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EST count

27 results

Library Name Percentage Expression
Ciona intestinalis whole animal Ciona intestinalis whole animal 0 clone(s) / 0
Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library 1 clone(s) / 5,577
Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult 2 clone(s) / 31,366
Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo 1 clone(s) / 15,579
Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg 0 clone(s) / 31,100
Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva 9 clone(s) / 26,704
Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo 8 clone(s) / 26,680
directional larval cDNA library directional larval cDNA library 0 clone(s) / 39
Ascidian hemocytes cDNA library Ascidian hemocytes cDNA library 0 clone(s) / 0
K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis 0 clone(s) / 5,468
Stratagene UniZAP whole-larva library Stratagene UniZAP whole-larva library 0 clone(s) / 0
Ciona intestinalis larva Ciona intestinalis larva 0 clone(s) / 0
Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells 0 clone(s) / 29,579
Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle 0 clone(s) / 2,556
Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo 0 clone(s) / 16,939
Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula 0 clone(s) / 25,258
Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad 0 clone(s) / 16,936
Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex 0 clone(s) / 10,463
Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart 0 clone(s) / 13,243
Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland 0 clone(s) / 17,765
Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal 1 clone(s) / 17,872
Yutaka Satou unpublished cDNA library, mature adult whole animal Yutaka Satou unpublished cDNA library, mature adult whole animal 1 clone(s) / 107,314
Nori Satoh unpublished cDNA library, juvenile whole animal Nori Satoh unpublished cDNA library, juvenile whole animal 0 clone(s) / 24,372
Nori Satoh unpublished cDNA library, mature adult whole animal Nori Satoh unpublished cDNA library, mature adult whole animal 0 clone(s) / 17,126
Ciona intestinalis whole animal stage3 juvenile Ciona intestinalis whole animal stage3 juvenile 0 clone(s) / 3,798
Yutaka Satou unpublished library (cicx) Yutaka Satou unpublished library (cicx) 0 clone(s) / 2,031
Gateway compatible cien cDNA library, Ciona intestinalis mixed embryonic stages (Egg to Neurula) Gateway compatible cien cDNA library, Ciona intestinalis mixed embryonic stages (Egg to Neurula) 0 clone(s) / 188,431

RNA-Seq transcriptome profiles (by Experiment)

2 results

OVERVIEW

   Expression profile summary from all experiments in WT and mutant conditions:
FPKM & RPKM

Click here to see the RNA-Seq Pipeline Protocol.
You can show/hide lines in the charts by clicking on it in the legend part.
You can see more details by clicking on a point and then, on the link which will appear.

Be careful, FPKM & RPKM does not permit you to compare a gene across different conditions or experiments.

Download FPKM & RPKM data

OVERVIEW

   Expression profile summary from all experiments in WT and mutant conditions:
Relative Log Expression RLE

Be careful, RLE and 2RLE does not permit you to compare a gene across different experiments.

Download RLE Relative Log Expression data

RNA-Seq Experiment n°34135

Read more…

Oocytes of a single individual of Ciona intestinalis (Roscoff, France) were fertilized by a mixture of sperm of two individuals and development was followed microscopically. Embryos were snapfrozen in liquid nitrogen at the appropriate stage and kept at -80°C. Samples at stage 0, 8, 12, 15, 21, 26 were collected from the same fertilzation, while sample from stage 11 was independently collected from a different individual. Total RNA was prepared with the RNA II kit of Magerey Nagel and the quality was checked with the Bioanalyzer, all samples had a RIN value of higher than 9. Strand specific libraries were constructed and the sequencing (50PE) was performed with Illumina HiSeq 2000 technology (BGI, Hong Kong, China). Reads were aligned onto C.robusta genome and considered to reflect the expression of the C.robusta orthologous genes.

