Additional file 1: of Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration

Additional file 9: of Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos

Han Rauwerda (563288)
Johanna Pagano (3919814)
Wim de Leeuw (3919811)
Wim Ensink (847356)
Ulrike Nehrdich (847358)
Mark de Jong (125452)
Martijs Jonker (715705)
Herman Spaink (3919817)
Timo Breit (3919808)

April 2017

Intensity distributions per type. A) Left panel: top 10 highest gene expression intensities per type...

Additional file 1: of Long non-coding RNA ZEB1-AS1 regulates miR-200b/FSCN1 signaling and enhances migration and invasion induced by TGF-Î˛1 in bladder cancer cells

Ruxu Gao (6417989)
Naiwen Zhang (6417992)
Jianyu Yang (651828)
Yuyan Zhu (46381)
Zhe Zhang (81603)
Jianfeng Wang (232744)
Xiaolong Xu (833921)
Zeliang Li (4689613)
Xiankui Liu (4689610)
Zhenhua Li (312199)
Jun Li (6494)
Chuize Kong (4118263)
Jianbin Bi (4689616)

March 2019

Table S1. Sequences of RNAi for transfection. Table S2. Sequences of primer pairs for qPCR. Table S3...

Additional file 2: of Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity

Beena Kamath-Rayne (3401888)
Yina Du (3513809)
Maria Hughes (3513812)
Erin Wagner (566195)
Louis Muglia (224816)
Emily DeFranco (706803)
Jeffrey Whitsett (3513806)
Nathan Salomonis (1526)
Yan Xu (14594)

October 2015

Detection of fetal specific sex chromosome associated gene expression in amniotic fluid RNA-Seq. (PD...

Additional file 4: of Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration

Joseph Brown (1784605)
Aaron Phillips (643730)
David Lewis (245511)
Michael-Andres Mans (6711890)
Yvonne Chang (4377181)
Robert Tanguay (2561101)
Elena Peterson (6711893)
Katrina Waters (2416138)
Susan Tilton (3404285)

May 2019

Human-zebrafish integration BRM output. Output from BRM after integrating human and zebrafish mRNA f...

Additional file 6: of Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration

Joseph Brown (1784605)
Aaron Phillips (643730)
David Lewis (245511)
Michael-Andres Mans (6711890)
Yvonne Chang (4377181)
Robert Tanguay (2561101)
Elena Peterson (6711893)
Katrina Waters (2416138)
Susan Tilton (3404285)

May 2019

Zebrafish miRNA list. List of differentially expressed miRNA in zebrafish after treatment with BAP. ...

Additional file 5: of Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration

Joseph Brown (1784605)
Aaron Phillips (643730)
David Lewis (245511)
Michael-Andres Mans (6711890)
Yvonne Chang (4377181)
Robert Tanguay (2561101)
Elena Peterson (6711893)
Katrina Waters (2416138)
Susan Tilton (3404285)

May 2019

HBEC miRNA list. List of differentially expressed miRNA in HBEC after treatment with BAP. (TXT 953 b...

Additional file 2: of Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration

Joseph Brown (1784605)
Aaron Phillips (643730)
David Lewis (245511)
Michael-Andres Mans (6711890)
Yvonne Chang (4377181)
Robert Tanguay (2561101)
Elena Peterson (6711893)
Katrina Waters (2416138)
Susan Tilton (3404285)

May 2019

HBEC mRNA list. List of differentially expressed mRNA in HBEC after treatment with BAP. (TXT 336 kb

Additional file 1: of A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes

Marzena Mura (6309653)
Roman Jaksik (6309656)
Anna Lalik (6309659)
Krzysztof Biernacki (1695766)
Marek Kimmel (39636)
Joanna Rzeszowska-Wolny (286036)
Krzysztof Fujarewicz (286030)

February 2019

Table S1. Summary of datasetÂ at our disposal downloaded from ArrayExpress database. Table includes ...

