Aniseed - RNA-Seq

Method

RNA-seq experiment

Expression Profile

Species

C. robusta formely Ciona int. type A

Assay platform

Ion Torrent PGM

Layout

Single-end

Stranded

Yes

Read length

20-365

Author

Satou team (2017-09-14)

Annotator

Justine Dardaillon (2017-05-17)

GEO Accession Number

PRJDB5237

SRA Accession Number

DRP003589

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).

Wild Type

Biomaterial		Number of reads	Library name
Stage 6a (early 32-cell)	whole embryo -	6078078	WT_Uninjected_control_32-cell_stage_embryos
Stage 8 (64-cell)	whole embryo -	6434364	WT_Uninjected_control_64-cell_stage_embryos
Stage 10 (112-cell)	whole embryo -	6227590	WT_Uninjected_control_112-cell_stage_embryos

Reference(s)

Tokuhiro et al. (2017). Differential gene expression along the animal-vegetal axis in the ascidian embryo is maintained by a dual functional protein Foxd. PLoS Genet. 13(5):e1006741

Experimentally perturbed expression(s) associated to this experiment

Mutant - 1 - Deregulation: FOXD1; FOXD3; FOXD4 from Stage 6a to Stage 10

Species

C. robusta formely Ciona int. type A

Read length

20-365

Assay platform

Ion Torrent PGM

Author

Justine Dardaillon (2016-11-23)

Annotator

Laetitia Sullivan (2016-11-23)

Curator

Justine Dardaillon (2016-11-23)

A morpholino oligonucleotide (MO; Gene Tools, LLC) for Foxd knock-down is designed to block translation of two paralogous Foxd genes, Foxd.a and Foxd.b (5 0-CACACAACACTGCACTGTCATCAT-3 0 ). The MO was introduced by microinjection under a microscope.

Mutant		Number of reads	Library name
Stage 6a (early 32-cell)	whole embryo -	5554372	Foxd_MO-injected_32-cell_stage_embryos
Stage 8 (64-cell)	whole embryo -	5847011	Foxd_MO-injected_64-cell_stage_embryos
Stage 10 (112-cell)	whole embryo -	6012401	Foxd_MO-injected_112-cell_stage_embryos

Deregulated Molecules

Name	Regulation type	Molecular Tool	From stage	To stage
KH2012:KH.C8.890 ( FOXD1; FOXD3; FOXD4)	Loss of function	FoxD-a_bMO (Imai's 25mer MO)	Stage 6a (early 32-cell)	Stage 10 (112-cell)

Embryo Manipulations

Removed anatomy part	From stage