Merrick (5479904)

June 2018

Figure S1. Exonic Variant Read Distribution. The distribution of all exonic variant reads across all...

Additional file 1: of Persistent accumulation of unrepaired DNA damage in rat cortical neurons: nuclear organization and ChIP-seq analysis of damaged DNA

Jorge Mata-Garrido (5563985)
Olga Tapia (705967)
Iñigo Casafont (5563988)
Maria Berciano (5563991)
Ana Cuadrado (5563994)
Miguel Lafarga (261451)

July 2018

Table S1. Primers used for ChIP-qPCR in different rat genomic regions. (XLSX 62 kb

Additional file 1: of Design and application of a target capture sequencing of exons and conserved non-coding sequences for the rat

Minako Yoshihara (3416264)
Daisuke Saito (575812)
Tetsuya Sato (2359468)
Osamu Ohara (3060)
Takashi Kuramoto (115452)
Mikita Suyama (17958)

August 2016

Table S1. Summary statistics for SNV and INDEL in various depths. Figure S1. Sequence coverage of th...

Additional file 1: Table S1. of Tracking the origin of simultaneous endometrial and ovarian cancer by next-generation sequencing â a case report

Nadejda Valtcheva (3682978)
Franziska Lang (3682987)
Aurelia Noske (321353)
Eleftherios Samartzis (3682981)
Anna-Maria Schmidt (3682990)
Elisa Bellini (758376)
Daniel Fink (337132)
Holger Moch (159876)
Markus Rechsteiner (802404)
Konstantin Dedes (3682984)
Peter Wild (18726)

January 2017

Sequences of the primers used for Sanger sequencing. Table S2. Comprehensive list of variants from t...

Whole exome sequencing in the rat

Julie F. Foley
Dhiral P. Phadke
Owen Hardy
Sara Hardy
Victor Miller
Anup Madan
Kellie Howard
Kimberly Kruse
Cara Lord
Sreenivasa Ramaiahgari
Gregory G. Solomon
Ruchir R. Shah
Arun R. Pandiri
Ronald A. Herbert
Robert C. Sills
B. Alex Merrick

June 2018

Abstract Background The rat genome was sequenced in 2004 with the aim to improve human health altere...

Additional file 21: of Genome-wide transcriptome analysis using RNA-Seq reveals a large number of differentially expressed genes in a transient MCAO rat model

Lyudmila Dergunova (5722535)
Ivan Filippenkov (5722541)
Vasily Stavchansky (5722544)
Alina Denisova (5722547)
Vadim Yuzhakov (5722550)
Sergey Mozerov (5722553)
Leonid Gubsky (4524799)
Svetlana Limborska (264231)

September 2018

Table S21. The characterization of the primers for real-time RT-PCR. (XLSX 12Â kb

Additional file 2: of Application of long single-stranded DNA donors in genome editing: generation and validation of mouse mutants

Gemma Codner (3407399)
Joffrey MiannĂŠ (3407429)
Adam Caulder (3407402)
Jorik Loeffler (5431574)
Rachel Fell (5431583)
Ruairidh King (5431589)
Alasdair Allan (5431595)
Matthew Mackenzie (5431592)
Fran Pike (5431568)
Christopher McCabe (206680)
Skevoulla Christou (5431577)
Sam Joynson (5431580)
Marie Hutchison (3578627)
Michelle Stewart (618852)
Saumya Kumar (530117)
Michelle Simon (530116)
Loranne Agius (2527249)
Quentin Anstee (5431571)
Kirill Volynski (5431598)
Dimitri Kullmann (5431586)
Sara Wells (106305)
Lydia Teboul (106309)

June 2018

Figure S1. Screening by Sanger sequencing of animals for the generation of a Syt7 conditional allele...

Additional file 2: Table S2. of Replicate exome-sequencing in a multiple-generation family: improved interpretation of next-generation sequencing data

Praveen Cherukuri (3492785)
Valerie Maduro (235138)
Karin Fuentes-Fajardo (3552710)
Kevin Lam (1404526)
David Adams (202540)
Cynthia Tifft (202569)
James Mullikin (374795)
William Gahl (3492812)
Cornelius Boerkoel (137810)

November 2015

Titration of percentage target exome sequenced as a function of depth of sequencing thresholds. (XLS...

Additional file 1: Table S1 of Unexpected effects of different genetic backgrounds on identification of genomic rearrangements via whole-genome next generation sequencing

Zhangguo Chen (3421043)
Katherine Gowan (477831)
Sonia Leach (3421034)
Sawanee Viboolsittiseri (3421046)
Ameet Mishra (3421040)
Tanya Kadoishi (3421037)
Katrina Diener (3421031)
Bifeng Gao (179750)
Kenneth Jones (781854)
Jing Wang (1228470)

October 2016

The numbers of CTXs in each sample after filtering process and chromosome coordinates of all CTXs. 1...

Additional file 2: Table S2. of Transcriptome profile of rat genes in injured spinal cord at different stages by RNA-sequencing

Ling-Ling Shi (439914)
Nan Zhang (46264)
Xiu-Mei Xie (3751375)
Yue-Juan Chen (3751372)
Rui Wang (52434)
Lin Shen (507259)
Jian-Sheng Zhou (3751366)
Jian-Guo Hu (3751363)
He-Zuo LĂź (3751378)

February 2017

The list of most relevant genes that are over-expressed or under-expressed in the different injured ...

Additional file 4: Table S4. of Genome-wide segregation of single nucleotide and structural variants into single cancer cells

John Easton (4615627)
Veronica Gonzalez-Pena (4615624)
Donald Yergeau (4615630)
Xiaotu Ma (44228)
Charles Gawad (186011)

November 2017

List of Amplicon Primers used in Resequencing. This file provides a list of the primers used for int...

Additional file 1: of Exonic duplication of the OTC gene by a complex rearrangement that likely occurred via a replication-based mechanism: a case report

Katsuyuki Yokoi (6080771)
Yoko Nakajima (6080777)
Hidehito Inagaki (560626)
Makiko Tsutsumi (177321)
Tetsuya Ito (667382)
Hiroki Kurahashi (560630)

December 2018

PCR primers and genomic coordinates. (a) Primers for Sanger sequences of OTC exons. (b) Primers for ...

Additional file 1: of The oncoprotein TBX3 is controlling severity in experimental arthritis

Samra Sardar (6197525)
Alish Kerr (6197528)
DaniĂŤlle Vaartjes (6197531)
Emilie Moltved (6197534)
Edita Karosiene (5392358)
Ramneek Gupta (437350)
Ăsa Andersson (6197537)

January 2019

Table S1. List of primers used for genotyping of mice. Table S2. List of primers for Tbx3 and Tbx5 s...

Additional file 1: Table S1. of Somatic loss of function mutations in neurofibromin 1 and MYC associated factor X genes identified by exome-wide sequencing in a wild-type GIST case

Martin Belinsky (3554900)
Lori Rink (277122)
Kathy Cai (3554894)
Stephen Capuzzi (3554897)
Yen Hoang (3554903)
Jeremy Chien (185202)
Andrew Godwin (811543)
Margaret Mehren (3554906)

November 2015

Primers for Sanger sequencing. Nucleotide sequences are listed for primers used for exon-based valid...

Additional file 2: of Whole exome sequencing in the rat

Abstract

Extracted data

Additional file 2: of Whole exome sequencing in the rat

Abstract

Extracted data

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