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GENE CARD

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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Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library 0 clone(s) / 5,577
Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult 1 clone(s) / 31,366
Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo 0 clone(s) / 15,579
Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg 0 clone(s) / 31,100
Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva 4 clone(s) / 26,704
Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo 0 clone(s) / 26,680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K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis 0 clone(s) / 5,468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Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells 0 clone(s) / 29,579
Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle 0 clone(s) / 2,556
Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo 0 clone(s) / 16,939
Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula 0 clone(s) / 25,258
Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad 0 clone(s) / 16,936
Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex 0 clone(s) / 10,463
Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart 0 clone(s) / 13,243
Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland 0 clone(s) / 17,765
Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal 1 clone(s) / 17,872
Yutaka Satou unpublished cDNA library, mature adult whole animal Yutaka Satou unpublished cDNA library, mature adult whole animal 0 clone(s) / 107,314
Nori Satoh unpublished cDNA library, juvenile whole animal Nori Satoh unpublished cDNA library, juvenile whole animal 1 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)

1 result

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

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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)

In Situ Experiment Data

15 results

Experiment data ( results)

C. robusta formely Ciona int. type A, Stage 26 (hatching larva)

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Control larvae electroporated with the pGsx>GFP2x construct.

Stained molecule KH2012:KH.S605.3 (CRYBB2; CRYGN; CRYGS)
Stained region(s)

C. robusta formely Ciona int. type A, Stage 26 (hatching larva)

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Conversion to Aniseed format of Ghost database entry from Kusakabe T et al., Dev Biol. 2002; 242:188-203. Original annotation: . Expression pattern: Papilla

Stained molecule KH2012:KH.S605.3 (CRYBB2; CRYGN; CRYGS)
Stained region(s) palp neurones -

C. robusta formely Ciona int. type A, Stage 26 (hatching larva)

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Ci-beta-gamma-crytallin mRNA was detected in the palps of late larva (p, palps; ot, otolith; oc, ocellus).

Stained molecule KH2012:KH.S605.3 (CRYBB2; CRYGN; CRYGS)
Stained region(s) otolith -

C. robusta formely Ciona int. type A, Stage 26 (hatching larva)

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Hatched early larva showing expression of Ci-beta-gamma-Crystallin mRNA in the palps (p, palps).

Stained molecule KH2012:KH.S605.3 (CRYBB2; CRYGN; CRYGS)
Stained region(s) otolith -

C. robusta formely Ciona int. type A, Stage 26 (hatching larva)

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Late larva showing localization of Ci-beta-gamma-crystallin protein (red) in the palps and the otolith (p, palps; ot, otolith).

Stained molecule KH2012:KH.S605.3 (CRYBB2; CRYGN; CRYGS)
Stained region(s) otolith -

C. robusta formely Ciona int. type A, Stage 26 (hatching larva)

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Early larva showing localization of Ci-beta-gamma-cristallin protein (red) in the palps (p, palps).

Stained molecule KH2012:KH.S605.3 (CRYBB2; CRYGN; CRYGS)
Stained region(s)

C. robusta formely Ciona int. type A, Stage 26 (hatching larva)

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Larva immediately before settlement, showing localization of Ci-beta-gamma-crytallin protein in the palps and otolith cells (p, palps; ot, otolith).

Stained molecule KH2012:KH.S605.3 (CRYBB2; CRYGN; CRYGS)
Stained region(s) otolith -

C. robusta formely Ciona int. type A, Stage 26 (hatching larva)

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Metamorph shortly after the initiation of metamorphosis. The tail has contracted (asterisk). Ci-beta-gamma-crystallin protein is located in the former palp cell (arrow) and the otolith cell.

Stained molecule KH2012:KH.S605.3 (CRYBB2; CRYGN; CRYGS)
Stained region(s) otolith -

C. robusta formely Ciona int. type A, Stage 26 (hatching larva)

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Picture 1 :The Ci-beta-gamma-Crystallin upstream region driving expression of GFP in transgenic Ciona intestinalis larvae. Staining is observed in one palp (p, out of focus), the otolith (ot), and in a cell adjacent to the ocellus (oc).

