Aniseed - Gene Card

Pub 'PMID:17959164'

EST count

No result

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 2^RLE does not permit you to compare a gene across different experiments.

Download RLE Relative Log Expression data

RNA-Seq Experiment n°34136

Oocytes of a single individual of Phallusia mammillata (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).

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)*	P.mammillata, Stage 0 (Unfertilized egg)
		P.mammillata, Stage 8 (64-cell)
		P.mammillata, Stage 11 (early gastrula)
		P.mammillata, Stage 12 (mid gastrula)
		P.mammillata, Stage 15 (mid neurula)
		P.mammillata, Stage 21 (mid tailbud I)
		P.mammillata, Stage 26 (hatching larva)

Wild type - Replica 2
	*Territories*	whole embryo -

	*Biomaterial(s)*	P.mammillata, Stage 0 (Unfertilized egg)
		P.mammillata, Stage 8 (64-cell)
		P.mammillata, Stage 11 (early gastrula)
		P.mammillata, Stage 12 (mid gastrula)
		P.mammillata, Stage 15 (mid neurula)
		P.mammillata, Stage 21 (mid tailbud I)
		P.mammillata, Stage 26 (hatching larva)

In Situ Experiment Data

27 results

Click here to visualize with MorphoNet

Experiment data ( results)

P.mammillata, Stage 0 (Unfertilized egg)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France). PEM RNA (located in vegetal cortex)
Gene name : Ephr1 (EPHA4; EPHA7; EPHB1)

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	whole egg -

P.mammillata, Stage 5a (early 16-cell)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : Ephr1 (EPHA4; EPHA7; EPHB1)

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	B5.2 cell pair -

P.mammillata, Stage 5a (early 16-cell)

Vegetal view of a WT Phallusia mammillata 16-cell stage embryo probed for Eph1 expression.
Eph1 maternal expression is observed in B5.2 blastomer pair

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	B5.2 cell pair -

P.mammillata, Stage 6b (late 32-cell)

Vegetal view of a WT Phallusia mammillata 32-cell stage embryo probed for Eph1 expression.
Maternal expression of Eph1 is observed in B6.

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	B6.3 cell pair -

P.mammillata, Stage 8 (64-cell)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : Ephr1 (EPHA4; EPHA7; EPHB1)

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	B7.6 cell pair -

P.mammillata, Stage 8 (64-cell)

Vegetal view of a Phallusia mammillata 64-cell stage embryo probed for Eph1 expression and treated with SB431542, a selective pharmacological inhibitor of the Nodal receptor ALK4/5/7, from the 16-cell stage.
Eph1 is expressed in B7.6 blastomer pair(presumptive germ cells, red arrowhead).
Second image is the HD raw picture sent by the authors.
Scale bar: 50 μm.

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	B7.6 cell pair -

P.mammillata, Stage 8 (64-cell)

Vegetal view of a WT Phallusia mammillata 64-cell stage embryo probed for Eph1 expression.
Eph1 maternal expression is observed in the presumptive germ cells (B7.6, red arrowhead).
Second image is the HD raw picture sent by the authors.
Scale bar: 50 μm.

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	B7.6 cell pair -

Vegetal view of a WT Phallusia mammillata 64-cell stage embryo probed for Eph1 expression.
Eph1 maternal expression is observed in the presumptive germ cells B7.6, and very weak zigotic expression in most of the vegetal blastomers.
Original comment: Eph1 is zygotically expressed from the 64-cell stage. Vegetal Eph1 expression, initially very low, increases during endoderm invagination.

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	A line - B7.6 cell pair - B line -

P.mammillata, Stage 8 (64-cell)

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	B7.6 cell pair -

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	A line - B7.6 cell pair - B line -

P.mammillata, Stage 9 (76-cell)

Vegetal view of a WT Phallusia mammillata 76-cell stage embryo probed for Eph1 expression.
Eph1 maternal expression is observed in the presumptive germ cells (B7.6, red arrowhead) and in B7.1, B7.2, B8.6, A7.1, A7.2, A7.5 and A7.6 bastomer pairs.
Second image is the HD raw picture sent by the authors.

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - A7.6 cell pair - B7.1 cell pair - B7.2 cell pair - B7.6 cell pair - B8.6 cell pair -

P.mammillata, Stage 9 (76-cell)

Vegetal view of a Phallusia mammillata 76-cell stage embryo probed for Eph1 expression and treated from the 16-cell stage with SB431542, a selective pharmacological inhibitor of the Nodal receptor ALK4/5/7.
Eph1 maternal expression is observed in the presumptive germ cells (B7.6, red arrowhead) and in B7.1, B7.2, B8.6, A7.1, A7.2, A7.5 and A7.6 bastomer pairs.
Original comment: Nodal signalling inhibition did not qualitatively change the spatial domain of zygotic Eph1 expression but did, however, markedly reduce the intensity of zygotic Eph1 in situ signal.
Second image is the HD raw picture sent by the authors.

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - A7.6 cell pair - B7.1 cell pair - B7.2 cell pair - B7.6 cell pair - B8.6 cell pair -

P.mammillata, Stage 9 (76-cell)

Vegetal view of a WT Phallusia mammillata 76-cell stage embryo probed for Eph1 expression.
Eph1 is expressed in B7.2, B7.6, B7.1, B7.5, A7.1, A7.2, A7.5 and A7.6 blastomer pairs. Expression in B7.6 is maternal.

