Additional file 6: Figure S9. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Additional file 4: Figure S4. of Two maternal duplications involving the CDKN1C gene are associated with contrasting growth phenotypes

Susanne Boonen (3420221)
Andrea Freschi (3420212)
Rikke Christensen (32108)
Federica Valente (3420209)
Dorte Lildballe (3420215)
Lucia Perone (3420218)
Orazio Palumbo (174177)
Massimo Carella (174251)
Niels Uldbjerg (500176)
Angela Sparago (272242)
Andrea Riccio (272246)
Flavia Cerrato (272244)

June 2016

FISH analysis on metaphase nuclei (top panel) of cultured cells derived from the umbilical cord of t...

Additional file 8: Figure S8. of Two maternal duplications involving the CDKN1C gene are associated with contrasting growth phenotypes

Susanne Boonen (3420221)
Andrea Freschi (3420212)
Rikke Christensen (32108)
Federica Valente (3420209)
Dorte Lildballe (3420215)
Lucia Perone (3420218)
Orazio Palumbo (174177)
Massimo Carella (174251)
Niels Uldbjerg (500176)
Angela Sparago (272242)
Andrea Riccio (272246)
Flavia Cerrato (272244)

June 2016

FISH analysis on metaphase nuclei (top panel) of cultured cells derived from peripheral blood leukoc...

Additional file 4: Figure S3. of Karyotype features of trematode Himasthla elongata

Anna Solovyeva (3456860)
Vera Stefanova (3456854)
Olga Podgornaya (297493)
Serghei Demin (3456857)

April 2016

Correspondence of Ag-NOR-staining and rDNA FISH signals at aneuploid metaphase spread of H. elongata...

Additional file 7: Figure S10. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Yoichiro Nakatani (10095)
Cecilia Mello (3577394)
Shin-ichi Hashimoto (26882)
Atsuko Shimada (247053)
Ryohei Nakamura (3577397)
Tatsuya Tsukahara (3577400)
Wei Qu (268253)
Jun Yoshimura (280993)
Yutaka Suzuki (1379)
Sumio Sugano (1380)
Hiroyuki Takeda (247055)
Andrew Fire (17358)
Shinichi Morishita (10016)

November 2015

Atypical evolution around nucleocyclic TSSs in liver. The definitions of graphs are similar to those...

Additional file 4: Figure S3. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Yoichiro Nakatani (10095)
Cecilia Mello (3577394)
Shin-ichi Hashimoto (26882)
Atsuko Shimada (247053)
Ryohei Nakamura (3577397)
Tatsuya Tsukahara (3577400)
Wei Qu (268253)
Jun Yoshimura (280993)
Yutaka Suzuki (1379)
Sumio Sugano (1380)
Hiroyuki Takeda (247055)
Andrew Fire (17358)
Shinichi Morishita (10016)

November 2015

Schematic illustration of asymmetric base composition coinciding with arrays of positioned nucleosom...

Additional file 2: Figure S4. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Yoichiro Nakatani (10095)
Cecilia Mello (3577394)
Shin-ichi Hashimoto (26882)
Atsuko Shimada (247053)
Ryohei Nakamura (3577397)
Tatsuya Tsukahara (3577400)
Wei Qu (268253)
Jun Yoshimura (280993)
Yutaka Suzuki (1379)
Sumio Sugano (1380)
Hiroyuki Takeda (247055)
Andrew Fire (17358)
Shinichi Morishita (10016)

November 2015

Characteristics of nucleocyclic TSSs in the blastulae. a. Representative TSSs in blastulae are clust...

Additional file 8: Figure S7. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Yoichiro Nakatani (10095)
Cecilia Mello (3577394)
Shin-ichi Hashimoto (26882)
Atsuko Shimada (247053)
Ryohei Nakamura (3577397)
Tatsuya Tsukahara (3577400)
Wei Qu (268253)
Jun Yoshimura (280993)
Yutaka Suzuki (1379)
Sumio Sugano (1380)
Hiroyuki Takeda (247055)
Andrew Fire (17358)
Shinichi Morishita (10016)

November 2015

Single nucleotide mutation rates and indel rates at positions within 500 bp around nucleocyclic/non-...

Additional file 3: Figure S5. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Yoichiro Nakatani (10095)
Cecilia Mello (3577394)
Shin-ichi Hashimoto (26882)
Atsuko Shimada (247053)
Ryohei Nakamura (3577397)
Tatsuya Tsukahara (3577400)
Wei Qu (268253)
Jun Yoshimura (280993)
Yutaka Suzuki (1379)
Sumio Sugano (1380)
Hiroyuki Takeda (247055)
Andrew Fire (17358)
Shinichi Morishita (10016)

November 2015

Characteristics of nucleocyclic TSSs in the liver. a-d. The definitions are similar to those in Figu...