Assay platform Illumina HiSeq 2000
Layout Paired-end
Stranded Yes
Read length 49
Normalized data types
  • FPKM
  • RLE
Wild type - Replica 1
Territories whole embryo -
Biomaterial(s) C. robusta formely Ciona int. type A, Stage 0 (Unfertilized egg)
C. robusta formely Ciona int. type A, Stage 8 (64-cell)
C. robusta formely Ciona int. type A, Stage 11 (early gastrula)
C. robusta formely Ciona int. type A, Stage 12 (mid gastrula)
C. robusta formely Ciona int. type A, Stage 15 (mid neurula)
C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)
C. robusta formely Ciona int. type A, Stage 26 (hatching larva)
Wild type - Replica 2
Territories whole embryo -
Biomaterial(s) C. robusta formely Ciona int. type A, Stage 0 (Unfertilized egg)
C. robusta formely Ciona int. type A, Stage 8 (64-cell)
C. robusta formely Ciona int. type A, Stage 11 (early gastrula)
C. robusta formely Ciona int. type A, Stage 12 (mid gastrula)
C. robusta formely Ciona int. type A, Stage 15 (mid neurula)
C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)
C. robusta formely Ciona int. type A, Stage 26 (hatching larva)

RNA-Seq Experiment n°34139

Read more…

The purpose of this project is to identify genes positively and negatively regulated by signaling molecules that belongs to the TGFbeta superfamily.

Assay platform Illumina HiSeq 2500
Layout Single-end
Stranded Yes
Read length 101
Normalized data types
  • RPKM
Wild type
Territories whole embryo -
Biomaterial(s) C. robusta formely Ciona int. type A, Stage 13 (late gastrula)
Mutant 1
Deregulated molecule(s) KH2012:KH.C4.125 -
Territories whole embryo -
Biomaterial(s) C. robusta formely Ciona int. type A, Stage 13 (late gastrula)
Mutant 2
Deregulated molecule(s) KH2012:KH.C2.573 -
Territories whole embryo -
Biomaterial(s) C. robusta formely Ciona int. type A, Stage 13 (late gastrula)

In Situ Experiment Data

55 results

Experiment data ( results)

C. robusta formely Ciona int. type A, Stage 1 (One cell)

Read more…

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :FoxF.
Expression pattern : No signal was detected.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) No expression -

C. robusta formely Ciona int. type A, Stage 5a (early 16-cell)

Read more…

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :FoxF.
Expression pattern : No distinct zygotic signal was detected.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) No expression -

C. robusta formely Ciona int. type A, Stage 6b (late 32-cell)

Read more…

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :FoxF.
Expression pattern : No distinct zygotic signal was detected.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) No expression -

C. robusta formely Ciona int. type A, Stage 8 (64-cell)

Read more…

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :FoxF.
Expression pattern : No distinct zygotic signal was detected.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) No expression -

C. robusta formely Ciona int. type A, Stage 10 (112-cell)

Read more…

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :FoxF.
Expression pattern : No distinct zygotic signal was detected.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) No expression -

C. robusta formely Ciona int. type A, Stage 13 (late gastrula)

Read more…

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :FoxF.
Expression pattern : No distinct zygotic signal was detected.

Aniseed annotation :
A signal might have been detected through the whole embryo.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) whole embryo -

C. robusta formely Ciona int. type A, Stage 15 (mid neurula)

Read more…

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :FoxF.
Expression pattern : epidermis.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis -

C. robusta formely Ciona int. type A, Stage 16 (late neurula)

Read more…

Ventral view of a late neurula stage embryo probed for FoxF (green) expression.
Nuclei of TVCs and ATMs are marked by β-gal antibody staining (red). Inset panels display magnified views of the B7.5 lineage. Note that the TVCs are the more anterior lineage, as marked by arrowheads in the first column.

Original annotation:
At stage 16, 8 h post fertilization (hpf), FoxF was robustly expressed in newly emerged TVCs (arrowheads) and trunk ectoderm.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis -

C. robusta formely Ciona int. type A, Stage 16 (late neurula)

Read more…

The two pictures show a lateral and a dorsal view of a 8hpf late neurula stained for FoxF expression by whole mount ISH. Arrowheads indicate the TVCs.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis -

C. robusta formely Ciona int. type A, Stage 19 (early tailbud I)

Read more…

Lateral view of an early tailbud stage embryo probed for FoxF (green) expression. Nuclei of TVCs and ATMs are marked by β-gal antibody staining (red). Inset panels display magnified views of the B7.5 lineage. Note that the TVCs are the more anterior lineage, as marked by arrowheads in the first column.

