Additional file 5: of Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos

Additional file 10: of Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish

Priyanjali Ghosh (5454407)
Jennifer Maurer (4968838)
Charles SagerstrĂśm (4968835)

June 2018

Figure S7. Scheme for generating gbx1 mutant line. (A) Schematic showing the 20 nucleotide (orange t...

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

Han Rauwerda
Johanna F. B. Pagano
Wim C. de Leeuw
Wim Ensink
Ulrike Nehrdich
Mark de Jong
Martijs Jonker
Herman P. Spaink
Timo M. Breit

April 2017

Abstract Background Recently, much progress has been made in the field of gene-expression in early e...

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 14: 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

High-variance genes of type five with a log2 variance > −1. On each page the left panel displays the...

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 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 15: 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

Comparison of this study with the zebrafish tomography study of [30] (study T), with the study on th...

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 18: 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

Example of the determination of a stopping point and a starting point. For an explanation see Method...

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

Rauwerda, H.
Pagano, J.F.B.
de Leeuw, W.C.
Ensink, W.
Nehrdich, U.
de Jong, M.
Jonker, M.
Spaink, H.P.
Breit, T.M.

April 2017

BACKGROUND: Recently, much progress has been made in the field of gene-expression in early embryogen...

Additional file 2: of Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish

Priyanjali Ghosh (5454407)
Jennifer Maurer (4968838)
Charles SagerstrĂśm (4968835)

June 2018

Table S1. Identification of additional r4, r5 and r6 genes. This file represents the data downloaded...

Additional file 3: Table S2. of Whole organism transcriptome analysis of zebrafish models of Bardet-Biedl Syndrome and Alström Syndrome provides mechanistic insight into shared and divergent phenotypes

Timothy Hostelley (3564659)
Sukanya Lodh (3564662)
Norann Zaghloul (3564656)

May 2016

Differentially expressed genes in BBS model. All genes exhibiting significant changes in bbs1-deplet...

Additional file 5: 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 S4. Enriched GO and INTERPRO domains for active gene group in zebrafish. (XLSX 15 kb

Additional file 8: Table S1. of Progenitor potential of nkx6.1-expressing cells throughout zebrafish life and during beta cell regeneration

Aurélie Ghaye (116951)
David Bergemann (3562187)
Estefania Tarifeño-Saldivia (3562202)
Lydie Flasse (3562190)
Virginie Von Berg (173736)
Bernard Peers (61486)
Marianne Voz (3562193)
Isabelle Manfroid (61481)

September 2015

Duct-specific genes listed by decreased expression level. We found 293 genes corresponding to the fo...

Functional mapping of the zebrafish early embryo proteome and transcriptome

Alli Shaik, Asfa
Wee, Sheena
Li, Rachel Hai Xia
Li, Zhen
Carney, Tom J.
Mathavan, Sinnakaruppan
Gunaratne, Jayantha

January 2014

Zebrafish is a popular system for studying vertebrate development and disease that shows high geneti...

Additional file 10: of Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish

Priyanjali Ghosh (5454407)
Jennifer Maurer (4968838)
Charles SagerstrĂśm (4968835)

June 2018

Figure S7. Scheme for generating gbx1 mutant line. (A) Schematic showing the 20 nucleotide (orange t...

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

Han Rauwerda
Johanna F. B. Pagano
Wim C. de Leeuw
Wim Ensink
Ulrike Nehrdich
Mark de Jong
Martijs Jonker
Herman P. Spaink
Timo M. Breit

April 2017

Abstract Background Recently, much progress has been made in the field of gene-expression in early e...

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 14: 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

High-variance genes of type five with a log2 variance > −1. On each page the left panel displays the...

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 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 15: 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

Comparison of this study with the zebrafish tomography study of [30] (study T), with the study on th...

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 18: 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

Example of the determination of a stopping point and a starting point. For an explanation see Method...

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

Rauwerda, H.
Pagano, J.F.B.
de Leeuw, W.C.
Ensink, W.
Nehrdich, U.
de Jong, M.
Jonker, M.
Spaink, H.P.
Breit, T.M.

April 2017

BACKGROUND: Recently, much progress has been made in the field of gene-expression in early embryogen...

Additional file 2: of Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish

Priyanjali Ghosh (5454407)
Jennifer Maurer (4968838)
Charles SagerstrĂśm (4968835)

June 2018

Table S1. Identification of additional r4, r5 and r6 genes. This file represents the data downloaded...

Additional file 3: Table S2. of Whole organism transcriptome analysis of zebrafish models of Bardet-Biedl Syndrome and Alström Syndrome provides mechanistic insight into shared and divergent phenotypes

Timothy Hostelley (3564659)
Sukanya Lodh (3564662)
Norann Zaghloul (3564656)

May 2016

Differentially expressed genes in BBS model. All genes exhibiting significant changes in bbs1-deplet...

Additional file 5: 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 S4. Enriched GO and INTERPRO domains for active gene group in zebrafish. (XLSX 15 kb

Additional file 8: Table S1. of Progenitor potential of nkx6.1-expressing cells throughout zebrafish life and during beta cell regeneration

Aurélie Ghaye (116951)
David Bergemann (3562187)
Estefania Tarifeño-Saldivia (3562202)
Lydie Flasse (3562190)
Virginie Von Berg (173736)
Bernard Peers (61486)
Marianne Voz (3562193)
Isabelle Manfroid (61481)

September 2015

Duct-specific genes listed by decreased expression level. We found 293 genes corresponding to the fo...

Functional mapping of the zebrafish early embryo proteome and transcriptome

Alli Shaik, Asfa
Wee, Sheena
Li, Rachel Hai Xia
Li, Zhen
Carney, Tom J.
Mathavan, Sinnakaruppan
Gunaratne, Jayantha

January 2014

Zebrafish is a popular system for studying vertebrate development and disease that shows high geneti...

Additional file 10: of Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish

Priyanjali Ghosh (5454407)
Jennifer Maurer (4968838)
Charles SagerstrĂśm (4968835)

June 2018

Figure S7. Scheme for generating gbx1 mutant line. (A) Schematic showing the 20 nucleotide (orange t...

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

Han Rauwerda
Johanna F. B. Pagano
Wim C. de Leeuw
Wim Ensink
Ulrike Nehrdich
Mark de Jong
Martijs Jonker
Herman P. Spaink
Timo M. Breit

April 2017

Abstract Background Recently, much progress has been made in the field of gene-expression in early e...

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

Abstract

Extracted data

Additional file 5: of Transcriptome dynamics in early zebrafish embryogenesis determined by high-resolution time course analysis of 180 successive, individual zebrafish embryos

Abstract

Extracted data

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