Additional file 1: Figure S1. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Yoichiro Nakatani (10095)
Cecilia Mello (3577394)
Shin-ichi Hashimoto (26882)
Atsuko Shimada (247053)
Ryohei Nakamura (3577397)
Tatsuya Tsukahara (3577400)
Wei Qu (268253)
Jun Yoshimura (280993)
Yutaka Suzuki (1379)
Sumio Sugano (1380)
Hiroyuki Takeda (247055)
Andrew Fire (17358)
Shinichi Morishita (10016)

November 2015

a. Phylogenetic tree of HNI, Hd-rR, and HSOK, deriving respectively from northern Japanese, southern...

Additional file 10: Figure S11. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Yoichiro Nakatani (10095)
Cecilia Mello (3577394)
Shin-ichi Hashimoto (26882)
Atsuko Shimada (247053)
Ryohei Nakamura (3577397)
Tatsuya Tsukahara (3577400)
Wei Qu (268253)
Jun Yoshimura (280993)
Yutaka Suzuki (1379)
Sumio Sugano (1380)
Hiroyuki Takeda (247055)
Andrew Fire (17358)
Shinichi Morishita (10016)

November 2015

Possible effect of transcription-coupled repair (TCR). a-c. We observed a significant excess of C to...

Additional file 11: Figure S2. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Yoichiro Nakatani (10095)
Cecilia Mello (3577394)
Shin-ichi Hashimoto (26882)
Atsuko Shimada (247053)
Ryohei Nakamura (3577397)
Tatsuya Tsukahara (3577400)
Wei Qu (268253)
Jun Yoshimura (280993)
Yutaka Suzuki (1379)
Sumio Sugano (1380)
Hiroyuki Takeda (247055)
Andrew Fire (17358)
Shinichi Morishita (10016)

November 2015

Estimating the average nucleosome core fragment length L. a. We calculated A/T mononucleotide distri...

Additional file 8: Figure S5. of Germ cell and tumor associated piRNAs in the medaka and Xiphophorus melanoma models

Susanne Kneitz (114893)
Rasmi R. Mishra (3541253)
Domitille Chalopin (668693)
John Postlethwait (841459)
Wesley C. Warren (230513)
Ronald B. Walter (225642)
Manfred Schartl (75405)

May 2016

Venn diagram of numbers of genes mapping to a piRNA. To compare gene lists, human homologes of medak...

Additional file 2: Figure S2. of Sox5 is involved in germ-cell regulation and sex determination in medaka following co-option of nested transposable elements

Manfred Schartl (75405)
Susanne Schories (4805310)
Yuko Wakamatsu (261917)
Yusuke Nagao (546940)
Hisashi Hashimoto (261854)
ChloĂŠ Bertin (4805313)
Brigitte Mourot (674108)
Cornelia Schmidt (253342)
Dagmar Wilhelm (105377)
Lazaro Centanin (243124)
Yann Guiguen (65559)
Amaury Herpin (80760)

January 2018

Comparison of medaka Rex1 reverse-transcriptase (RT) sequence with other non-LTR retrotransposons. R...

Additional file 6: of Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development

P. Fabre (5754794)
M. Leleu (5754797)
B. Mascrez (5754800)
Q. Lo Giudice (5754803)
J. Cobb (5754806)
D. Duboule (5754812)

September 2018

Figure S5. Cyclone analysis of the cell cycle in single cells from autopod and zeugopod. A-B. Graphi...

Additional file 1: of Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye

Richard Harrington (499440)
Brant Faircloth (3250557)
Ron Eytan (3575135)
W. Smith (3575132)
Thomas Near (3575129)
Michael Alfaro (762174)
Matt Friedman (453708)

October 2016

Extended descriptions of protocols for DNA isolation, library preparation, sequencing, and data pipe...

Additional file 4: Figure S4. of Two maternal duplications involving the CDKN1C gene are associated with contrasting growth phenotypes

Susanne Boonen (3420221)
Andrea Freschi (3420212)
Rikke Christensen (32108)
Federica Valente (3420209)
Dorte Lildballe (3420215)
Lucia Perone (3420218)
Orazio Palumbo (174177)
Massimo Carella (174251)
Niels Uldbjerg (500176)
Angela Sparago (272242)
Andrea Riccio (272246)
Flavia Cerrato (272244)

June 2016

FISH analysis on metaphase nuclei (top panel) of cultured cells derived from the umbilical cord of t...