Original annotation:
Between stages 18 and 19 (9 hpf) the expression patterns of FoxF remained unaltered.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 19 (early tailbud I)

Read more…

Lateral view of a tailbud stage wild type embryo probed for FoxF expression.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) dorso lateral head epidermis -

C. robusta formely Ciona int. type A, Stage 19 (early tailbud I)

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Lateral view of a tailbud stage embryo probed for FoxF expression following egg micro-injection of a Mesp MO. FoxF expression was down-regulated in mesenchyme. Expression in trunk epidermal cells was not affected.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis -

C. robusta formely Ciona int. type A, Stage 19 (early tailbud I)

Read more…

Aniseed Comment : update of annotation of (Imai et al.,2004), based on (Imai et al.,2006).

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) dorso lateral head epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 19 (early tailbud I)

Read more…

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :FoxF.
Expression pattern : epidermis.
Comment : trunk epidermis except for epidermis along the dorsal midline. Epidermis above TVC or mesenchyme is especially stained deeply.

Aniseed annotation :
According to the picture, a staining has been detected in part of the head epidermis and more precisely in dorso lateral head epidermis, ventral head epidermis and in part of the mesenchyme.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) dorso lateral head epidermis -

C. robusta formely Ciona int. type A, Stage 19 (early tailbud I)

Read more…

Lateral and dorsal views of an early tailbud stage embryo, showing expression of ci-FoxF in lateral head epidermis and in mesenchyme . Expression of ci-FoxF is revealed by whole-mount in situ hybridization.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) dorso lateral head epidermis - ventral head epidermis -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Lateral view of a mid tailbud stage embryo probed for FoxF (green) expression. Nuclei of TVCs and ATMs are marked by β-gal antibody staining (red). Inset panels display magnified views of the B7.5 lineage. Note that the TVCs are the more anterior lineage, as marked by arrowheads in the first column.

Original annotation:
FoxF expression domains were unchanged.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Lateral view of a mid tailbud stage embryo co-electroporated with Mesp-lacZ (red) and Hl-GATAa-DBD and probed for FoxF (green) expression.
The construct Hl-GATAa-DBD was included in embryos for a more rigourous control : this construct contains the GATAa DNA binding domain alone which is expressed in the TVCs.

Original annotation:
In Hl-GATAa- DBD control embryos, FoxF was consistently expressed in the trunk ventral cells.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Lateral view of a mid tailbud stage embryo co-electroporated with Mesp-lacZ (red) and Hl-GATAa-WRPW and probed for FoxF (green) expression.
Construct Hl-GATAa-WRPW was used to disrup GATAa activity.

Original annotation:
In Hl-GATAa-WRPW embryos, TVC expression of FoxF was eliminated or significantly reduced while expression in adjacent lineages was not affected.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Lateral view of a mid tailbud stage embryo co-electroporated with Mesp-lacZ (red) and Ttf-GATAa-DBD and probed for FoxF (green) expression. The construct Ttf-GATAa-DBD was used as a control.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Lateral view of a mid tailbud stage embryo co-electroporated with Mesp-lacZ (red) and Ttf-GATAa-WRPW and probed for FoxF (green) expression. The construct Ttf-GATAa-DBD was used as a control.

Original annotation:
There was no detectable difference in the TVC expression of FoxF between Ttf-GATAa-WRPW and control embryos.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Aniseed Comment : update of annotation of (Imai et al.,2004), based on (Imai et al.,2006).

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) dorso lateral head epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Conversion to Aniseed format of data from Yutaka Satou's gene expression profiles of transcription factors and signalling molecule ISH screen (Development. 2004 131:4047-58).

Original annotation :
Gene name :FoxF.
Expression pattern : epidermis.

Aniseed annotation :
According to the picture, a staining has been detected in part of the head epidermis and more precisely in dorso lateral head epidermis, ventral head epidermis and in part of mesenchyme.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) dorso lateral head epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Lateral view of a mid tailbud embryo (10hpf) stained for the presence of FoxF transcripts by whole mount ISH. The arrowheads point to the TVC.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Sagittal section through a mid tailbud embryo.

