Additional file 2: of Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm

Excel file containing RNA-seq results (ΔcamS versus WT, camSΔ69–391 versus WT, ΔcamS versus ΔcamS::camS).

Katrin Schilcher (17743038)
Morgan M. Severn (17743041)
Christian Jenul (17743044)
Young-Saeng C. Avina (17743047)
Rebecca A. Keogh (14636318)
Alexander R. Horswill (45837)

January 2024

Excel file containing RNA-seq results (ΔcamS versus WT, camSΔ69–391 versus WT, ΔcamS versus ΔcamS::c...

Additional file 1: of Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency

Scott Adamson (5331245)
Lijun Zhan (326110)
Brenton Graveley (5331248)

June 2018

This document contains Table S1., which kists the oligo sequences used to assemble the splicing repo...

Additional file 2: of SpliceV: analysis and publication quality printing of linear and circular RNA splicing, expression and regulation

Nathan Ungerleider (5598377)
Erik Flemington (404193)

May 2019

An example pipeline to generate the required files for SpliceV analysis. (PDF 148 kb

Additional file 1: of Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm

Juan Romero (516524)
MarĂa Ortiz-EstĂŠvez (5791583)
Ander Muniategui (183724)
Soraya Carrancio (341408)
Fernando de Miguel (5077766)
Fernando Carazo (5791574)
Luis Montuenga (3405611)
Remco Loos (5791577)
RubĂŠn PĂo (5791586)
Matthew Trotter (188553)
Angel Rubio (46993)

September 2018

Vignette on the comparison based on expression analysis. Figure S1 to S9. Experiment design and cont...

Additional file 3: of Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm

Juan Romero (516524)
MarĂa Ortiz-EstĂŠvez (5791583)
Ander Muniategui (183724)
Soraya Carrancio (341408)
Fernando de Miguel (5077766)
Fernando Carazo (5791574)
Luis Montuenga (3405611)
Remco Loos (5791577)
RubĂŠn PĂo (5791586)
Matthew Trotter (188553)
Angel Rubio (46993)

September 2018

Compressed file including the GTF files generated for the matched events. (ZIP 15 kb

Supplementary excel 1

Huo Lei (5245121)
Lei Wang (6656)
Zhaoyao Yang (5245118)
Pingyuan Li (5245112)
Dechun Geng (5245115)
Yaozeng Xu (5245109)

May 2018

This file contains all the difference expression genes from RNA-seq analysis. This file was made wit...

Additional file 2: of Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data

Yongsheng Bai (49362)
Jeff Kinne (3529151)
Brandon Donham (3529148)
Feng Jiang (95012)
Lizhong Ding (3455855)
Justin Hassler (592429)
Randal Kaufman (3529154)

August 2016

Spliced regions identified by RSR for the Dtt sample. This file contains all supplementary results f...

Additional file 2: of Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes

Boas Pucker (3202233)
Samuel Brockington (4959529)

December 2018

RNA-Seq data sets. List of Sequence Read Archive accession numbers of all included RNA-Seq data sets...

Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm

Romero, J.P. (Juan P.)
Ortiz-Estévez, M. (Maria)
Muniategui, A. (Ander)
Carrancio, S. (Soraya)
Miguel, F.J. (Fernando J.) de
Carazo Melo, F.(Fernando)
Montuenga-Badia, L.M. (Luis M.)
Loos, R. (Remco)
Pio, R. (Rubén)
Trotter, M. (Matthew)
Rubio, A. (Ángel)

January 2018

Background: RNA-seq is a reference technology for determining alternative splicing at genome-wide le...

Additional file 2: of Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance

Alyssa Baccarella (3095256)
Claire Williams (2513419)
Jay Parrish (1834015)
Charles Kim (2529652)

November 2018

Sample combinations for each iteration at varying sample numbers. The same sample combinations were ...

Additional file 1: of Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers

Yu Fu (16582)
Pei-Hsuan Wu (5511056)
Timothy Beane (5511050)
Phillip Zamore (5511053)
Zhiping Weng (51233)

July 2018

Mapping and UMI statistics of (A) RNA-seq and (B) small RNA-seq data generated in this study. (XLSX ...

