1 result
OVERVIEW
Click here to see the RNA-Seq Pipeline Protocol.
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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 Halocynthia roretzi (Aomori, Japan) were fertilized by sperms of an another single individual and development was followed microscopically. Embryos were snapfrozen in liquid nitrogen at the appropriate stage and kept at -80°C. Total RNA was prepared with the AGPC method and the quality was checked with the Bioanalyzer, most 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 |
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| Wild type - Replica 1 | ||
| Territories | whole embryo - | |
| Biomaterial(s) | H.roretzi, Stage 0 (Unfertilized egg) | |
| H.roretzi, Stage 8 (64-cell) | ||
| H.roretzi, Stage 12 (mid gastrula) | ||
| H.roretzi, Stage 21 (mid tailbud I) | ||
| H.roretzi, Stage 26 (hatching larva) | ||
| Wild type - Replica 2 | ||
| Territories | whole embryo - | |
| Biomaterial(s) | H.roretzi, Stage 0 (Unfertilized egg) | |
| H.roretzi, Stage 8 (64-cell) | ||
| H.roretzi, Stage 12 (mid gastrula) | ||
| H.roretzi, Stage 15 (mid neurula) | ||
| H.roretzi, Stage 21 (mid tailbud I) | ||
| H.roretzi, Stage 26 (hatching larva) | ||
17 results
MAGEST annotation : a4.2, b4.2.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | a4.2 cell pair - b4.2 cell pair - |
Vegetal view of a control Halocynthia roretzi 110-cell stage embryo probed for ETR-1 expression and treated with DMSO.
ETR-1 is expressed in A8.7, A8.8 and A8.15 nerve cord precursors (blue arrows).
Yellow arrows indicate the absence of ectopic gene expression in germline cells.
The numbers represent the proportion of embryos showing ectopic gene expression in the germline.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | A8.15 cell pair - A8.7 cell pair - A8.8 cell pair - |
Vegetal view of a Halocynthia roretzi 110-cell stage embryo probed for ETR-1 expression, injected with morpholinos against Pem and treated with GSK126, a selective inhibitor of EZH2 used to inhibit H3K27me3.
ETR-1 is expressed in A8.7, A8.8 and A8.15 nerve cord precursors, as in WT conditions.
Original comment: No ectopic ETR-1 expression in the germline was observed in Pem- and H3K27me3-deficient germline cells (0%, n = 19; yellow arrows).
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | A8.15 cell pair - A8.7 cell pair - A8.8 cell pair - |
MAGEST annotation : brain, nerve cord.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | A8.15 cell pair - A8.16 cell pair - a8.17 cell pair - a8.19 cell pair - a8.25 cell pair - A8.7 cell pair - A8.8 cell pair - b8.17 cell pair - b8.19 cell pair - |
Vegetal view of a WT Halocynthia roretzi gastrula stage embryo probed for ETR-1 expression.
ETR-1 is expressed in the a-line neural plate.
Original comment: The expression of Hr-ETR-1 at the early neural stage is detected in a four by six sheet of
a-line cells with two rows of the cells (daughter cells of
a8.17, a8.19, and a8.25) having the strongest expression
(white arrows). Hr-ETR-1 is also expressed in fourteen A-
line cells (A-line neural plate).
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | a9.33 cell pair - a9.34 cell pair - a9.35 cell pair - a9.36 cell pair - a9.37 cell pair - a9.38 cell pair - a9.39 cell pair - a9.40 cell pair - a9.49 cell pair - a9.50 cell pair - a9.51 cell pair - a9.52 cell pair - a line neural plate - A line neural plate - row III neural plate - row IV neural plate - row VI neural plate - row V neural plate - |
Vegetal view of a Halocynthia roretzi gastrula stage embryo probed for ETR-1 expression and injected with a control MO in left A5.1 at the 16-cell stage.
ETR-1 is expressed in the A- and a- neural plate.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | a line neural plate - A line neural plate - |
Vegetal view of a Halocynthia roretzi gastrula stage embryo probed for ETR-1 expression and injected with a control MO in left A5.2 at the 16-cell stage.
