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Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library 0 clone(s) / 5,577
Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult 0 clone(s) / 31,366
Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo 0 clone(s) / 15,579
Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg 0 clone(s) / 31,100
Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva 4 clone(s) / 26,704
Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo 0 clone(s) / 26,680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K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis 0 clone(s) / 5,468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Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells 0 clone(s) / 29,579
Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle 0 clone(s) / 2,556
Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo 0 clone(s) / 16,939
Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula 0 clone(s) / 25,258
Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad 0 clone(s) / 16,936
Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex 0 clone(s) / 10,463
Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart 0 clone(s) / 13,243
Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland 0 clone(s) / 17,765
Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal 0 clone(s) / 17,872
Yutaka Satou unpublished cDNA library, mature adult whole animal Yutaka Satou unpublished cDNA library, mature adult whole animal 0 clone(s) / 107,314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

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)

In Situ Experiment Data

17 results

Experiment data ( results)

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

Read more…

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16)

Original annotation :
Gene name: Lhx1.
Expression pattern: No signal was detected.

Aniseed annotation :
A weak staining is detected through the embryo.

Stained molecule KH2012:KH.L107.7 (LHX1; LHX5)
Stained region(s) whole embryo -

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

Read more…

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16)

Original annotation :
Gene name: Lhx1.
Expression pattern: No signal was detected.

Aniseed annotation :
A weak staining is detected through the embryo.

Stained molecule KH2012:KH.L107.7 (LHX1; LHX5)
Stained region(s) whole embryo -

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

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Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16)

Original annotation :
Gene name: Lhx1.
Expression pattern: No signal was detected.

Aniseed annotation :
A weak staining is detected through the embryo.

Stained molecule KH2012:KH.L107.7 (LHX1; LHX5)
Stained region(s) whole embryo -

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

Read more…

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16)

Original annotation :
Gene name: Lhx1.
Expression pattern: No signal was detected.

Aniseed annotation :
A weak staining is detected through the embryo.

Stained molecule KH2012:KH.L107.7 (LHX1; LHX5)
Stained region(s) whole embryo -

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

Read more…

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16)

Original annotation :
Gene name: Lhx1.
Expression pattern: No signal was detected.

Stained molecule KH2012:KH.L107.7 (LHX1; LHX5)
Stained region(s) whole embryo -

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

Read more…

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16)

Original annotation :
Gene name: Lhx1.
Expression pattern: No signal was detected.

Aniseed annotation :
A weak staining is detected through the embryo.

Stained molecule KH2012:KH.L107.7 (LHX1; LHX5)
Stained region(s) whole embryo -

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

Read more…

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16)

Original annotation :
Gene name: Lhx1.
Expression pattern: No signal was detected.

Aniseed annotation :
A weak staining is detected through the embryo.

Stained molecule KH2012:KH.L107.7 (LHX1; LHX5)
Stained region(s) whole embryo -

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

Read more…

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16)

Original annotation :
Gene name: Lhx1.
Expression pattern: No signal was detected.

Aniseed annotation :
A weak staining is detected through the embryo.

Stained molecule KH2012:KH.L107.7 (LHX1; LHX5)
Stained region(s) whole embryo -

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

Read more…

Dorsal view of a mid tailbud stage wild type embryo probed for Lhx1.
Red and yellow arrowheads indicate boundaries between the neck and the visceral ganglion, and between the visceral ganglion and the caudal nerve cord, respectively.

Original Annotation :
Lhx1 was expressed in the visceral ganglion( more precisely in A12.238 cell pair).

Stained molecule KH2012:KH.L107.7 (LHX1; LHX5)
Stained region(s) visceral ganglion -

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

Read more…

Dorsal view of a mid tailbud stage embryo probed for Lhx1, following the injection of Pax3/7 MO.
Red and yellow arrowheads indicate boundaries between the neck and the visceral ganglion, and between the visceral ganglion and the caudal nerve cord, respectively.

Original Annotation :
Expression in the visceral ganglion was lost (white arrow).

Stained molecule KH2012:KH.L107.7 (LHX1; LHX5)
Stained region(s) No expression -

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

Read more…

Dorsal view of a mid tailbud stage embryo probed for Lhx1, following the injection of Neurogenin MO.
Red and yellow arrowheads indicate boundaries between the neck and the visceral ganglion, and between the visceral ganglion and the caudal nerve cord, respectively.

Original Annotation :
Expression in the visceral ganglion was lost (white arrow).

Stained molecule KH2012:KH.L107.7 (LHX1; LHX5)
Stained region(s) No expression -

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

Read more…

Lateral views of WT Ciona robusta mid tailbud stage embryos probed for Lhx5 expression.
Lhx5 is expressed in the sensory vesicle.
"n" is the number of scored embryos ; % corresponds to the proportion of embryos showing similar staining patterns.

Stained molecule KH2012:KH.L107.7 (LHX1; LHX5)
Stained region(s) anterior sensory vesicle - posterior sensory vesicle -

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

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Lateral views of Ciona robusta mid tailbud stage embryos probed for Lhx5 expression and electroporated with pGsx>OC::VP16.
Expression is lost in 63% of the embryos and strongly reduced in 18% of the embryos.
Overexpression of constitutively active Onecut in the sensory vesicle downregulated Lhx5 expression.
"n" is the number of scored embryos ; % corresponds to the proportion of embryos showing similar staining patterns.

Stained molecule KH2012:KH.L107.7 (LHX1; LHX5)
Stained region(s) No expression -

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

Read more…

Lateral views of Ciona robusta mid tailbud stage embryos probed for Lhx5 expression and electroporated with pGsx>OC::WRPW.
Strong expression is observed in the sensory vesicle and in the palps of 65% of the embryos in which Onecut dominant negative was overexpressed in the sensory vesicle.
"n" is the number of scored embryos ; % corresponds to the proportion of embryos showing similar staining patterns.

Stained molecule KH2012:KH.L107.7 (LHX1; LHX5)
Stained region(s) anterior sensory vesicle - palps - posterior sensory vesicle -

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

Read more…

Conversion to Aniseed format of Ghost database entry from Imai et al. (2004) Development 131(16)

Original annotation :
Gene name: Lhx1.
Expression pattern: nervous system .
Comment : a part of the brain.

Stained molecule KH2012:KH.L107.7 (LHX1; LHX5)
Stained region(s) anterior anterior sensory vesicle -

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

Read more…

No data shown in the article for this developmental stage.
Lhx1/5 is expressed in A12.239 at the late tailbud stage.

Stained molecule KH2012:KH.L107.7 (LHX1; LHX5)
Stained region(s) visceral ganglion -

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

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Lateral view of the motor ganglion of a Ciona robusta late tailbud embryo probed for Lhx1/5 expression (green) and electroporated with FGF8/17/18>mCherry reporter construct (red nuclei) and FGF8/17/18>Su(H)-DBM overexpression construct.
Lhx1/5 is expressed in A12.239 and A12.237.
Original comment: Inhibition of Notch signaling (FGF8/17/18>Su(H)-DBM) also results in OFF-ON-OFF-ON pattern of expression of A12.239 marker Lhx1/5.
The A9.30 lineage is visualized using the FGF8/17/18 reporter construct (red).

Stained molecule KH2012:KH.L107.7 (LHX1; LHX5)
Stained region(s) visceral ganglion -