Aniseed - Gene Card

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

19 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).
Gene name : lhx3

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	No expression -

P.mammillata, Stage 3 (4-cell)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : lhx3

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	No expression -

P.mammillata, Stage 4 (8-cell)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : lhx3

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	No expression -

P.mammillata, Stage 5b (late 16-cell)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : lhx3

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	No expression -

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

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : lhx3

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	No expression -

P.mammillata, Stage 10 (112-cell)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : lhx3

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - B7.1 cell pair - B7.2 cell pair -

P.mammillata, Stage 10 (112-cell)

Vegetal view of a WT Phallusia mammillata 110-cell stage embryo probed for Lhx3 expression.
Lhx3 is expressed in B7.1, B7.2, A7.1, A7.2 and A7.5 bastomer pairs.
Scale bar: 50 μm.

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - B7.1 cell pair - B7.2 cell pair -

Vegetal view of a WT Phallusia mammillata 110-cell stage embryo probed for Lhx3 expression.
Lhx3 is expressed in B7.1, B7.2, A7.1, A7.2 and A7.5 bastomer pairs.

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - B7.1 cell pair - B7.2 cell pair -

P.mammillata, Stage 10 (112-cell)

Vegetal view of a WT Phallusia mammillata 110-cell stage embryo probed for Lhx3 expression.
Lhx3 is expressed in B7.1, B7.2, A7.1, A7.2 and A7.5 bastomer pairs.
Scale bar: 50 μm.

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - B7.1 cell pair - B7.2 cell pair -

Vegetal view of a WT Phallusia mammillata 110-cell stage embryo probed for Lhx3 expression.
Lhx3 is expressed in B7.1, B7.2, A7.1, A7.2 and A7.5 bastomer pairs.

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - B7.1 cell pair - B7.2 cell pair -

P.mammillata, Stage 10 (112-cell)

Vegetal view of a Phallusia mammillata 112-cell stage embryo probed for Lhx3 expression and treated from the 16-cell stage with SB431542, a selective pharmacological inhibitor of the Nodal receptor ALK4/5/7.
Lhx3 is expressed in B7.1, B7.2, A7.1, A7.2 and A7.5 bastomer pairs.
Original comment: Expression level of Lhx3 was not reduced by Nodal inhibition.

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - B7.1 cell pair - B7.2 cell pair -

P.mammillata, Stage 10 (112-cell)

Vegetal view of a Phallusia mammillata 112-cell stage embryo probed for Lhx3 expression and treated with 6 μM NVPBHG712 from the 8-cell stage to inhibit Eph-mediated signalling.
Lhx3 is expressed in B7.1, B7.2, A7.1, A7.2 and A7.5 bastomer pairs, as in WT conditions.

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - B7.1 cell pair - B7.2 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 : lhx3

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair -

P.mammillata, Stage 11 (early gastrula)

Primary expression in A7.1, A7.5, B7.2 cell pairs
Secondary expression in A7.2 cell pair.

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	A7.1 cell pair - A7.2 cell pair - A7.5 cell pair - B7.2 cell pair -

P.mammillata, Stage 12 (mid gastrula)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : lhx3

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	No expression -

P.mammillata, Stage 15 (mid neurula)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : lhx3

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	tail muscles -

P.mammillata, Stage 17 (initial tailbud I)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : lhx3

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	neck - posterior sensory vesicle - visceral ganglion -

P.mammillata, Stage 21 (mid tailbud I)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : lhx3

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	anterior sensory vesicle - visceral ganglion -

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 : lhx3

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	anterior sensory vesicle - ventral posterior sensory vesicle - visceral ganglion -

P.mammillata, Stage 23 (late tailbud I)

Conversion to Aniseed format of data from Remi Dumollard et al. (Ascidian BioCell Team, LBDV, Villefranche-sur-mer, France).
Gene name : lhx3

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	anterior sensory vesicle - posterior sensory vesicle - tail nerve cord - visceral ganglion -

P.mammillata, Stage 26 (hatching larva)

Stained molecule	Phmamm.CG.MTP2014.S2332.g16546 (LHX1; LHX3; LHX4)
Stained region(s)	head endoderm -