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

Additional file 1: of Comprehensive off-target analysis of dCas9-SAM-mediated HIV reactivation via long noncoding RNA and mRNA profiling

Yonggang Zhang (38357)
Gustavo Arango (5735267)
Fang Li (41162)
Xiao Xiao (99147)
Raj Putatunda (4870147)
Jun Yu (5904)
Xiao-Feng Yang (177016)
Hong Wang (13528)
Layne Watson (3497636)
Liqing Zhang (16090)
Wenhui Hu (80326)

September 2018

Table S1. Statistics of RNA-Seq quality reads. Table S2. Mapping results. Table S3. Validation of dC...

Additional file 10: 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

Number of significant genes by number of biological replicates. Bar represents average number of sig...

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 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 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 1 of Expression and splicing mediate distinct biological signals

Søren Helweg Dam (17256847)
Lars Rønn Olsen (1633549)
Kristoffer Vitting-Seerup (15113390)

October 2023

Additional file 1: Figure S1. Summary of the manual literature review of articles from 2020 that ana...

Additional file 2: of RNA-seq assistant: machine learning based methods to identify more transcriptional regulated genes

Likai Wang (783629)
Yanpeng Xi (4288414)
Sibum Sung (3357308)
Hong Qiao (235938)

July 2018

Figure S1. RNA-seq quality detection of differential regulated genes in air and ethylene treatment. ...

Supplemental Data Set 1. Read Statistics of RNA-Seq Data and Computational Analysis of Transcriptome-Wide AS and Gene Expression.

Gabriele Drechsel (3252561)
André Kahles (481273)
Anil K. Kesarwani (3252549)
Eva Stauffer (3252555)
Jonas Behr (86040)
Philipp Drewe (3252552)
Gunnar Rätsch (54319)
Andreas Wachter (3252558)

October 2016

(A) Alignment statistics of all RNA-seq reads derived from Illumina sequencing. (B) - (E) Event base...

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...

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 3: of Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq

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

January 2017

Figure of similarity in performance characteristics of significant gene identification by limma and ...

Additional file 2: of Comprehensive off-target analysis of dCas9-SAM-mediated HIV reactivation via long noncoding RNA and mRNA profiling

Yonggang Zhang (38357)
Gustavo Arango (5735267)
Fang Li (41162)
Xiao Xiao (99147)
Raj Putatunda (4870147)
Jun Yu (5904)
Xiao-Feng Yang (177016)
Hong Wang (13528)
Layne Watson (3497636)
Liqing Zhang (16090)
Wenhui Hu (80326)

September 2018

Figure S1. Distributions of the mapped reads in the genome for the six samples. Figure S2. Workflow ...

Additional file 1:Table S1. of Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap

Shanrong Zhao (509890)
Ying Zhang (1235337)
William Gordon (150154)
Jie Quan (3549545)
Hualin Xi (78547)
Sarah Du (3549542)
David von Schack (227633)
Baohong Zhang (108942)

September 2015

Reports the related metrics for all eight RNA-seq samples, including library sizes, the mapping summ...

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 1: of RNA-seq assistant: machine learning based methods to identify more transcriptional regulated genes

Likai Wang (783629)
Yanpeng Xi (4288414)
Sibum Sung (3357308)
Hong Qiao (235938)

July 2018

Table S1. Primers for qPCR. Table S2. The list of all features considered prior to feature selection...

Additional file 1: of Comprehensive off-target analysis of dCas9-SAM-mediated HIV reactivation via long noncoding RNA and mRNA profiling

Yonggang Zhang (38357)
Gustavo Arango (5735267)
Fang Li (41162)
Xiao Xiao (99147)
Raj Putatunda (4870147)
Jun Yu (5904)
Xiao-Feng Yang (177016)
Hong Wang (13528)
Layne Watson (3497636)
Liqing Zhang (16090)
Wenhui Hu (80326)

September 2018

Table S1. Statistics of RNA-Seq quality reads. Table S2. Mapping results. Table S3. Validation of dC...

Additional file 10: 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

Number of significant genes by number of biological replicates. Bar represents average number of sig...

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 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 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 1 of Expression and splicing mediate distinct biological signals

Søren Helweg Dam (17256847)
Lars Rønn Olsen (1633549)
Kristoffer Vitting-Seerup (15113390)

October 2023

Additional file 1: Figure S1. Summary of the manual literature review of articles from 2020 that ana...

Additional file 2: of RNA-seq assistant: machine learning based methods to identify more transcriptional regulated genes

Likai Wang (783629)
Yanpeng Xi (4288414)
Sibum Sung (3357308)
Hong Qiao (235938)

July 2018

Figure S1. RNA-seq quality detection of differential regulated genes in air and ethylene treatment. ...

Supplemental Data Set 1. Read Statistics of RNA-Seq Data and Computational Analysis of Transcriptome-Wide AS and Gene Expression.

Gabriele Drechsel (3252561)
André Kahles (481273)
Anil K. Kesarwani (3252549)
Eva Stauffer (3252555)
Jonas Behr (86040)
Philipp Drewe (3252552)
Gunnar Rätsch (54319)
Andreas Wachter (3252558)

October 2016

(A) Alignment statistics of all RNA-seq reads derived from Illumina sequencing. (B) - (E) Event base...

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...

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 3: of Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq

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

January 2017

Figure of similarity in performance characteristics of significant gene identification by limma and ...

Additional file 2: of Comprehensive off-target analysis of dCas9-SAM-mediated HIV reactivation via long noncoding RNA and mRNA profiling

Yonggang Zhang (38357)
Gustavo Arango (5735267)
Fang Li (41162)
Xiao Xiao (99147)
Raj Putatunda (4870147)
Jun Yu (5904)
Xiao-Feng Yang (177016)
Hong Wang (13528)
Layne Watson (3497636)
Liqing Zhang (16090)
Wenhui Hu (80326)

September 2018

Figure S1. Distributions of the mapped reads in the genome for the six samples. Figure S2. Workflow ...

Additional file 1:Table S1. of Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap

Shanrong Zhao (509890)
Ying Zhang (1235337)
William Gordon (150154)
Jie Quan (3549545)
Hualin Xi (78547)
Sarah Du (3549542)
David von Schack (227633)
Baohong Zhang (108942)

September 2015

Reports the related metrics for all eight RNA-seq samples, including library sizes, the mapping summ...

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 1: of RNA-seq assistant: machine learning based methods to identify more transcriptional regulated genes

Likai Wang (783629)
Yanpeng Xi (4288414)
Sibum Sung (3357308)
Hong Qiao (235938)

July 2018

Table S1. Primers for qPCR. Table S2. The list of all features considered prior to feature selection...

Additional file 1: of Comprehensive off-target analysis of dCas9-SAM-mediated HIV reactivation via long noncoding RNA and mRNA profiling

Yonggang Zhang (38357)
Gustavo Arango (5735267)
Fang Li (41162)
Xiao Xiao (99147)
Raj Putatunda (4870147)
Jun Yu (5904)
Xiao-Feng Yang (177016)
Hong Wang (13528)
Layne Watson (3497636)
Liqing Zhang (16090)
Wenhui Hu (80326)

September 2018

Table S1. Statistics of RNA-Seq quality reads. Table S2. Mapping results. Table S3. Validation of dC...

Additional file 10: 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

Number of significant genes by number of biological replicates. Bar represents average number of sig...

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

Abstract

Extracted data

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

Abstract

Extracted data

Related items

Related items