Picture D: The green FoxF ISH signal was visualised using TSA-Fluorescein and the picture obtained by confocal laser scanning microscopy.

Picture D': In red, the position of the B7.5 progeny, visualised through mesp::LacZ electroporation and LacZ immunohistochemistry.

Picture D": overlay of D and D'.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Sagittal section through a mid tailbud embryo in which Ets1/2-VP16 was overexpressed under control of the mesp driver.

Picture E: The green FoxF ISH signal was visualised using TSA-Fluorescein and the picture obtained by confocal laser scanning microscopy.

Picture E': In red, the position of the B7.5 progeny, visualised through mesp::LacZ electroporation and LacZ immunohistochemistry.

Picture E": overlay of D and D'. Note that the posterior B7.5 lineage have migrated into the trunk and formed supernumerary heart precursors and that all B7.5 progeny have now been transformed into FoxF-expressing TVC and that. The control picture (D, D', D") shows Fox F and B7.5 in a wild-type embryo.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Sagittal section through a mid tailbud embryo in which Ets1/2-WRPW was overexpressed under control of the mesp driver.

Picture F: the green FoxF ISH signal was visualised using TSA-Fluorescein and the picture obtained by confocal laser scanning microscopy.

Picture F': in red, the position of the B7.5 progeny, visualised through mesp::LacZ electroporation and LacZ immunohistochemistry.

Picture F": overlay of F and F'. Note that all B7.5 progeny have now been transformed into FoxF-negative tail muscle. The control picture (D, D', D") shows Fox F and B7.5 in a wild-type embryo.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Sagittal section through a mid tailbud embryo in which Mesp-VP16 was overexpressed under control of the mesp driver.

Picture G: the green FoxF ISH signal was visualised using TSA-Fluorescein and the picture obtained by confocal laser scanning microscopy.

Picture G': in red, the position of the B7.5 progeny, visualised through mesp::LacZ electroporation and LacZ immunohistochemistry.

Picture G": overlay of G and G'. Note that B7.5 lineage cells that failed to migrate into the trunk did not express FoxF. The control picture (D, D', D") shows Fox F and B7.5 in a wild-type embryo.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Lateral view of a mid tailbud embryo, showing nuclear X gal staining in the head and tail epidermis (coordinates and corresponding name in the paper of this region : -3052/+1 delta E-box.)

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) epidermis -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Lateral view of a mid tailbud embryo showing transgene activity in the TVCs and head epidermis (coordinates and corresponding name in the paper : -3052/+1).

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Lateral view of a mid tailbud embryo, showing transgene activity in the 2 TVCs (coordinates and corresponding name in the paper : -1135/-840).

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Lateral view of a mid tailbud embryo showing no activity of the reporter construct (mesenchymal activity is most likely due to the minimal promoter used). This shows that the E box is required for the enhancer activity (coordinates and corresponding name in the paper : -1135/-840 delta E box).

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) No expression -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

No picture available in article. this construct has no significant enhancer activity in WT embryos (coordinates in the paper : -1135/-840).

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) No expression -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

No picture presented in the article. This construct shows no activity in WT embryos (coordinates in the paper : -1135/-840).

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) No expression -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

No picture available in article. Mutation of EtsA and EtsB causes the complete suppression of the enhancer activity of region -7072/-777 (coordinates in the paper : -1135/-840).

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) No expression -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

No picture available. Although some TVC expression is detected, a 5 fold reduction in enhancer activity is caused by the mutation of this EtsA site (coordinates in the paper : -1135/-840).

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

No Picture available in article. Mutation of the EtsB site causes a 2.5 fold reduction in the enhancer activity of the -1072/-777 region (coordinates in the paper : -1135/-840).

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

This is the construct (coordinates in the paper : -1054/-840) made to test the sequence shown on Fig. 2C. No picture was provided, but in a mail to the Aniseed curator, the authors attest that this construct has the same activity as pFoxF -1072/-777::LacZ (coordinates in the paper : -1135/-840).