Picture 2 :A different tadpole transgenic for the same construct. Staining is observed in one palp and in the ocellus.

Stained molecule KH2012:KH.S605.3 (CRYBB2; CRYGN; CRYGS)
Stained region(s) lens cells - ocellus - otolith -

C. robusta formely Ciona int. type A, Stage 26 (hatching larva)

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Original annotation :Larva expressing FoxC>H2B:mCherry (red) and palp differentiation marker βγ-crystallin>GFP (green). Control larva (co-electroporated with DMRT>LAcZ and FoxC>LacZ) shows βγ-crystallin reporter in two of the three palps but not in the intervening palp domain marked by FoxC reporter.
Under control conditions, we detect the βγ-crystallin>GFP reporter in the palps (Fig. 6D) in 73% of larvae; it is always specifically expressed in 1-2 cells per palp.

Stained molecule KH2012:KH.S605.3 (CRYBB2; CRYGN; CRYGS)
Stained region(s)

C. robusta formely Ciona int. type A, Stage 27 (swimming larva I)

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Lateral view of a tadpole larva electroporated with the -315/+110 extended promoter of βγ-crystallin (S605.3)
Original annotation : A transgenic larva with fluorescent reporter detected in palp (p) and otolith (ot). Only one palp is labelled, a common occurrence reflecting mosaicism.
Aniseed warning: Due to a lack of ontology at stage 30, the "Stained region(s)" field cannot be completed.

Stained molecule KH2012:KH.S605.3 (CRYBB2; CRYGN; CRYGS)
Stained region(s)

C. robusta formely Ciona int. type A, Stage 30 (swimming larva IV)

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Lateral view of a tadpole larva probed for βγ-crystallin (S605.3) expression.
Original annotation : Localisation of Ci-βγcrys protein detected by immunohistochemistry. D shows a larval head imaged by DIC microscopy, and E a fluorescent image of the same larva with protein localised in palps (p) and otolith (ot).
Aniseed warning: Due to a lack of ontology at stage 30, the "Stained region(s)" field cannot be completed.

Stained molecule KH2012:KH.S605.3 (CRYBB2; CRYGN; CRYGS)
Stained region(s)

C. robusta formely Ciona int. type A, Stage 30 (swimming larva IV)

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Lateral view of a tadpole larva electroporated with the -1115bp/+110bp cis-regulatory region of βγ-crystallin (S605.3). LacZ staining is observed in palps and pigment cells.
Original comment : Ciona larvae electroporated with Ci-βγcrys pCES. A shows reporter expression in the palps (p). B shows reporter expression in the otolith (ot). In C, expression includes the otolith (ot) but extends more towards the ocellus (oc) as described previously. Reporter expression faithfully reproduced endogenous protein localisation and original transgene expression.
Aniseed warning: Due to a lack of ontology at stage 30, the "Stained region(s)" field cannot be completed.

Stained molecule KH2012:KH.S605.3 (CRYBB2; CRYGN; CRYGS)
Stained region(s)

C. robusta formely Ciona int. type A, Stage 48 (young adult)

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Metamorphs in which the stalk that connects the animal to the substrate has begun to elongate. Ci-beta-gamma-crystallin protein is weakly detected in the otolith cell and the remnants of the palps (arrow)(ot, otolith).

Stained molecule KH2012:KH.S605.3 (CRYBB2; CRYGN; CRYGS)
Stained region(s)

C. robusta formely Ciona int. type A, Stage 48 (young adult)

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Metamorphs in which the Ci-beta-gamma-crystallin positive cells (arrow) begin to disperse.

Stained molecule KH2012:KH.S605.3 (CRYBB2; CRYGN; CRYGS)
Stained region(s)