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| Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library |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| Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult |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| Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo |
|
4 clone(s) / 15,579 |
| Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg |
|
3 clone(s) / 31,100 |
| Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva |
|
0 clone(s) / 26,704 |
| Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo |
|
1 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| K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis |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| Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells |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| Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle |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| Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo |
|
3 clone(s) / 16,939 |
| Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula |
|
7 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| Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad |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| Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex |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| Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart |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| Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland |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| Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal |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 |
|
0 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) |
|
1 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 |
3 results
OVERVIEW
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.
OVERVIEW
Be careful, RLE and 2RLE does not permit you to compare a gene across different experiments.
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 |
|
|
| 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) | ||
Ciona robusta adults were obtained from the National Bio-Resource Project for Ciona (NBRP, Japan). 50 unperturbed and Foxd-morphant embryos were collected at the 32-, 64-, and 112-cell stages. RNA was extracted using a Dynabeads mRNA DIRECT Purification Kit (Thermo Fischer Scientific) and libraries were made with an Ion Total RNA-Seq kit ver 2 (Thermo Fischer Scientific). The libraries were sequenced with an Ion PGM instrument (Thermo Fischer Scientific).
| Assay platform | Ion Torrent PGM | |
| Layout | Single-end | |
| Stranded | Yes | |
| Read length | 20-365 | |
| Normalized data types |
|
|
| Wild type | ||
| Territories | whole embryo - | |
| Biomaterial(s) | C. robusta formely Ciona int. type A, Stage 6a (early 32-cell) | |
| C. robusta formely Ciona int. type A, Stage 8 (64-cell) | ||
| C. robusta formely Ciona int. type A, Stage 10 (112-cell) | ||
| Mutant | ||
| Deregulated molecule(s) | KH2012:KH.C8.890 - | |
| Territories | whole embryo - | |
| Biomaterial(s) | C. robusta formely Ciona int. type A, Stage 6a (early 32-cell) | |
| C. robusta formely Ciona int. type A, Stage 8 (64-cell) | ||
| C. robusta formely Ciona int. type A, Stage 10 (112-cell) | ||
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 |
|
|
| 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) | |
24 results
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 :Emc.
Expression pattern : Unlocalized signal was detected
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | whole embryo - |
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 :Emc.
Expression pattern : No distinct zygotic signal was detected
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | No expression - |
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 :Emc.
Expression pattern : No distinct zygotic signal was detected
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | No expression - |
Vegetal view of a WT Ciona robusta late 32-cell stage embryo probed for Emc/Id-b expression.
No expression is observed.
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | No expression - |
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 :Emc.
Expression pattern : a7.11, a7.12, a7.14, a7.15, a7.16, b7.12, b7.15, b7.16
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | a7.11 cell pair - a7.12 cell pair - a7.14 cell pair - a7.15 cell pair - a7.16 cell pair - b7.12 cell pair - b7.15 cell pair - b7.16 cell pair - |
Vegetal view of a WT Ciona robusta 64-cell stage embryo probed for Emc/Id-b expression.
No expression is observed.
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | No expression - |
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 :Emc.
Expression pattern : a8.17, a8.18, a8.19, a8.20, a8.21, a8.22, a8.23, a8.24, a8.25, a8.26, a8.27, a8.28, a8.29, a8.30, a8.31, a8.32
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | a8.17 cell pair - a8.18 cell pair - a8.19 cell pair - a8.20 cell pair - a8.21 cell pair - a8.22 cell pair - a8.23 cell pair - a8.24 cell pair - a8.25 cell pair - a8.26 cell pair - a8.27 cell pair - a8.28 cell pair - a8.29 cell pair - a8.30 cell pair - a8.31 cell pair - a8.32 cell pair - |
Vegetal view of a WT Ciona robusta 112-cell stage embryo probed for Emc/Id-b expression.
Expression is observed in A8.6, A8.7, A8.15, b8.17 and b8.19 blastomere pairs.
In schematic representation of gene expression, nerve cord precursors are shown in blue. Blastomeres with gene expression are marked by dots.
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | A8.15 cell pair - A8.6 cell pair - A8.7 cell pair - b8.17 cell pair - b8.19 cell pair - |
A late gastrula wild type embryo probed for Emc expression.
Original Annotation :
Emc was expressed in A9.16 and A9.32 cell pairs.