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

No picture provided in the article (coordinates in the paper : -845/+1).

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

No picture available in article. Mutation of EtsC site causes a 1.5 fold reduction in enhancer activity of region -1135/-840.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

(Data not shown in the article)
At the tailbud stage, in WT conditions, Mesp enhancer drives reporter activity in the B7.5 lineage of Ciona robusta embryos.

Stained molecule KH2012:KH.C3.100 (MESP2; MSGN1; PTF1A)
Stained region(s) anterior ventral primary muscle lineage (B7.5 line) - trunk ventral cells (B7.5 line) -

(Data not shown in the article)
At the tailbud stage, in WT conditions, FoxF enhancer drives reporter activity in th trunk ventral cells and the head epidermis of Ciona robusta embryos.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

Read more…

Lateral view of a Ciona robusta mid tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs and treated with the MEK inhibitor U0126 at the late gastrula stage (6hpf). FoxF enhancer drives RFP expression in the epidermis and in one trunk ventral cell precursor cell.
Original annotation: One B7.5 lineage cell on the right side expresses FoxF-RFP (line) and one on the left appears to undergo partial migration (arrow).

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) trunk ventral cells (B7.5 line) -

Lateral view of a Ciona robusta mid tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs and treated with the MEK inhibitor U0126 at the late gastrula stage (6hpf). Mesp enhancer drives GFP expression the B7.5 lineage.
Original annotation: One B7.5 lineage cell on the right side expresses FoxF-RFP (line) and one on the left appears to undergo partial migration (arrow).

Stained molecule KH2012:KH.C3.100 (MESP2; MSGN1; PTF1A)
Stained region(s) anterior ventral primary muscle lineage (B7.5 line) - trunk ventral cells (B7.5 line) -

Lateral view of a Ciona robusta mid tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs and treated with the MEK inhibitor U0126 at the late gastrula stage (6hpf). Mesp-driven GFP staining is observed in the B7.5 lineage.
(B) Green channel.
(B') Red channel.
(B'') Red and green channels

Stained molecule KH2012:KH.C3.100 (MESP2; MSGN1; PTF1A)
Stained region(s) anterior ventral primary muscle lineage (B7.5 line) - trunk ventral cells (B7.5 line) -

Lateral view of a Ciona robusta mid tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs and treated with the MEK inhibitor U0126 at the late gastrula stage (6hpf). FoxF enhancer drives RFP expression in the epidermis.
Original annotation: When gastrulating embryos were treated with the MEK inhibitor, U0126, the rostral cells fail to activate the FoxF enhancer.
(B) Green channel.
(B') Red channel. Note FoxF reporter expression in the epidermis (FoxF is expressed in both heart precursors and epidermis in WT embryos.)
(B'') Red and green channels.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) epidermis -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

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Lateral view of a Ciona robusta mid tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs and treated with the MEK inhibitor U0126 at the neurula stage (7hpf). Mesp enhancer drives GFP expression in the B7.5 lineage.
Original annotation: Although U0126 blocked heart induction up to the late gastrula stage, application at later time points (7–9hpf) failed to block induction.
(C) Green channel.
(C') Red channel.
(C'') Red and green channels.

Stained molecule KH2012:KH.C3.100 (MESP2; MSGN1; PTF1A)
Stained region(s) anterior ventral primary muscle lineage (B7.5 line) - trunk ventral cells (B7.5 line) -

Lateral view of a WT Ciona robusta mid tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs and treated with the MEK inhibitor U0126 at the neurula stage (7hpf). FoxF enhancer drives RFP expression in epidermis and trunk ventral cells.
Original annotation: Although U0126 blocked heart induction up to the late gastrula stage (6hpf) application at later time points (7–9H) failed to block induction.
(C) Green channel.
(C') Red channel.
(C'') Red and green channels.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

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Lateral view of a Ciona robusta mid tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs and Mesp>FGFR-DN. Mesp enhancer drives GFP expression in the B7.5 lineage.
Original annotation: Targeted expression of FGFRDN in the B7.5 lineage blocks migration of the anterior heart precursors.
(F) Red channel.
(F') Red and green channels.