Additional file 1: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Hannah Dueck (3461837)
Rizi Ai (2343607)
Adrian Camarena (3461816)
Bo Ding (210928)
Reymundo Dominguez (3461819)
Oleg Evgrafov (392965)
Jian-Bing Fan (28237)
Stephen Fisher (3461825)
Jennifer Herstein (3461804)
Tae Kim (3405566)
Jae Kim (2100565)
Ming-Yi Lin (237662)
Rui Liu (54031)
William Mack (3461807)
Sean McGroty (3461831)
Joseph Nguyen (3461810)
Neeraj Salathia (18709)
Jamie Shallcross (3461834)
Tade Souaiaia (3291015)
Jennifer Spaethling (3461813)
Christopher Walker (200465)
Jinhui Wang (37220)
Kai Wang (21246)
Wei Wang (17594)
Andre Wildberg (3461828)
Lina Zheng (331151)
Robert Chow (3443600)
James Eberwine (253973)
James Knowles (3461822)
Kun Zhang (108291)
Junhyong Kim (6423)

November 2016

Control dataset sample identification, protocol information, and RNA sequencing stats. Experimental ...

Additional file 2: of Efficient identification of CRISPR/Cas9-induced insertions/deletions by direct germline screening in zebrafish

Isabel Brocal (436318)
Richard White (138360)
Christopher Dooley (23947)
Samantha Carruthers (63033)
Richard Clark (45325)
Amanda Hall (210816)
Elisabeth Busch-Nentwich (23944)
Derek Stemple (183414)
Ross Kettleborough (3474797)

March 2016

Tutorial for the bioinformatics including sgRNA/primer deisgn and MiSeq analysis. (PDF 7778Â kb

Additional file 1: of Network analysis reveals stage-specific changes in zebrafish embryo development using time course whole transcriptome profiling and prior biological knowledge

Yuji Zhang (250069)

August 2015

A list of altered genes identified along with the days on which they were differentially expressed. ...

Additional file 1: of Predicting microRNA targeting efficacy in Drosophila

Vikram Agarwal (5560100)
Alexander Subtelny (4558381)
Prathapan Thiru (5820533)
Igor Ulitsky (28697)
David Bartel (4558375)

October 2018

Table S1. Processed mRNA abundances (measured in fragments per kilobase per million mapped reads (FP...

Additional file 12: of Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos

Han Rauwerda (563288)
Johanna Pagano (3919814)
Wim de Leeuw (3919811)
Wim Ensink (847356)
Ulrike Nehrdich (847358)
Mark de Jong (125452)
Martijs Jonker (715705)
Herman Spaink (3919817)
Timo Breit (3919808)

April 2017

Multi-level genes. On each page the left panel displays the expression intensities of a gene in deve...

Additional file 4: of Reprogramming histone modification patterns to coordinate gene expression in early zebrafish embryos

Wei Zhu (23646)
Xiaocui Xu (6525593)
Xinxin Wang (134010)
Jiang Liu (197069)

March 2019

Table S3. Enriched GO and INTERPRO domains for co-occupied gene group in zebrafish. (XLSX 11 kb

Additional file 2: of Determination of dosage compensation and comparison of gene expression in a triploid hybrid fish

Li Ren (417022)
Chenchen Tang (3620012)
Wuhui Li (3483701)
Jialin Cui (3620009)
Xingjun Tan (3620006)
Yafeng Xiong (3620003)
Jie Chen (5892)
Jun Wang (5906)
Jun Xiao (179459)
Yi Zhou (2723)
Jing Wang (1228470)
Min Tao (143985)
Chun Zhang (29010)
Shaojun Liu (282495)

January 2017

Gene ontology (GO) assignments for the GC, BSB and GB. GO assignments (level 2) were used to predict...

Additional file 9: of Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos

Han Rauwerda (563288)
Johanna Pagano (3919814)
Wim de Leeuw (3919811)
Wim Ensink (847356)
Ulrike Nehrdich (847358)
Mark de Jong (125452)
Martijs Jonker (715705)
Herman Spaink (3919817)
Timo Breit (3919808)

April 2017

Intensity distributions per type. A) Left panel: top 10 highest gene expression intensities per type...

Additional file 1: of Long non-coding RNA ZEB1-AS1 regulates miR-200b/FSCN1 signaling and enhances migration and invasion induced by TGF-Î˛1 in bladder cancer cells

Ruxu Gao (6417989)
Naiwen Zhang (6417992)
Jianyu Yang (651828)
Yuyan Zhu (46381)
Zhe Zhang (81603)
Jianfeng Wang (232744)
Xiaolong Xu (833921)
Zeliang Li (4689613)
Xiankui Liu (4689610)
Zhenhua Li (312199)
Jun Li (6494)
Chuize Kong (4118263)
Jianbin Bi (4689616)

March 2019

Table S1. Sequences of RNAi for transfection. Table S2. Sequences of primer pairs for qPCR. Table S3...

