Aniseed - Gene Card

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Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library		4 clone(s) / 5,577
Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult		0 clone(s) / 31,366
Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo		0 clone(s) / 15,579
Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg		0 clone(s) / 31,100
Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva		15 clone(s) / 26,704
Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo		20 clone(s) / 26,680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K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis		0 clone(s) / 5,468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Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells		0 clone(s) / 29,579
Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle		0 clone(s) / 2,556
Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo		2 clone(s) / 16,939
Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula		3 clone(s) / 25,258
Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad		0 clone(s) / 16,936
Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex		0 clone(s) / 10,463
Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart		0 clone(s) / 13,243
Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland		0 clone(s) / 17,765
Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal		3 clone(s) / 17,872
Yutaka Satou unpublished cDNA library, mature adult whole animal Yutaka Satou unpublished cDNA library, mature adult whole animal		0 clone(s) / 107,314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)		5 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 2^RLE does not permit you to compare a gene across different experiments.

Download RLE Relative Log Expression data

RNA-Seq Experiment n°34135

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

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

35 results

Click here to visualize with MorphoNet

Experiment data ( results)

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

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 :Cdx.
Expression pattern : No signal was detected

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	No expression -

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

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 :Cdx.
Expression pattern : No distinct zygotic signal was detected

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	No expression -

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

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 :Cdx.
Expression pattern : No distinct zygotic signal was detected

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	No expression -

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

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 :Cdx.
Expression pattern : No distinct zygotic signal was detected

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	No expression -

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

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 :Cdx.
Expression pattern : No distinct zygotic signal was detected

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	No expression -

C. robusta formely Ciona int. type A, Stage 12 (mid gastrula)

Vegetal view of a late gastrula embryo probed for Ci-Cdx expression following the injection of Delta-MO.

Original annotation:
Cdx expression was lost following the injection of Delta-MO (white arrow).

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	No expression -

C. robusta formely Ciona int. type A, Stage 12 (mid gastrula)

Vegetal view of a mid gastrula stage embryo treated with DMSO from the 16-cell stage and showing expression of Ci-cdx.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	A9.15 cell pair - A9.29 cell pair - posterior secondary muscle lineage (A9.31 line) - tail epidermis -

C. robusta formely Ciona int. type A, Stage 12 (mid gastrula)

Vegetal view of a mid gastrula stage embryo treated with SB431542 from the 16-cell stage and showing expression of Ci-cdx.

Original annotation :
Ci-cdx was diminished in the A-line nerve cord-lineage cells.
Blue arrowhead indicates blastomeres in which the expression was diminished.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	tail epidermis -

C. robusta formely Ciona int. type A, Stage 12 (mid gastrula)

Vegetal view of a mid gastrula stage embryo treated with SB431542 from the 64-cell stage and showing expression of Ci-cdx.

Original annotation :
SB431542 treatment from the 64-cell stage did not affect the expression pattern.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	A9.15 cell pair - A9.29 cell pair - posterior secondary muscle lineage (A9.31 line) - tail epidermis -

C. robusta formely Ciona int. type A, Stage 12 (mid gastrula)

Vegetal view of a late gastrula wild type embryo probed for Ci-Cdx expression.

Original Annotation :
Cdx was expressed in A line in row I : A9.29 and A9.15 cell pairs.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	A9.15 cell pair - A9.29 cell pair -

C. robusta formely Ciona int. type A, Stage 12 (mid gastrula)

Vegetal view of a mid gastrula stage wild type embryo probed for Ci-Cdx expression.

Original Annotation : Ci-Cdx expression was detected in A9.29, A9.15 and A9.31 cell pairs.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	A9.15 cell pair - A9.29 cell pair - posterior secondary muscle lineage (A9.31 line) -

C. robusta formely Ciona int. type A, Stage 12 (mid gastrula)

Vegetal view of a mid gastrula stage embryo probed for Ci-Cdx and treated with U0126 from the 112-cell stage.

Original Annotation : Ci-Cdx expression was lost following the inhibition of MEK/ERK signaling (due to U0126).

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	No expression -

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

Vegetal view of a late gastrula stage embryo showing expression of Ci-cdx.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	A9.15 cell pair - A9.29 cell pair - posterior secondary muscle lineage (A9.31 line) -

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

Vegtal view of a late gastrula stage embryo. Ci-cdx expression was examined in embryos that expressed Ci-FoxD/Ci-nodal transgene.

Original annotation:
Ci-FoxD/Ci-Nodal transgene mediated ectopic activation of Ci-cdx expression in A9.13 cell pair.
Red arrowheads indicates ectopic expression.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	A9.13 cell pair - A9.15 cell pair - A9.29 cell pair - posterior secondary muscle lineage (A9.31 line) -

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

Vegetal view of a late gastrula stage embryo. Ci-cdx expression was examined in embryos that expressed Ci-FoxD/Ci-lefty transgene.