Stained molecule KH2012:KH.C3.100 (MESP2; MSGN1; PTF1A)
Stained region(s) anterior ventral primary muscle lineage (B7.5 line) - trunk ventral cells (B7.5 line) -

Lateral view of a Ciona robusta mid tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs and Mesp>FGFR-DN. FoxF enhancer drives RFP expression in the epidermis.
Original annotation: Targeted expression of FGFRDN in the B7.5 lineage blocks migration of the anterior heart precursors and prevents activation of the FoxF enhancer in these cells.
(F) Red channel.
(F') Red and green channels.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) epidermis -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

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Lateral view of a Ciona robusta mid tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs and Mesp>Ets1/2-WRPW. Mesp enhancer drives GFP expression in the B7.5 lineage.
Original annotation: The repressor form, EtsWRPW, causes a block in heart migration, so that both the anterior and posterior B7.5 lineages remain in the tail.
(F) Red channel.
(F') Red and green channels.

Stained molecule KH2012:KH.C3.100 (MESP2; MSGN1; PTF1A)
Stained region(s) anterior ventral primary muscle lineage (B7.5 line) - trunk ventral cells (B7.5 line) -

Lateral view of a Ciona robusta mid tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs and Mesp>Ets1/2-WRPW. FoxF enhancer drives RFP expression in the head epidermis.
Original annotation: The repressor form, EtsWRPW, causes a block in heart migration, so that both the anterior and posterior B7.5 lineages remain in the tail. The anterior lineage fails to activate the FoxF enhancer.
(F) Red channel.
(F') Red and green channels.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

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Lateral view of a Ciona robusta mid tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs and Mesp>Ets1/2-VP16. Mesp enhancer drives GFP expression in the B7.5 lineage.
Original annotation: Targeted expression of constitutively active Ets1/2 (EtsVp16) in the B7.5 lineage doubles the number of heart progenitor cells by transforming the proximal tail muscle lineage into supernumerary heart cells.
(D) Red channel.
(D') Red and green channels.

Stained molecule KH2012:KH.C3.100 (MESP2; MSGN1; PTF1A)
Stained region(s) anterior ventral primary muscle lineage (B7.5 line) - trunk ventral cells (B7.5 line) -

Lateral view of a Ciona robusta mid tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs and Mesp>Ets1/2-VP16. FoxF enhancer drives RFP expression in the B7.5 lineage.
Original annotation: A constitutively activated form of Ets1/2, EtsVp16, activate the FoxF enhancer in the whole B7.5 lineage.
(D) Red channel.
(D') Red and green channels.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) anterior ventral primary muscle lineage (B7.5 line) - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 21 (mid tailbud I)

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Lateral view of a Ciona robusta mid tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs and treated with the MEK inhibitor U0126 at the late gastrula stage (6hpf). FoxF enhancer drives RFP expression in the epidermis and in one trunk ventral cell precursor cell.
Original annotation: One B7.5 lineage cell on the right side expresses FoxF-RFP (line) and one on the left appears to undergo partial migration (arrow).

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) trunk ventral cells (B7.5 line) -

Lateral view of a Ciona robusta mid tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs and treated with the MEK inhibitor U0126 at the late gastrula stage (6hpf). Mesp enhancer drives GFP expression the B7.5 lineage.
Original annotation: One B7.5 lineage cell on the right side expresses FoxF-RFP (line) and one on the left appears to undergo partial migration (arrow).

