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

Additional file 2: 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

Excel file with characteristics of the validated events and PCR primers. (XLSX 27 kb

Additional file 4: of Conserved regulation of RNA processing in somatic cell reprogramming

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

February 2019

Table of comparisons for differential analyses. The file contains an XLSX spreadsheet describing sam...

Additional file 1: of XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data

Roelof Kluin (5820728)
Kristel Kemper (362317)
Thomas Kuilman (682262)
Julian de Ruiter (5820731)
Vivek Iyer (572160)
Josep Forment (5820734)
Paulien Cornelissen-Steijger (167454)
Iris de Rink (5820737)
Petra ter Brugge (1677586)
Ji-Ying Song (167443)
Sjoerd Klarenbeek (5820740)
Ultan McDermott (213251)
Jos Jonkers (13239)
Arno Velds (23633)
David Adams (202540)
Daniel Peeper (5820743)
Oscar Krijgsman (680688)

October 2018

Table S1. WGS of mouse strains mapped to human. Number of sequence reads from 3 mouse strains mapped...

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 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...

Additional file 4: 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

Statistics reported by RSR for 64 test cases for the Dtt sample. This file contains all supplementar...

Additional file 4: 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

U12-type and U2-type intron sequences used in the study. This file contains U12-type and U2-type 5â...

Additional file 1: of Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes

Boas Pucker (3202233)
Samuel Brockington (4959529)

December 2018

Analysed data sets. List of investigated genome sequences and corresponding annotation. Md5sums are ...

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...

Additional file 2: of Long genes and genes with multiple splice variants are enriched in pathways linked to cancer and other multigenic diseases

Aleksandr Sahakyan (3521390)
Shankar Balasubramanian (9301)

March 2016

The calculated lengths (nt) of all the mRNA-coding nuclear transcripts (GRCh37) along with the numbe...

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

Additional file 5: of Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes

Boas Pucker (3202233)
Samuel Brockington (4959529)

December 2018

Genome statistics. Statistical information about each analyzed genome sequence and the average value...

Additional file 1: of RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

Amy Webb (791450)
Audrey Papp (252886)
Amanda Curtis (3437192)
Leslie Newman (3437204)
Maciej Pietrzak (212740)
Michal Seweryn (791451)
Samuel Handelman (3437207)
Grzegorz Rempala (212741)
Daqing Wang (406452)
Erica Graziosa (3437201)
Rachel Tyndale (3437195)
Caryn Lerman (264866)
John Kelsoe (3437189)
Deborah Mash (3437198)
Wolfgang Sadee (179657)

November 2015

Table S1. Sequencing and mapping statistics. Listed are the sequencing details and mapping statistic...

Additional file 2: of CRISPR directed evolution of the spliceosome for resistance to splicing inhibitors

Haroon Butt (3864433)
Ayman Eid (777468)
Afaque Momin (6648473)
Jeremie Bazin (6648476)
Martin Crespi (231072)
Stefan Arold (487269)
Magdy Mahfouz (777477)

April 2019

Table S1. Sequences of sgRNAs with PAM targeting SF3B1. Table S2. List of primers annealed to synthe...

Additional file 2: 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

Excel file with characteristics of the validated events and PCR primers. (XLSX 27 kb

Additional file 4: of Conserved regulation of RNA processing in somatic cell reprogramming

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

February 2019

Table of comparisons for differential analyses. The file contains an XLSX spreadsheet describing sam...

Additional file 1: of XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data

Roelof Kluin (5820728)
Kristel Kemper (362317)
Thomas Kuilman (682262)
Julian de Ruiter (5820731)
Vivek Iyer (572160)
Josep Forment (5820734)
Paulien Cornelissen-Steijger (167454)
Iris de Rink (5820737)
Petra ter Brugge (1677586)
Ji-Ying Song (167443)
Sjoerd Klarenbeek (5820740)
Ultan McDermott (213251)
Jos Jonkers (13239)
Arno Velds (23633)
David Adams (202540)
Daniel Peeper (5820743)
Oscar Krijgsman (680688)

October 2018

Table S1. WGS of mouse strains mapped to human. Number of sequence reads from 3 mouse strains mapped...

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 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...

Additional file 4: 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

Statistics reported by RSR for 64 test cases for the Dtt sample. This file contains all supplementar...

Additional file 4: 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

U12-type and U2-type intron sequences used in the study. This file contains U12-type and U2-type 5â...

Additional file 1: of Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes

Boas Pucker (3202233)
Samuel Brockington (4959529)

December 2018

Analysed data sets. List of investigated genome sequences and corresponding annotation. Md5sums are ...

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...

Additional file 2: of Long genes and genes with multiple splice variants are enriched in pathways linked to cancer and other multigenic diseases

Aleksandr Sahakyan (3521390)
Shankar Balasubramanian (9301)

March 2016

The calculated lengths (nt) of all the mRNA-coding nuclear transcripts (GRCh37) along with the numbe...

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

Additional file 5: of Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes

Boas Pucker (3202233)
Samuel Brockington (4959529)

December 2018

Genome statistics. Statistical information about each analyzed genome sequence and the average value...

Additional file 1: of RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

Amy Webb (791450)
Audrey Papp (252886)
Amanda Curtis (3437192)
Leslie Newman (3437204)
Maciej Pietrzak (212740)
Michal Seweryn (791451)
Samuel Handelman (3437207)
Grzegorz Rempala (212741)
Daqing Wang (406452)
Erica Graziosa (3437201)
Rachel Tyndale (3437195)
Caryn Lerman (264866)
John Kelsoe (3437189)
Deborah Mash (3437198)
Wolfgang Sadee (179657)

November 2015

Table S1. Sequencing and mapping statistics. Listed are the sequencing details and mapping statistic...

Additional file 2: of CRISPR directed evolution of the spliceosome for resistance to splicing inhibitors

Haroon Butt (3864433)
Ayman Eid (777468)
Afaque Momin (6648473)
Jeremie Bazin (6648476)
Martin Crespi (231072)
Stefan Arold (487269)
Magdy Mahfouz (777477)

April 2019

Table S1. Sequences of sgRNAs with PAM targeting SF3B1. Table S2. List of primers annealed to synthe...

Additional file 2: 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

Excel file with characteristics of the validated events and PCR primers. (XLSX 27 kb

Additional file 4: of Conserved regulation of RNA processing in somatic cell reprogramming

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

February 2019

Table of comparisons for differential analyses. The file contains an XLSX spreadsheet describing sam...

Additional file 1: of XenofilteR: computational deconvolution of mouse and human reads in tumor xenograft sequence data

Roelof Kluin (5820728)
Kristel Kemper (362317)
Thomas Kuilman (682262)
Julian de Ruiter (5820731)
Vivek Iyer (572160)
Josep Forment (5820734)
Paulien Cornelissen-Steijger (167454)
Iris de Rink (5820737)
Petra ter Brugge (1677586)
Ji-Ying Song (167443)
Sjoerd Klarenbeek (5820740)
Ultan McDermott (213251)
Jos Jonkers (13239)
Arno Velds (23633)
David Adams (202540)
Daniel Peeper (5820743)
Oscar Krijgsman (680688)

October 2018

Table S1. WGS of mouse strains mapped to human. Number of sequence reads from 3 mouse strains mapped...

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

Abstract

Extracted data

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

Abstract

Extracted data

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