Additional file 1: of Whole exome sequencing in the rat

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: of Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction

Alex Genshaft (3485744)
Shuqiang Li (228142)
Caroline Gallant (3485738)
Spyros Darmanis (203309)
Sanjay Prakadan (3485741)
Carly Ziegler (3485747)
Martin Lundberg (584387)
Simon Fredriksson (29917)
Joyce Hong (3485750)
Aviv Regev (147110)
Kenneth Livak (3485735)
Ulf Landegren (7959)
Alex Shalek (3424427)

September 2016

Supplementary Table. Supplementary tables with legends in the first sheet called "Supplementary Tabl...

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 2: 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 S2. PCR forward and reverse primer pairs for Sanger sequencing. (XLSX 10 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 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

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 1: Table S1. of Multi-class computational evolution: development, benchmark evaluation and application to RNA-Seq biomarker discovery

Nathaniel Crabtree (3948155)
Jason Moore (377082)
John Bowyer (3547901)
Nysia George (3948158)

April 2017

Genes chosen by CES using all 12,549 genes expressed in rat blood. Description of data: A list of th...

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 Comprehensive transcriptional landscape of aging mouse liver

Ryan White (513000)
Brandon Milholland (455326)
Sheila MacRae (3499064)
Mingyan Lin (139065)
Deyou Zheng (7943)
Jan Vijg (31744)

November 2015

Sequencing and alignment metrics for each young and old liver sample. (XLSX 44 kb

Additional file 3: 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

Figure S1. RNA-Seq analysis of differentially expressed genes (DEGs) in tMCAO model conditions. (PPT...

Additional file 1: Table S1. of Programming of mouse obesity by maternal exposure to concentrated ambient fine particles

Minjie Chen (561735)
Xiaoke Wang (548086)
Ziying Hu (4034651)
Huifen Zhou (4170631)
Yanyi Xu (741187)
Lianglin Qiu (307501)
Xiaobo Qin (4170634)
Yuhao Zhang (123122)
Zhekang Ying (115022)

June 2017

Primer sequences for real-time RT-PCR. Table S2 Primer sequences for leptin promoter methylation ass...

Additional file 1: of Cognitive impairment in metabolically-obese, normal-weight rats: identification of early biomarkers in peripheral blood mononuclear cells

Margalida Cifre (4996952)
Andreu Palou (219347)
Paula Oliver (2741743)

March 2018

Nucleotide sequences of primers used for real-time RT-qPCR amplification. (DOCX 17 kb

Additional file 15: 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 S15. The RNA-Seq analysis of DEGs associated with the functional category âRibosomal protein...

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: of Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction

Alex Genshaft (3485744)
Shuqiang Li (228142)
Caroline Gallant (3485738)
Spyros Darmanis (203309)
Sanjay Prakadan (3485741)
Carly Ziegler (3485747)
Martin Lundberg (584387)
Simon Fredriksson (29917)
Joyce Hong (3485750)
Aviv Regev (147110)
Kenneth Livak (3485735)
Ulf Landegren (7959)
Alex Shalek (3424427)

September 2016

Supplementary Table. Supplementary tables with legends in the first sheet called "Supplementary Tabl...

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 2: 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 S2. PCR forward and reverse primer pairs for Sanger sequencing. (XLSX 10 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 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

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 1: Table S1. of Multi-class computational evolution: development, benchmark evaluation and application to RNA-Seq biomarker discovery

Nathaniel Crabtree (3948155)
Jason Moore (377082)
John Bowyer (3547901)
Nysia George (3948158)

April 2017

Genes chosen by CES using all 12,549 genes expressed in rat blood. Description of data: A list of th...

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 Comprehensive transcriptional landscape of aging mouse liver

Ryan White (513000)
Brandon Milholland (455326)
Sheila MacRae (3499064)
Mingyan Lin (139065)
Deyou Zheng (7943)
Jan Vijg (31744)

November 2015

Sequencing and alignment metrics for each young and old liver sample. (XLSX 44 kb

Additional file 3: 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

Figure S1. RNA-Seq analysis of differentially expressed genes (DEGs) in tMCAO model conditions. (PPT...

Additional file 1: Table S1. of Programming of mouse obesity by maternal exposure to concentrated ambient fine particles

Minjie Chen (561735)
Xiaoke Wang (548086)
Ziying Hu (4034651)
Huifen Zhou (4170631)
Yanyi Xu (741187)
Lianglin Qiu (307501)
Xiaobo Qin (4170634)
Yuhao Zhang (123122)
Zhekang Ying (115022)

June 2017

Primer sequences for real-time RT-PCR. Table S2 Primer sequences for leptin promoter methylation ass...

Additional file 1: of Cognitive impairment in metabolically-obese, normal-weight rats: identification of early biomarkers in peripheral blood mononuclear cells

Margalida Cifre (4996952)
Andreu Palou (219347)
Paula Oliver (2741743)

March 2018

Nucleotide sequences of primers used for real-time RT-qPCR amplification. (DOCX 17 kb

Additional file 15: 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 S15. The RNA-Seq analysis of DEGs associated with the functional category âRibosomal protein...

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: of Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction

Alex Genshaft (3485744)
Shuqiang Li (228142)
Caroline Gallant (3485738)
Spyros Darmanis (203309)
Sanjay Prakadan (3485741)
Carly Ziegler (3485747)
Martin Lundberg (584387)
Simon Fredriksson (29917)
Joyce Hong (3485750)
Aviv Regev (147110)
Kenneth Livak (3485735)
Ulf Landegren (7959)
Alex Shalek (3424427)

September 2016

Supplementary Table. Supplementary tables with legends in the first sheet called "Supplementary Tabl...

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: of Whole exome sequencing in the rat

Abstract

Extracted data

Additional file 1: of Whole exome sequencing in the rat

Abstract

Extracted data

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