Additional file 8: Figure S8. of Two maternal duplications involving the CDKN1C gene are associated with contrasting growth phenotypes

Susanne Boonen (3420221)
Andrea Freschi (3420212)
Rikke Christensen (32108)
Federica Valente (3420209)
Dorte Lildballe (3420215)
Lucia Perone (3420218)
Orazio Palumbo (174177)
Massimo Carella (174251)
Niels Uldbjerg (500176)
Angela Sparago (272242)
Andrea Riccio (272246)
Flavia Cerrato (272244)

June 2016

FISH analysis on metaphase nuclei (top panel) of cultured cells derived from peripheral blood leukoc...

Additional file 4: Figure S3. of Karyotype features of trematode Himasthla elongata

Anna Solovyeva (3456860)
Vera Stefanova (3456854)
Olga Podgornaya (297493)
Serghei Demin (3456857)

April 2016

Correspondence of Ag-NOR-staining and rDNA FISH signals at aneuploid metaphase spread of H. elongata...

Additional file 7: Figure S10. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Yoichiro Nakatani (10095)
Cecilia Mello (3577394)
Shin-ichi Hashimoto (26882)
Atsuko Shimada (247053)
Ryohei Nakamura (3577397)
Tatsuya Tsukahara (3577400)
Wei Qu (268253)
Jun Yoshimura (280993)
Yutaka Suzuki (1379)
Sumio Sugano (1380)
Hiroyuki Takeda (247055)
Andrew Fire (17358)
Shinichi Morishita (10016)

November 2015

Atypical evolution around nucleocyclic TSSs in liver. The definitions of graphs are similar to those...

Additional file 4: Figure S3. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Yoichiro Nakatani (10095)
Cecilia Mello (3577394)
Shin-ichi Hashimoto (26882)
Atsuko Shimada (247053)
Ryohei Nakamura (3577397)
Tatsuya Tsukahara (3577400)
Wei Qu (268253)
Jun Yoshimura (280993)
Yutaka Suzuki (1379)
Sumio Sugano (1380)
Hiroyuki Takeda (247055)
Andrew Fire (17358)
Shinichi Morishita (10016)

November 2015

Schematic illustration of asymmetric base composition coinciding with arrays of positioned nucleosom...

Additional file 2: Figure S4. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Yoichiro Nakatani (10095)
Cecilia Mello (3577394)
Shin-ichi Hashimoto (26882)
Atsuko Shimada (247053)
Ryohei Nakamura (3577397)
Tatsuya Tsukahara (3577400)
Wei Qu (268253)
Jun Yoshimura (280993)
Yutaka Suzuki (1379)
Sumio Sugano (1380)
Hiroyuki Takeda (247055)
Andrew Fire (17358)
Shinichi Morishita (10016)

November 2015

Characteristics of nucleocyclic TSSs in the blastulae. a. Representative TSSs in blastulae are clust...

Additional file 8: Figure S7. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Yoichiro Nakatani (10095)
Cecilia Mello (3577394)
Shin-ichi Hashimoto (26882)
Atsuko Shimada (247053)
Ryohei Nakamura (3577397)
Tatsuya Tsukahara (3577400)
Wei Qu (268253)
Jun Yoshimura (280993)
Yutaka Suzuki (1379)
Sumio Sugano (1380)
Hiroyuki Takeda (247055)
Andrew Fire (17358)
Shinichi Morishita (10016)

November 2015

Single nucleotide mutation rates and indel rates at positions within 500 bp around nucleocyclic/non-...

Additional file 3: Figure S5. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Yoichiro Nakatani (10095)
Cecilia Mello (3577394)
Shin-ichi Hashimoto (26882)
Atsuko Shimada (247053)
Ryohei Nakamura (3577397)
Tatsuya Tsukahara (3577400)
Wei Qu (268253)
Jun Yoshimura (280993)
Yutaka Suzuki (1379)
Sumio Sugano (1380)
Hiroyuki Takeda (247055)
Andrew Fire (17358)
Shinichi Morishita (10016)

November 2015

Characteristics of nucleocyclic TSSs in the liver. a-d. The definitions are similar to those in Figu...

Additional file 1: Figure S1. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Yoichiro Nakatani (10095)
Cecilia Mello (3577394)
Shin-ichi Hashimoto (26882)
Atsuko Shimada (247053)
Ryohei Nakamura (3577397)
Tatsuya Tsukahara (3577400)
Wei Qu (268253)
Jun Yoshimura (280993)
Yutaka Suzuki (1379)
Sumio Sugano (1380)
Hiroyuki Takeda (247055)
Andrew Fire (17358)
Shinichi Morishita (10016)

November 2015

a. Phylogenetic tree of HNI, Hd-rR, and HSOK, deriving respectively from northern Japanese, southern...