Aniseed Annotation :
According to the picture and to Imai et al. 2006, there is also expression in a9.33, a9.34, a9.49, a9.50 cell pairs.
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | A9.16 cell pair - A9.32 cell pair - a9.33 cell pair - a9.34 cell pair - a9.49 cell pair - a9.50 cell pair - |
Vegetal view of a late gastrula stage embryo probed for Emc expression following the injection of Delta-like MO.
Original Annotation :
Emc expression was lost in A9.32 cell pair (white arrow).
Aniseed Annotation :
It seems that expression in a-line neural plate and in A9.16 cell pair is also lost.
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | A9.16 cell pair - |
Vegetal view of a late gastrula stage embryo probed for Emc expression following the injection of neurogenin-MO.
Original annotation:
Emc expression was lost in A9.32 (white arrow).
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | A9.16 cell pair - a9.33 cell pair - a9.34 cell pair - a9.49 cell pair - a9.50 cell pair - |
Conversion to Aniseed format of data from Yutaka Satou s gene expression profiles of transcription factors and signalling molecule ISH screen
ANISEED annotation : Expression in a9.49, A10.31, A10.32, a9.34, a9.33 and a9.50 cell pairs.
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | A10.31 cell pair - A10.32 cell pair - a9.33 cell pair - a9.34 cell pair - a9.49 cell pair - a9.50 cell pair - No expression - |
Vegetal view of a late gastrula stage probed for Emc expression.
Original annotation:
Ci-emc was expressed in neural plate and CNS cells but not in A7.6/TLC lineage.
Aniseed annotation:
According to the picture, it seems that the staining is localized in a9.35 and a9.39 cell pairs.
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | a9.35 cell pair - a9.39 cell pair - |
Vegetal view of a late gastrula stage wild type embryo probed for emc expression.
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | A10.31 cell pair - A10.32 cell pair - a9.33 cell pair - a9.34 cell pair - a9.49 cell pair - a9.50 cell pair - |
Vegetal view of a late gastrula stage embryo probed for emc expression following egg micro-injection of a Nodal MO.
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | No expression - |
Vegetal view of a late gastrula stage embryo probed for emc expression following egg micro-injection of a AP2-like2 MO.
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | epidermis - |
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 :Emc.
Expression pattern : No distinct zygotic signal was detected
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | No expression - |
Dorsal view of an initial tailbud stage probed for Emc expression.
Original annotation:
Ci-emc was expressed in neural plate and CNS cells but not in A7.6/TLC lineage.
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | anterior sensory vesicle - |
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 :Emc.
Expression pattern : nervous system, nerve cord.
Comment : epidermal neurons, brain, palp.
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | nervous system - |
Dorsal view of an early tailbud wild type embryo probed for Emc expression.
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 :
Emc expression was detected in A11.120, A11.119, A11.118, A11.117 cell pairs (visceral ganglion).
Aniseed Annotation :
According to the picture and to others data in ANISEED, it seems that there is also expression in the anterior sensory vesicle.
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | anterior sensory vesicle - visceral ganglion - |
Dorsal view of an early tailbud embryo probed for Emc expression following the injection of Emc-MO.
Rred and yellow arrowheads indicate boundaries between the neck and the visceral ganglion, and between the visceral ganglion and the caudal nerve cord, respectively on the control picture.
Original Annotation :
Emc expression became ectopic (black arrow) following the injection of Emc-MO.
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | central nervous system - |
Dorsal view of an early tailbud embryo probed for Emc expression 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 in the control picture.
Original Annotation :
Emc expression was lost in the visceral ganglion (white arrow) following the injection of neurogenin-MO.
Aniseed Annotation :
It seems that expression persists in the anterior sensory vesicle.
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | anterior sensory vesicle - |
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 :Emc.
Expression pattern : nervous system, nerve cord.
Comment : epidermal neurons, brain, palp.
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | nervous system - tail epidermis - |
Mid tailbud stage wild type embryo probed for Emc expression. No picture available in the article.
Original Annotation :
Emc expression was detected in A12.240, A12.238, A13.474, A13.473, A12.239, A11.118 and A11.117 cell pairs (visceral ganglion).
Aniseed Annotation :
According to others data in ANISEED, it seems that there is also expression in the anterior sensory vesicle.
| Stained molecule | KH2012:KH.C7.157 (ID1; ID2; ID3) |
| Stained region(s) | anterior sensory vesicle - visceral ganglion - |