ETR-1 is expressed in the A- and a- neural plate.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | a line neural plate - A line neural plate - |
Vegetal view of a WT Halocynthia roretzi gastrula stage embryo probed for ETR-1 expression.
ETR-1 is expressed in the a-line neural plate.
Original comment: The expression of Hr-ETR-1 at the early neural stage is detected in a four by six sheet of
a-line cells with two rows of the cells (daughter cells of
a8.17, a8.19, and a8.25) having the strongest expression
(white arrows). Hr-ETR-1 is also expressed in fourteen A-
line cells (A-line neural plate).
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | a9.33 cell pair - a9.34 cell pair - a9.35 cell pair - a9.36 cell pair - a9.37 cell pair - a9.38 cell pair - a9.39 cell pair - a9.40 cell pair - a9.49 cell pair - a9.50 cell pair - a9.51 cell pair - a9.52 cell pair - a line neural plate - A line neural plate - row III neural plate - row IV neural plate - row VI neural plate - row V neural plate - |
Vegetal view of a Halocynthia roretzi gastrula stage embryo probed for ETR-1 expression and injected with a control MO in left A5.1 at the 16-cell stage.
ETR-1 is expressed in the A- and a- neural plate.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | a line neural plate - A line neural plate - |
Vegetal view of a Halocynthia roretzi gastrula stage embryo probed for ETR-1 expression and injected with a control MO in left A5.2 at the 16-cell stage.
ETR-1 is expressed in the A- and a- neural plate.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | a line neural plate - A line neural plate - |
Vegetal view of a WT Halocynthia roretzi gastrula stage embryo probed for ETR-1 expression.
ETR-1 is expressed in the a-line neural plate.
Original comment: The expression of Hr-ETR-1 at the early neural stage is detected in a four by six sheet of
a-line cells with two rows of the cells (daughter cells of
a8.17, a8.19, and a8.25) having the strongest expression
(white arrows). Hr-ETR-1 is also expressed in fourteen A-
line cells (A-line neural plate).
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | a9.33 cell pair - a9.34 cell pair - a9.35 cell pair - a9.36 cell pair - a9.37 cell pair - a9.38 cell pair - a9.39 cell pair - a9.40 cell pair - a9.49 cell pair - a9.50 cell pair - a9.51 cell pair - a9.52 cell pair - a line neural plate - A line neural plate - row III neural plate - row IV neural plate - row VI neural plate - row V neural plate - |
Vegetal view of a Halocynthia roretzi gastrula stage embryo probed for ETR-1 expression and injected with a control MO in left A5.1 at the 16-cell stage.
ETR-1 is expressed in the A- and a- neural plate.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | a line neural plate - A line neural plate - |
Vegetal view of a Halocynthia roretzi gastrula stage embryo probed for ETR-1 expression and injected with a control MO in left A5.2 at the 16-cell stage.
ETR-1 is expressed in the A- and a- neural plate.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | a line neural plate - A line neural plate - |
Vegetal view of a Halocynthia roretzi gastrula stage embryo probed for ETR-1 expression and injected with Hr-Fgf9/16/20 MO in left A5.1 at the 16-cell stage.
ETR-1 is expressed in the A-neural plate and in a9.49, a9.50, a9.51 and a9.52 from the a-neural plate (black arrowhead). Domains of the a-line in which the expression is eliminated by local inhibition of FGF9/16/20 signaling is shown by white arrowheads.
Original comment: Inhibition of Hr-FGF9/16/20 signaling from the descendants of A5.1 affected brain formation in the a5.3 lineage but not in the a5.4 lineage with respect to Hr-ETR-1 expression (100%, n=12 for A5.1 MO
injection).
The diagram is in vegetal view (anterior up), injected blastomere is in red.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | a9.49 cell pair - a9.50 cell pair - a9.51 cell pair - a9.52 cell pair - A line neural plate - |
Vegetal view of a Halocynthia roretzi gastrula stage embryo probed for ETR-1 expression and injected with Hr-Fgf9/16/20 MO in left A5.2 at the 16-cell stage.
ETR-1 is expressed in the A-neural plate and in the a-neural plate (black arrowheads) minus a9.49, a9.50, a9.51 and a9.52 blastomers (white arrowhead).