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - A7.6 cell pair - B7.1 cell pair - B7.2 cell pair - B7.5 cell pair - B7.6 cell pair -

P.mammillata, Stage 10 (112-cell)

Vegetal view of a WT Phallusia mammillata 110-cell stage embryo probed for Eph1 expression.
Eph1 maternal expression is observed in the presumptive germ cells (B8.11, red arrowhead) and in B7.1, B7.2, B8.6, A7.1, A7.2, A7.5 and A7.6 bastomer pairs.
Second image is the HD raw picture sent by the authors.

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - A8.11 cell pair - B7.1 cell pair - B7.2 cell pair - B7.6 cell pair - B8.6 cell pair -

Vegetal view of a WT Phallusia mammillata 110-cell stage embryo probed for Eph1 expression.
Eph1 is expressed in B7.2, B7.6, B7.1, B7.5, B8.6, A7.1, A7.2, A7.5 and A8.11 blastomer pairs.

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - A8.11 cell pair - B7.1 cell pair - B7.2 cell pair - B7.5 cell pair - B7.6 cell pair - B8.6 cell pair -

P.mammillata, Stage 10 (112-cell)

Vegetal view of a Phallusia mammillata 110-cell stage embryo probed for Eph1 expression and treated from the 16-cell stage with SB431542, a selective pharmacological inhibitor of the Nodal receptor ALK4/5/7.
Eph1 maternal expression is observed in the presumptive germ cells (B7.6, red arrowhead) and in B7.1, B7.2, B8.6, A7.1, A7.2, A7.5 and A7.6 bastomer pairs.
Original comment: Nodal signalling inhibition did not qualitatively change the spatial domain of zygotic Eph1 expression but did, however, markedly reduce the intensity of zygotic Eph1 in situ signal.
Second image is the HD raw picture sent by the authors.

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - A8.11 cell pair - A8.12 cell pair - B7.1 cell pair - B7.2 cell pair - B7.6 cell pair - B8.6 cell pair -

P.mammillata, Stage 10 (112-cell)

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - A8.11 cell pair - B7.1 cell pair - B7.2 cell pair - B7.6 cell pair - B8.6 cell pair -

Vegetal view of a WT Phallusia mammillata 110-cell stage embryo probed for Eph1 expression.
Eph1 is expressed in B7.2, B7.6, B7.1, B7.5, B8.6, A7.1, A7.2, A7.5 and A8.11 blastomer pairs.

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - A8.11 cell pair - B7.1 cell pair - B7.2 cell pair - B7.5 cell pair - B7.6 cell pair - B8.6 cell pair -

P.mammillata, Stage 11 (early gastrula)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : Ephr1 (EPHA4; EPHA7; EPHB1)

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - A8.11 cell pair - A8.12 cell pair - A8.13 cell pair - A8.14 cell pair - A8.5 cell pair - A8.6 cell pair - B7.1 cell pair - B7.2 cell pair - B7.5 cell pair - B7.7 cell pair -

P.mammillata, Stage 11 (early gastrula)

Original annotation:
In 10-50% of stained embryos, main expression is observed in endoderm and notochord ; weaker expression is observed in A7.6 cell pair.
Aniseed annotation:
At early gastrula :
- Endoderm corresponds to B7.1, B7.2, B7.5, A7.1, A7.2 and A7.5 cell pairs.
- Part of notochord corresponds to A8.5 and A8.6 cell pairs.
- A7.6 corresponds to A8.11 and A8.12 cell pairs.

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - A8.11 cell pair - A8.12 cell pair - A8.5 cell pair - A8.6 cell pair - B7.1 cell pair - B7.2 cell pair - B7.5 cell pair -

P.mammillata, Stage 11 (early gastrula)

Original annotation:
In 10-50% of stained embryos, main expression is observed in endoderm, secondary expression in B7.7 cell pair.
Aniseed annotation: At early gastrula : - Part of endoderm corresponds to B7.1, B7.2, A7.1 and A7.2 cell pairs.

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - B7.1 cell pair - B7.2 cell pair - B7.7 cell pair -

P.mammillata, Stage 13 (late gastrula)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : Ephr1 (EPHA4; EPHA7; EPHB1)

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	A line neural plate - endoderm -

P.mammillata, Stage 14 (early neurula)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : Ephr1 (EPHA4; EPHA7; EPHB1)

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	neural plate -

P.mammillata, Stage 16 (late neurula)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : Ephr1 (EPHA4; EPHA7; EPHB1)

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	neural plate - posterior tail epidermis -

P.mammillata, Stage 22 (mid tailbud II)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : Ephr1 (EPHA4; EPHA7; EPHB1)

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	central nervous system -

P.mammillata, Stage 24 (late tailbud II)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : Ephr1 (EPHA4; EPHA7; EPHB1)

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	central nervous system -

P.mammillata, Stage 26 (hatching larva)

Original annotation:
In >50% of stained embryos, expression is observed in endoderm, TLCs, mesenchyme, notochord and brain.

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	anterior sensory vesicle - endoderm - neck - notochord - posterior sensory vesicle - trunk lateral cells (A7.6 line) - visceral ganglion -

P.mammillata, Stage 26 (hatching larva)

Original annotation:
In 10-50% of stained embryos, expression is observed endoderm, mesenchyme, notochord, brain, muscle and neurones.

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	anterior sensory vesicle - endoderm - notochord - peripheral nervous system - posterior sensory vesicle - tail muscles - visceral ganglion -

P.mammillata, Stage 26 (hatching larva)

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	endoderm -

P.mammillata, Stage 26 (hatching larva)

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)	anterior sensory vesicle - peripheral nervous system - posterior sensory vesicle -

P.mammillata, Stage 26 (hatching larva)

No expression is observed.

Stained molecule	Phmamm.CG.MTP2014.S160.g04451 (EPHA4; EPHA7; EPHB1)
Stained region(s)