Stained molecule KH2012:KH.C3.100 (MESP2; MSGN1; PTF1A)
Stained region(s) anterior ventral primary muscle lineage (B7.5 line) - trunk ventral cells (B7.5 line) -

Lateral view of a Ciona robusta mid tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs and treated with the MEK inhibitor U0126 at the late gastrula stage (6hpf). Mesp-driven GFP staining is observed in the B7.5 lineage.
(B) Green channel.
(B') Red channel.
(B'') Red and green channels

Stained molecule KH2012:KH.C3.100 (MESP2; MSGN1; PTF1A)
Stained region(s) anterior ventral primary muscle lineage (B7.5 line) - trunk ventral cells (B7.5 line) -

Lateral view of a Ciona robusta mid tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs and treated with the MEK inhibitor U0126 at the late gastrula stage (6hpf). FoxF enhancer drives RFP expression in the epidermis.
Original annotation: When gastrulating embryos were treated with the MEK inhibitor, U0126, the rostral cells fail to activate the FoxF enhancer.
(B) Green channel.
(B') Red channel. Note FoxF reporter expression in the epidermis (FoxF is expressed in both heart precursors and epidermis in WT embryos.)
(B'') Red and green channels.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) epidermis -

C. robusta formely Ciona int. type A, Stage 22 (mid tailbud II)

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Dorsal confocal projections (Anterior to the left) of a Ciona robusta embryo electroporated with Mesp>GFP (green) and FoxF>RFP (red), arrested at the 110-cell stage (4hpf) through treatment with cytochalasin and fixed at 10hpf. Mesp reporter drives GFP expression in the B7.5 lineage.

Stained molecule KH2012:KH.C3.100 (MESP2; MSGN1; PTF1A)
Stained region(s) anterior ventral primary muscle lineage (B7.5 line) - trunk ventral cells (B7.5 line) -

Dorsal confocal projections (Anterior to the left) of a Ciona robusta embryo electroporated with Mesp>GFP (green) and FoxF>RFP (red), arrested at the 110-cell stage (4hpf) through treatment with cytochalasin and fixed at 10hpf. The FoxF enhancer drives some reporter expression in the epidermis (faint red staining) and strong expression in the B7.5 lineage.
Original annotation: Treatment of 4H embryos with cytochalasin causes a block in the division of the B7.5 blastomeres at the 110-cell stage. Despite this block, FoxF reporter gene expression is observed in the B7.5 cells “on schedule,” ∼10 h after fertilization at the equivalent of the tailbud stage.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) anterior ventral primary muscle lineage (B7.5 line) - epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 22 (mid tailbud II)

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Dorsal confocal projections (Anterior to the left) of a Ciona robusta embryo electroporated with Mesp>GFP (green) and FoxF>RFP (red), arrested at the 110-cell stage (4hpf) through treatment with cytochalasin and fixed at 10hpf and treated with the MEK inhibitor U0126 from 16-cell stage (2hpf).
The Mesp enhancer drives GFP expression in the B7.5 lineage.
Original annotation: Treatment of 4hpf embryos with cytochalasin causes a block in the division of the B7.5 blastomeres at the 110-cell stage.

Stained molecule KH2012:KH.C3.100 (MESP2; MSGN1; PTF1A)
Stained region(s) anterior ventral primary muscle lineage (B7.5 line) - trunk ventral cells (B7.5 line) -

Dorsal confocal projections (Anterior to the left) of a Ciona robusta embryo electroporated with Mesp>GFP (green) and FoxF>RFP (red), arrested at the 110-cell stage (4hpf) through treatment with cytochalasin and fixed at 10hpf and treated with the MEK inhibitor U0126 from 16-cell stage (2hpf).
The FoxF enhancer drives RFP expression in the epidermis.
Original annotation: Treatment of 4hpf embryos with cytochalasin causes a block in the division of the B7.5 blastomeres at the 110-cell stage. Note lack of FoxF-RFP expression in the B7.5 cells (marked by Mesp>GFP). Also note that FoxF>RFP expression is significantly stronger in the epidermis, indicating that RTK signaling normally represses epidermal expression in arrested embryos.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) epidermis -

C. robusta formely Ciona int. type A, Stage 23 (late tailbud I)

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Aniseed Comment : update of annotation of (Imai et al.,2004), based on (Imai et al.,2006).

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) dorso lateral head epidermis - trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 23 (late tailbud I)

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Lateral view of a late tailbud stage embryo probed for FoxF (green) expression. Nuclei of TVCs and ATMs are marked by β-gal antibody staining (red). Inset panels display magnified views of the B7.5 lineage. Note that the TVCs are the more anterior lineage, as marked by arrowheads in the first column.