Original comment: Injection of the A5.2 blastomere with Hr-FGF9/16/20 MO eliminated Hr-ETR-1 expression in the daughters of a8.25.
The diagram is in vegetal view (anterior up), injected blastomere is in red.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | a9.33 cell pair - a9.34 cell pair - a9.35 cell pair - a9.36 cell pair - a9.37 cell pair - a9.38 cell pair - a9.39 cell pair - a9.40 cell pair - A line neural plate - |
Vegetal view of a Halocynthia roretzi gastrula stage embryo probed for ETR-1 expression and injected with Hr-Fgf9/16/20 MO in left B5.1 at the 16-cell stage.
ETR-1 is expressed in the a- and A-neural plate as in WT conditions.
The diagram is in vegetal view (anterior up), injected blastomere is in red.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | a line neural plate - A line neural plate - |
Vegetal view of a Halocynthia roretzi gastrula stage embryo probed for ETR-1 expression and injected with Hr-Fgf9/16/20 MO in left A6.1 at the 24-cell stage.
ETR-1 is expressed in the a- and A-neural plate as in WT conditions.
The diagram is in vegetal view (anterior up), injected blastomere is in red and brain precursors in blue.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | a line neural plate - A line neural plate - |
Vegetal view of a Halocynthia roretzi gastrula stage embryo probed for ETR-1 expression and injected with Hr-Fgf9/16/20 MO in left A6.2 at the 24-cell stage.
ETR-1 is expressed in the A-neural plate and in a9.49, a9.50, a9.51 and a9.52 from the a-neural plate (black arrowhead). Domains of the a-line in which the expression is eliminated or reduced by local inhibition of FGF9/16/20 signaling is shown by white arrowheads.
Original comment: Inhibition of Hr-FGF9/16/20 signaling from the descendants of A6.2 affected brain formation in the a5.3 lineage but not in the a5.4 lineage with respect to Hr-ETR-1 expression (69.6%, n=23 for A6.2 MO
injection).
The diagram is in vegetal view (anterior up), injected blastomere is in red and brain precursors in blue.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | a9.49 cell pair - a9.50 cell pair - a9.51 cell pair - a9.52 cell pair - A line neural plate - |
Vegetal view of a Halocynthia roretzi gastrula stage embryo probed for ETR-1 expression and injected with Hr-Fgf9/16/20 MO in left A6.4 at the 24-cell stage.
ETR-1 is expressed in the A-neural plate and in the a-neural plate (black arrowheads) minus a9.49, a9.50, a9.51 and a9.52 blastomers (white arrowhead).
Original comment: Injection of the A6.4 blastomere with Hr-FGF9/16/20 MO eliminated Hr-ETR-1 expression in the daughters of a8.25 (72.7% eliminated, n=22).
The diagram is in vegetal view (anterior up), injected blastomere is in red and brain precursors in blue.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | a9.33 cell pair - a9.34 cell pair - a9.35 cell pair - a9.36 cell pair - a9.37 cell pair - a9.38 cell pair - a9.39 cell pair - a9.40 cell pair - A line neural plate - |
Vegetal view of a Halocynthia roretzi gastrula stage embryo probed for ETR-1 expression and injected with Hr-Fgf9/16/20 MO in left A6.2 at the 32-cell stage.
ETR-1 is expressed in the a- and A-neural plate as in WT conditions.
The diagram is in vegetal view (anterior up), injected blastomere is in red and brain precursors in blue.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | a line neural plate - A line neural plate - |
An image of a cleavage-arrested Halocynthia roretzi embryo at the equivalent of the early neurula stage. ETR-1 expression is restricted to the anterior edge of the embryo. Vegetal view with anterior to the top.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | A line neural plate - |
Cleavage-arrested (at the equivalent of the neurula stage) Halocynthia roretzi embryo probed for ETR-1 expression and injected with PEM MO. Ectopic expression is observed in the posterior edge of the embryo (arrow heads). Vegetal view with anterior up.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | A line neural plate - |
MAGEST annotation : brain, nerve cord.
| Stained molecule | Harore.CG.MTP2014.S5.g02306 (CELF3; CELF4; CELF5) |
| Stained region(s) | anterior sensory vesicle - posterior sensory vesicle - tail nerve cord - |