Additional file 13: of Conserved regulation of RNA processing in somatic cell reprogramming

Alexander Kanitz (121360)
Afzal Syed (6286067)
Keisuke Kaji (403022)
Mihaela Zavolan (16626)

February 2019

Top ranked alternative splicing events for human and mouse reprogramming. The file contains an XLSX ...

2

Michael C. Ryan
James Cleland
Ryangguk Kim
Wing Chung Wong
John N

October 2016

Summary: SpliceSeq is a resource for RNA-Seq data that provides a clear view of alternative splicing...

Additional file 1: of Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly

Yongsheng Bai (49362)
Jeff Kinne (3529151)
Lizhong Ding (3455855)
Ethan Rath (3455867)
Aaron Cox (4489708)
Siva Naidu (4489711)

October 2017

Comparison of running time and memory usage between RSR and RSF for 70 ENCODE samples. This file con...

Additional file 1: of Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data

Yongsheng Bai (49362)
Jeff Kinne (3529151)
Brandon Donham (3529148)
Feng Jiang (95012)
Lizhong Ding (3455855)
Justin Hassler (592429)
Randal Kaufman (3529154)

August 2016

Spliced regions identified by RSR for the Tg sample. This file contains all supplementary results fo...

Excel file containing RNA-seq results (ΔcamS versus WT, camSΔ69–391 versus WT, ΔcamS versus ΔcamS::camS).

Katrin Schilcher (17743038)
Morgan M. Severn (17743041)
Christian Jenul (17743044)
Young-Saeng C. Avina (17743047)
Rebecca A. Keogh (14636318)
Alexander R. Horswill (45837)

January 2024

Excel file containing RNA-seq results (ΔcamS versus WT, camSΔ69–391 versus WT, ΔcamS versus ΔcamS::c...

Additional file 1: of Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency

Scott Adamson (5331245)
Lijun Zhan (326110)
Brenton Graveley (5331248)

June 2018

This document contains Table S1., which kists the oligo sequences used to assemble the splicing repo...

Additional file 2: of SpliceV: analysis and publication quality printing of linear and circular RNA splicing, expression and regulation

Nathan Ungerleider (5598377)
Erik Flemington (404193)

May 2019

An example pipeline to generate the required files for SpliceV analysis. (PDF 148 kb

Additional file 1: of Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm

Juan Romero (516524)
MarĂa Ortiz-EstĂŠvez (5791583)
Ander Muniategui (183724)
Soraya Carrancio (341408)
Fernando de Miguel (5077766)
Fernando Carazo (5791574)
Luis Montuenga (3405611)
Remco Loos (5791577)
RubĂŠn PĂo (5791586)
Matthew Trotter (188553)
Angel Rubio (46993)

September 2018

Vignette on the comparison based on expression analysis. Figure S1 to S9. Experiment design and cont...

Additional file 3: of Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm

Juan Romero (516524)
MarĂa Ortiz-EstĂŠvez (5791583)
Ander Muniategui (183724)
Soraya Carrancio (341408)
Fernando de Miguel (5077766)
Fernando Carazo (5791574)
Luis Montuenga (3405611)
Remco Loos (5791577)
RubĂŠn PĂo (5791586)
Matthew Trotter (188553)
Angel Rubio (46993)

September 2018

Compressed file including the GTF files generated for the matched events. (ZIP 15 kb

Supplementary excel 1

Huo Lei (5245121)
Lei Wang (6656)
Zhaoyao Yang (5245118)
Pingyuan Li (5245112)
Dechun Geng (5245115)
Yaozeng Xu (5245109)

May 2018

This file contains all the difference expression genes from RNA-seq analysis. This file was made wit...

Additional file 2: of Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data

Yongsheng Bai (49362)
Jeff Kinne (3529151)
Brandon Donham (3529148)
Feng Jiang (95012)
Lizhong Ding (3455855)
Justin Hassler (592429)
Randal Kaufman (3529154)

August 2016

Spliced regions identified by RSR for the Dtt sample. This file contains all supplementary results f...