Additional file 10: Figure S11. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Yoichiro Nakatani (10095)
Cecilia Mello (3577394)
Shin-ichi Hashimoto (26882)
Atsuko Shimada (247053)
Ryohei Nakamura (3577397)
Tatsuya Tsukahara (3577400)
Wei Qu (268253)
Jun Yoshimura (280993)
Yutaka Suzuki (1379)
Sumio Sugano (1380)
Hiroyuki Takeda (247055)
Andrew Fire (17358)
Shinichi Morishita (10016)

November 2015

Possible effect of transcription-coupled repair (TCR). a-c. We observed a significant excess of C to...

Additional file 11: Figure S2. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Yoichiro Nakatani (10095)
Cecilia Mello (3577394)
Shin-ichi Hashimoto (26882)
Atsuko Shimada (247053)
Ryohei Nakamura (3577397)
Tatsuya Tsukahara (3577400)
Wei Qu (268253)
Jun Yoshimura (280993)
Yutaka Suzuki (1379)
Sumio Sugano (1380)
Hiroyuki Takeda (247055)
Andrew Fire (17358)
Shinichi Morishita (10016)

November 2015

Estimating the average nucleosome core fragment length L. a. We calculated A/T mononucleotide distri...

Additional file 8: Figure S5. of Germ cell and tumor associated piRNAs in the medaka and Xiphophorus melanoma models

Susanne Kneitz (114893)
Rasmi R. Mishra (3541253)
Domitille Chalopin (668693)
John Postlethwait (841459)
Wesley C. Warren (230513)
Ronald B. Walter (225642)
Manfred Schartl (75405)

May 2016

Venn diagram of numbers of genes mapping to a piRNA. To compare gene lists, human homologes of medak...

Additional file 2: Figure S2. of Sox5 is involved in germ-cell regulation and sex determination in medaka following co-option of nested transposable elements

Manfred Schartl (75405)
Susanne Schories (4805310)
Yuko Wakamatsu (261917)
Yusuke Nagao (546940)
Hisashi Hashimoto (261854)
ChloĂŠ Bertin (4805313)
Brigitte Mourot (674108)
Cornelia Schmidt (253342)
Dagmar Wilhelm (105377)
Lazaro Centanin (243124)
Yann Guiguen (65559)
Amaury Herpin (80760)

January 2018

Comparison of medaka Rex1 reverse-transcriptase (RT) sequence with other non-LTR retrotransposons. R...

Additional file 6: of Heterogeneous combinatorial expression of Hoxd genes in single cells during limb development

P. Fabre (5754794)
M. Leleu (5754797)
B. Mascrez (5754800)
Q. Lo Giudice (5754803)
J. Cobb (5754806)
D. Duboule (5754812)

September 2018

Figure S5. Cyclone analysis of the cell cycle in single cells from autopod and zeugopod. A-B. Graphi...

Additional file 1: of Phylogenomic analysis of carangimorph fishes reveals flatfish asymmetry arose in a blink of the evolutionary eye

Richard Harrington (499440)
Brant Faircloth (3250557)
Ron Eytan (3575135)
W. Smith (3575132)
Thomas Near (3575129)
Michael Alfaro (762174)
Matt Friedman (453708)

October 2016

Extended descriptions of protocols for DNA isolation, library preparation, sequencing, and data pipe...

Additional file 4: Figure S4. of Two maternal duplications involving the CDKN1C gene are associated with contrasting growth phenotypes

Susanne Boonen (3420221)
Andrea Freschi (3420212)
Rikke Christensen (32108)
Federica Valente (3420209)
Dorte Lildballe (3420215)
Lucia Perone (3420218)
Orazio Palumbo (174177)
Massimo Carella (174251)
Niels Uldbjerg (500176)
Angela Sparago (272242)
Andrea Riccio (272246)
Flavia Cerrato (272244)

June 2016

FISH analysis on metaphase nuclei (top panel) of cultured cells derived from the umbilical cord of t...

Additional file 8: Figure S8. of Two maternal duplications involving the CDKN1C gene are associated with contrasting growth phenotypes

Susanne Boonen (3420221)
Andrea Freschi (3420212)
Rikke Christensen (32108)
Federica Valente (3420209)
Dorte Lildballe (3420215)
Lucia Perone (3420218)
Orazio Palumbo (174177)
Massimo Carella (174251)
Niels Uldbjerg (500176)
Angela Sparago (272242)
Andrea Riccio (272246)
Flavia Cerrato (272244)

June 2016

FISH analysis on metaphase nuclei (top panel) of cultured cells derived from peripheral blood leukoc...

Additional file 4: Figure S3. of Karyotype features of trematode Himasthla elongata

Anna Solovyeva (3456860)
Vera Stefanova (3456854)
Olga Podgornaya (297493)
Serghei Demin (3456857)

April 2016

Correspondence of Ag-NOR-staining and rDNA FISH signals at aneuploid metaphase spread of H. elongata...

Additional file 6: Figure S9. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Abstract

Extracted data

Additional file 6: Figure S9. of Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species

Abstract

Extracted data

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