Additional file 2: of Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity

Beena Kamath-Rayne (3401888)
Yina Du (3513809)
Maria Hughes (3513812)
Erin Wagner (566195)
Louis Muglia (224816)
Emily DeFranco (706803)
Jeffrey Whitsett (3513806)
Nathan Salomonis (1526)
Yan Xu (14594)

October 2015

Detection of fetal specific sex chromosome associated gene expression in amniotic fluid RNA-Seq. (PD...

Additional file 4: of Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration

Joseph Brown (1784605)
Aaron Phillips (643730)
David Lewis (245511)
Michael-Andres Mans (6711890)
Yvonne Chang (4377181)
Robert Tanguay (2561101)
Elena Peterson (6711893)
Katrina Waters (2416138)
Susan Tilton (3404285)

May 2019

Human-zebrafish integration BRM output. Output from BRM after integrating human and zebrafish mRNA f...

Additional file 6: of Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration

Joseph Brown (1784605)
Aaron Phillips (643730)
David Lewis (245511)
Michael-Andres Mans (6711890)
Yvonne Chang (4377181)
Robert Tanguay (2561101)
Elena Peterson (6711893)
Katrina Waters (2416138)
Susan Tilton (3404285)

May 2019

Zebrafish miRNA list. List of differentially expressed miRNA in zebrafish after treatment with BAP. ...

Additional file 5: of Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration

Joseph Brown (1784605)
Aaron Phillips (643730)
David Lewis (245511)
Michael-Andres Mans (6711890)
Yvonne Chang (4377181)
Robert Tanguay (2561101)
Elena Peterson (6711893)
Katrina Waters (2416138)
Susan Tilton (3404285)

May 2019

HBEC miRNA list. List of differentially expressed miRNA in HBEC after treatment with BAP. (TXT 953 b...

Additional file 2: of Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration

Joseph Brown (1784605)
Aaron Phillips (643730)
David Lewis (245511)
Michael-Andres Mans (6711890)
Yvonne Chang (4377181)
Robert Tanguay (2561101)
Elena Peterson (6711893)
Katrina Waters (2416138)
Susan Tilton (3404285)

May 2019

HBEC mRNA list. List of differentially expressed mRNA in HBEC after treatment with BAP. (TXT 336 kb

Additional file 1: of A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes

Marzena Mura (6309653)
Roman Jaksik (6309656)
Anna Lalik (6309659)
Krzysztof Biernacki (1695766)
Marek Kimmel (39636)
Joanna Rzeszowska-Wolny (286036)
Krzysztof Fujarewicz (286030)

February 2019

Table S1. Summary of datasetÂ at our disposal downloaded from ArrayExpress database. Table includes ...

Additional file 1: of Assessing characteristics of RNA amplification methods for single cell RNA sequencing

Hannah Dueck (3461837)
Rizi Ai (2343607)
Adrian Camarena (3461816)
Bo Ding (210928)
Reymundo Dominguez (3461819)
Oleg Evgrafov (392965)
Jian-Bing Fan (28237)
Stephen Fisher (3461825)
Jennifer Herstein (3461804)
Tae Kim (3405566)
Jae Kim (2100565)
Ming-Yi Lin (237662)
Rui Liu (54031)
William Mack (3461807)
Sean McGroty (3461831)
Joseph Nguyen (3461810)
Neeraj Salathia (18709)
Jamie Shallcross (3461834)
Tade Souaiaia (3291015)
Jennifer Spaethling (3461813)
Christopher Walker (200465)
Jinhui Wang (37220)
Kai Wang (21246)
Wei Wang (17594)
Andre Wildberg (3461828)
Lina Zheng (331151)
Robert Chow (3443600)
James Eberwine (253973)
James Knowles (3461822)
Kun Zhang (108291)
Junhyong Kim (6423)

November 2016

Control dataset sample identification, protocol information, and RNA sequencing stats. Experimental ...