Additional file 2: of Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes

Boas Pucker (3202233)
Samuel Brockington (4959529)

December 2018

RNA-Seq data sets. List of Sequence Read Archive accession numbers of all included RNA-Seq data sets...

Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm

Romero, J.P. (Juan P.)
Ortiz-Estévez, M. (Maria)
Muniategui, A. (Ander)
Carrancio, S. (Soraya)
Miguel, F.J. (Fernando J.) de
Carazo Melo, F.(Fernando)
Montuenga-Badia, L.M. (Luis M.)
Loos, R. (Remco)
Pio, R. (Rubén)
Trotter, M. (Matthew)
Rubio, A. (Ángel)

January 2018

Background: RNA-seq is a reference technology for determining alternative splicing at genome-wide le...

Additional file 2: of Empirical assessment of the impact of sample number and read depth on RNA-Seq analysis workflow performance

Alyssa Baccarella (3095256)
Claire Williams (2513419)
Jay Parrish (1834015)
Charles Kim (2529652)

November 2018

Sample combinations for each iteration at varying sample numbers. The same sample combinations were ...

Additional file 1: of Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers

Yu Fu (16582)
Pei-Hsuan Wu (5511056)
Timothy Beane (5511050)
Phillip Zamore (5511053)
Zhiping Weng (51233)

July 2018

Mapping and UMI statistics of (A) RNA-seq and (B) small RNA-seq data generated in this study. (XLSX ...

Additional file 13: of Conserved regulation of RNA processing in somatic cell reprogramming

Alexander Kanitz (121360)
Afzal Syed (6286067)
Keisuke Kaji (403022)
Mihaela Zavolan (16626)

February 2019

Top ranked alternative splicing events for human and mouse reprogramming. The file contains an XLSX ...

2

Michael C. Ryan
James Cleland
Ryangguk Kim
Wing Chung Wong
John N

October 2016

Summary: SpliceSeq is a resource for RNA-Seq data that provides a clear view of alternative splicing...

Additional file 1: of Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly

Yongsheng Bai (49362)
Jeff Kinne (3529151)
Lizhong Ding (3455855)
Ethan Rath (3455867)
Aaron Cox (4489708)
Siva Naidu (4489711)

October 2017

Comparison of running time and memory usage between RSR and RSF for 70 ENCODE samples. This file con...

Additional file 1: of Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data

Yongsheng Bai (49362)
Jeff Kinne (3529151)
Brandon Donham (3529148)
Feng Jiang (95012)
Lizhong Ding (3455855)
Justin Hassler (592429)
Randal Kaufman (3529154)

August 2016

Spliced regions identified by RSR for the Tg sample. This file contains all supplementary results fo...

Excel file containing RNA-seq results (ΔcamS versus WT, camSΔ69–391 versus WT, ΔcamS versus ΔcamS::camS).

Katrin Schilcher (17743038)
Morgan M. Severn (17743041)
Christian Jenul (17743044)
Young-Saeng C. Avina (17743047)
Rebecca A. Keogh (14636318)
Alexander R. Horswill (45837)

January 2024

Excel file containing RNA-seq results (ΔcamS versus WT, camSΔ69–391 versus WT, ΔcamS versus ΔcamS::c...

Additional file 1: of Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency

Scott Adamson (5331245)
Lijun Zhan (326110)
Brenton Graveley (5331248)

June 2018

This document contains Table S1., which kists the oligo sequences used to assemble the splicing repo...

Additional file 2: of SpliceV: analysis and publication quality printing of linear and circular RNA splicing, expression and regulation

Nathan Ungerleider (5598377)
Erik Flemington (404193)

May 2019

An example pipeline to generate the required files for SpliceV analysis. (PDF 148 kb

Additional file 2: of Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm

Abstract

Extracted data

Additional file 2: of Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm

Abstract

Extracted data

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