Original annotation:
FoxF was no longer detected in the TVC lineage.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis -

C. robusta formely Ciona int. type A, Stage 23 (late tailbud I)

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Lateral view of a Ciona robusta late tailbud embryo transfected with MesP>lacZ (red) and FoxF[TVCenhancer]>H2B::mCherry (red) transgenes.
Mesp enhancer is active in B7.5 progeny and FoxF[TVCenhancer] drives mCherry expression in the trunk ventral cells.
Scale bar: 50 μm.

Stained molecule KH2012:KH.C3.100 (MESP2; MSGN1; PTF1A)
Stained region(s) anterior ventral primary muscle lineage (B7.5 line) - trunk ventral cells (B7.5 line) -

Lateral view of a Ciona robusta late tailbud embryo transfected with MesP>lacZ (red) and FoxF[TVCenhancer]>H2B::mCherry (red) transgenes.
Mesp enhancer is active in B7.5 progeny and FoxF[TVCenhancer] drives mCherry expression in the trunk ventral cells (white arrowheads).
Scale bar: 50 μm.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) trunk ventral cells (B7.5 line) -

C. robusta formely Ciona int. type A, Stage 25 (late tailbud III)

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Late tailbud embryos expressing FoxF>Cherry-caax (Red) and FoxF>lacZ (control construct), and stained with phalloidin (Green). MChery staining is observed in trunk and tail ectoderm.
Original annotation : A′ and A′′ show close-up view of surface ectodermal cells (shown in white brackets) on electroporated and unelectroporated sides, respectively, of the FoxF>lacZ control. Cells on either side are of similar length.
Pannels shows a set of 20 embryos expressing FoxF>LacZ. Images show a single confocal section and denote the measurements used to calculate normalized cell lengths.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) epidermis -

C. robusta formely Ciona int. type A, Stage 25 (late tailbud III)

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Ventral view of the head of a Ciona robusta late tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs. Mesp enhancers drives GFP staining in B7.5 lineage.
(D) Green channel.
(D') Red channel.(D'') Red and green channels.

Stained molecule KH2012:KH.C3.100 (MESP2; MSGN1; PTF1A)
Stained region(s) anterior ventral primary muscle lineage (B7.5 line) - first heart precursors -

Ventral view of the head of a Ciona robusta late tailbud stage embryo co-electroporated with Mesp>GFP (green) and FoxF>RFP (red) reporter constructs. FoxF enhancers drives GFP staining in the trunk ventral cells and in epidermis.
(D) Green channel.
(D') Red channel.(D'') Red and green channels.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) first heart precursors - head epidermis -

C. robusta formely Ciona int. type A, Stage 25 (late tailbud III)

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Ventral view of the head of a Ciona robusta late tailbud stage embryo co-electroporated with FoxF>RFP (red) reporter construct and Mesp>FGFR-DN::VENUS (green) overexpression construct. FoxF enhancer drives RFP staining in the epidermis. Trunk lateral cells (green) did not migrate.
Original annotation: The dominant-negative form of the FGF receptor (FGFRDN) causes a block in heart cell migration and differentiation when expressed throughout the heart field using the Mesp B7.5 enhancer.
(E) Green channel.
(E') Red channel.(E'') Red and green channels.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) head epidermis -

C. robusta formely Ciona int. type A, Stage 25 (late tailbud III)

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Ventral view of the head of a Ciona robusta late tailbud stage embryo co-electroporated with FoxF>RFP (red) reporter construct and Mesp>FGFR-DN::VENUS (green) and Mesp>Ets1/2-VP16 overexpression constructs. FoxF enhancer drives RFP staining in epidermis and migrating heart cell precursors (labelled in green by Mesp reporter construct).
Original annotation: Migration and FoxF reporter gene activity were restored when both constitutively active Ets (Ets-Vp16) and dominant negative FGFR were simultaneously expressed in the B7.5 lineage
(F) Green channel.
(F') Red channel.(F'') Red and green channels.

Stained molecule KH2012:KH.C3.170 (FOXF1; FOXF2; FOXL1)
Stained region(s) first heart precursors - head epidermis -