Additional file 2: of Efficient identification of CRISPR/Cas9-induced insertions/deletions by direct germline screening in zebrafish

Isabel Brocal (436318)
Richard White (138360)
Christopher Dooley (23947)
Samantha Carruthers (63033)
Richard Clark (45325)
Amanda Hall (210816)
Elisabeth Busch-Nentwich (23944)
Derek Stemple (183414)
Ross Kettleborough (3474797)

March 2016

Tutorial for the bioinformatics including sgRNA/primer deisgn and MiSeq analysis. (PDF 7778Â kb

Additional file 1: of Network analysis reveals stage-specific changes in zebrafish embryo development using time course whole transcriptome profiling and prior biological knowledge

Yuji Zhang (250069)

August 2015

A list of altered genes identified along with the days on which they were differentially expressed. ...

Additional file 1: of Predicting microRNA targeting efficacy in Drosophila

Vikram Agarwal (5560100)
Alexander Subtelny (4558381)
Prathapan Thiru (5820533)
Igor Ulitsky (28697)
David Bartel (4558375)

October 2018

Table S1. Processed mRNA abundances (measured in fragments per kilobase per million mapped reads (FP...

Additional file 12: of Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos

Han Rauwerda (563288)
Johanna Pagano (3919814)
Wim de Leeuw (3919811)
Wim Ensink (847356)
Ulrike Nehrdich (847358)
Mark de Jong (125452)
Martijs Jonker (715705)
Herman Spaink (3919817)
Timo Breit (3919808)

April 2017

Multi-level genes. On each page the left panel displays the expression intensities of a gene in deve...

Additional file 4: of Reprogramming histone modification patterns to coordinate gene expression in early zebrafish embryos

Wei Zhu (23646)
Xiaocui Xu (6525593)
Xinxin Wang (134010)
Jiang Liu (197069)

March 2019

Table S3. Enriched GO and INTERPRO domains for co-occupied gene group in zebrafish. (XLSX 11 kb

Additional file 2: of Determination of dosage compensation and comparison of gene expression in a triploid hybrid fish

Li Ren (417022)
Chenchen Tang (3620012)
Wuhui Li (3483701)
Jialin Cui (3620009)
Xingjun Tan (3620006)
Yafeng Xiong (3620003)
Jie Chen (5892)
Jun Wang (5906)
Jun Xiao (179459)
Yi Zhou (2723)
Jing Wang (1228470)
Min Tao (143985)
Chun Zhang (29010)
Shaojun Liu (282495)

January 2017

Gene ontology (GO) assignments for the GC, BSB and GB. GO assignments (level 2) were used to predict...

Additional file 9: of Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos

Han Rauwerda (563288)
Johanna Pagano (3919814)
Wim de Leeuw (3919811)
Wim Ensink (847356)
Ulrike Nehrdich (847358)
Mark de Jong (125452)
Martijs Jonker (715705)
Herman Spaink (3919817)
Timo Breit (3919808)

April 2017

Intensity distributions per type. A) Left panel: top 10 highest gene expression intensities per type...

Additional file 1: of Long non-coding RNA ZEB1-AS1 regulates miR-200b/FSCN1 signaling and enhances migration and invasion induced by TGF-Î˛1 in bladder cancer cells

Ruxu Gao (6417989)
Naiwen Zhang (6417992)
Jianyu Yang (651828)
Yuyan Zhu (46381)
Zhe Zhang (81603)
Jianfeng Wang (232744)
Xiaolong Xu (833921)
Zeliang Li (4689613)
Xiankui Liu (4689610)
Zhenhua Li (312199)
Jun Li (6494)
Chuize Kong (4118263)
Jianbin Bi (4689616)

March 2019

Table S1. Sequences of RNAi for transfection. Table S2. Sequences of primer pairs for qPCR. Table S3...

Additional file 2: of Systems biology evaluation of cell-free amniotic fluid transcriptome of term and preterm infants to detect fetal maturity

Beena Kamath-Rayne (3401888)
Yina Du (3513809)
Maria Hughes (3513812)
Erin Wagner (566195)
Louis Muglia (224816)
Emily DeFranco (706803)
Jeffrey Whitsett (3513806)
Nathan Salomonis (1526)
Yan Xu (14594)

October 2015

Detection of fetal specific sex chromosome associated gene expression in amniotic fluid RNA-Seq. (PD...

Additional file 1: of Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration

Abstract

Extracted data

Additional file 1: of Bioinformatics Resource Manager: a systems biology web tool for microRNA and omics data integration

Abstract

Extracted data

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