Original annotation:
The Ci-FoxD/Ci-lefty transgene suppressed the Ci-cdx expression.
Blue arrowhead indicates blastomeres in which the expression was diminished.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	No expression -

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

Vegetal view of a late gastrula stage embryo. Ci-cdx expression was examined in SB431542-treated embryos.

Original annotation:
SB431542 suppressed the Ci-cdx expression.
Blue arrowhead indicates blastomeres in which the expression was diminished.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	No expression -

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

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 :Cdx.
Expression pattern : epidermis, unidentifiable.
Comment : posterior epidermis; nervous system, A9.15, A9.29

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	A9.15 cell pair - A9.29 cell pair - posterior tail epidermis -

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

Vegetal view of a late gastrula stage wild type embryo probed for Cdx expression.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	A9.15 cell pair - A9.29 cell pair -

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

Vegetal view of a late gastrula stage embryo probed for Cdx expression following egg micro-injection of a FoxB MO. Cdx was ectopically expressed in medial part of A-line nerve cord cells.

Aniseed annotation : Staining is also observed in two cells that maybe correspond to Trunk Lateral Cells.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	A line neural plate -

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

Vegetal view of a late gastrula stage embryo probed for Cdx expression following egg micro-injection of a SoxC MO. Cdx is ectopically expressed in medial part of A-line nerve cord cells.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	A line neural plate -

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

Vegetal view of a late gastrula stage embryo probed for Cdx expression following egg micro-injection of a ZicL MO. Cdx is down-regulated in A-line nerve cord cells.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	No expression -

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

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 :Cdx.
Expression pattern : epidermis.
Comment : posterior epidermis

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	tail epidermis -

C. robusta formely Ciona int. type A, Stage 17 (initial tailbud I)

Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904. Original annotation: tail epidermis. Expression pattern: Epidermis Endodermal strand Nerve cord

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	endodermal strand - epidermis - tail nerve cord -

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

Lateral view of an early tailbud stage wild type embryo probed for Ci-Cdx expression.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	endodermal strand - tail epidermis - tail nerve cord -

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

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 :Cdx.
Expression pattern : epidermis.
Comment : posterior.

Aniseed annotation : Expression is also detected in the endodermal strand and nerve cord.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	endodermal strand - tail epidermis - tail nerve cord -

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

Mid tailbud wild type embryos treated with DMSO, probed for Ci-Cdx expression.

Aniseed annotation:
Cdx was expressed in the tail epidermis, endordermal strand and tail nerve cord.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	endodermal strand - tail epidermis - tail nerve cord -

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

Mid tailbud wild type embryos treated with DMSO, probed for Ci-Cdx expression.

Aniseed annotation:
Cdx was expressed in the tail epidermis, endordermal strand and tail nerve cord.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	endodermal strand - tail epidermis - tail nerve cord -

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

Mid tailbud wild type embryos treated with DMSO, probed for Ci-Cdx expression.

Aniseed annotation:
Cdx was expressed in the tail epidermis, endordermal strand and tail nerve cord.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	endodermal strand - tail epidermis - tail nerve cord -

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

Conversion to Aniseed format of Ghost database entry from Satou Y et al., Development 2001; 128:2893-2904. Original annotation: tail epidermis, but not in the tip of the tail. Expression pattern: Epidermis Endodermal strand Nerve cord

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	endodermal strand - epidermis - tail nerve cord -

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

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 :Cdx.
Expression pattern : epidermis.
Comment : posterior epidermis

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	endodermal strand - tail epidermis - tail nerve cord -

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

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)

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

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	endodermal strand - epidermis - tail nerve cord -

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

Conversion to aniseed format of DBTGR database entry from Kusakabe team.

Original annotation:
Tail epidermis; nerve cord; posterior trunk epidermis; endodermal strand.

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	endodermal strand - posterior dorsal midline head epidermis (b8.20 line) - posterior ventral head epidermis (a7.16 line) - tail epidermis - tail nerve cord -

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

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

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)	tail nerve cord -

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

Expression signals were assessed by whole-mount in situ hybridization (WISH) and the NBT/BCIP coloring system under the stereomicroscope. Bars 100 μm (a–c), 20 μm (d,e)
“Cdx expression is detected in the intestine in juveniles (c) and is restricted to the anterior intestine (e).”

Stained molecule	KH2012:KH.C14.408 (CDX1; CDX2; CDX4)
Stained region(s)