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| Nori Satoh unpublished cDNA library Nori Satoh unpublished cDNA library |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| Nori Satoh unpublished cDNA library, young adult Nori Satoh unpublished cDNA library, young adult |
|
6 clone(s) / 31,366 |
| Nori Satoh unpublished cDNA library, cleavage stage embryo Nori Satoh unpublished cDNA library, cleavage stage embryo |
|
3 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| Nori Satoh unpublished cDNA library, egg Nori Satoh unpublished cDNA library, egg |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| Nori Satoh unpublished cDNA library, larva Nori Satoh unpublished cDNA library, larva |
|
12 clone(s) / 26,704 |
| Nori Satoh unpublished cDNA library, tailbud embryo Nori Satoh unpublished cDNA library, tailbud embryo |
|
15 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| K. Inaba unpublished cDNA library, testis K. Inaba unpublished cDNA library, testis |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| Nori Satoh unpublished cDNA library, blood cells Nori Satoh unpublished cDNA library, blood cells |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| Nori Satoh unpublished cDNA library, endostyle Nori Satoh unpublished cDNA library, endostyle |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| Nori Satoh unpublished cDNA library, cleaving embryo Nori Satoh unpublished cDNA library, cleaving embryo |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| Nori Satoh unpublished cDNA library, gastrula and neurula Nori Satoh unpublished cDNA library, gastrula and neurula |
|
2 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| Nori Satoh unpublished cDNA library, gonad Nori Satoh unpublished cDNA library, gonad |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| Nori Satoh unpublished cDNA library, neural complex Nori Satoh unpublished cDNA library, neural complex |
|
6 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| Nori Satoh unpublished cDNA library, heart Nori Satoh unpublished cDNA library, heart |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| Yutaka Satou unpublished cDNA library, adult digestive gland Yutaka Satou unpublished cDNA library, adult digestive gland |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| Yutaka Satou unpublished cDNA library, embryo whole animal Yutaka Satou unpublished cDNA library, embryo whole animal |
|
2 clone(s) / 17,872 |
| Yutaka Satou unpublished cDNA library, mature adult whole animal Yutaka Satou unpublished cDNA library, mature adult whole animal |
|
7 clone(s) / 107,314 |
| Nori Satoh unpublished cDNA library, juvenile whole animal Nori Satoh unpublished cDNA library, juvenile whole animal |
|
2 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 |
|
3 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) |
|
2 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) | |
27 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 :Orphan bHLH1.
Expression pattern : No signal was detected
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| 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 :Orphan bHLH1.
Expression pattern : No distinct zygotic signal was detected
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| 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 :Orphan bHLH1.
Expression pattern : No distinct zygotic signal was detected
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | No expression - |
Animal view of a 32-cell stage embryo probed for Orphan_bHLH1 expression.
Original annotation: Orphan bHLH1 is expressed in b-line cells of the 32-cell stage embryo.
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | b line - |
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 :Orphan bHLH1.
Expression pattern : No distinct zygotic signal was detected
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| 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 :Orphan bHLH1.
Expression pattern : No distinct zygotic signal was detected
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | No expression - |
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | No expression - |
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| 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 :Orphan bHLH1.
Expression pattern : notochord, nervous system
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | neural plate - notochord - |
“Orphan bHLH-1 was expressed in the notochord.”
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | notochord - |
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 :Orphan bHLH1.
Expression pattern : notochord, nervous system
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | neural plate - notochord - |
“Orphan bHLH-1 was expressed in the notochord.”
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | notochord - |
“Orphan bHLH-1 was expressed in anterior trunk ectoderm and the notochord .”
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | notochord - |
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 :Orphan bHLH1.
Expression pattern : notochord, nervous system, epidermis.
Comment : plap, brain, notochord, dorsal midline epidermis, ventral midline tail
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | epidermis - nervous system - notochord - |
“Orphan bHLH-1 was expressed in the notochord.”
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - notochord - ventral midline anterior tail epidermis - ventral midline posterior tail epidermis - |
“Orphan bHLH-1 was expressed in anterior trunk ectoderm and the notochord .”
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - notochord - ventral midline anterior tail epidermis - ventral midline posterior tail 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 :Orphan bHLH1.
Expression pattern : notochord, nervous system, epidermis.
Comment : plap, brain, notochord, dorsal midline epidermis, ventral midline tail
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | epidermis - nervous system - notochord - |
“Orphan bHLH-1 was expressed in anterior trunk ectoderm and the notochord .”
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - notochord - ventral midline anterior tail epidermis - ventral midline posterior tail epidermis - |
“Orphan bHLH-1 was expressed in anterior trunk ectoderm and the notochord .”
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - notochord - ventral midline anterior tail epidermis - ventral midline posterior tail epidermis - |
“Orphan bHLH-1 was expressed in anterior trunk ectoderm and the notochord .”
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - notochord - ventral midline anterior tail epidermis - ventral midline posterior tail epidermis - |
"At late tailbud stages, Orphan bHLH-1 expression was downregulated in irregularly spaced cells that are presumably ESNs (white asterisks).
“Orphan bHLH-1 displayed a downregulation of expression in discrete cells within the midlines. The random location of these non-expressing cells suggests that they correspond to the ESNs.”
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - ventral midline anterior tail epidermis - ventral midline posterior tail epidermis - |
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - ventral midline anterior tail epidermis - ventral midline posterior tail epidermis - |
“Overexpression of Klf1/2/4 using the pFog driver led to activation or inhibition of Orphan bHLH-1 at the late tailbud stage compared to control.”
Embryos are in lateral views with anterior to the left and dorsal to the top.
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - ventral midline anterior tail epidermis - ventral midline posterior tail epidermis - |
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - ventral midline anterior tail epidermis - ventral midline posterior tail epidermis - |
“Overexpression of Msxb with either pFog or pSoxB2 can activate the other six genes (Nkx-C, Klf1/2/4, Achaete-scute a like-2, Cagf9/tox, Dll-C and Orphan bHLH-1) in the lateral epidermis.”
Embryos are in lateral views with anterior to the left and dorsal to the top.
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - ventral midline anterior tail epidermis - ventral midline posterior tail epidermis - |
“Overexpression of Nkx-C with pSoxB2 can activate the other six genes (Nkx-C, Klf1/2/4, Achaete-scute a like-2, Cagf9/tox, Dll-C and Orphan bHLH-1) in the lateral epidermis.
Embryos are in lateral views with anterior to the left and dorsal to the top.
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | dorsal midline anterior tail epidermis - dorsal midline head epidermis - dorsal midline posterior tail epidermis - ventral midline anterior tail epidermis - ventral midline posterior tail epidermis - |
Conversion to Aniseed format of Ghost database entry from Kusakabe T et al., Dev Biol. 2002; 242:188-203. Original annotation: . Expression pattern: Papilla Brain
| Stained molecule | KH2012:KH.C7.269 (KH.C7.269) |
| Stained region(s) | anterior sensory vesicle - neck - palp neurones - posterior sensory vesicle - |
