GEO DataSets

(Submitter supplied) Larvacean tunicates feature a spectacular innovation not seen in other animals - the trunk oikoplastic epithelium (OE). This epithelium produces a house, a large and complex extracellular structure used for filtering and concentrating food particles. Previously we identified several homeobox transcription factors expressed during early OE patterning. Among these are two Pax3/7 duplicates that we named Pax37A and Pax37B. more...

Organism:

Oikopleura dioica

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25139 GPL34192

14 Samples

Download data: TSV

(Submitter supplied) The larvacean, Oikopleura dioica, is a planktonic chordate and belongs to tunicate that is the closest relative to vertebrates. Its simple and transparent body, invariant embryonic cell lineages and short life cycle of five days make it a promising model organism for research in developmental biology. The genome browser, OikoBase, has been established in 2013 using Norwegian O. dioica. However, genome information of other populations is not available, despite that many researchers have used local populations. more...

Organism:

Oikopleura dioica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19577

67 Samples

Download data: XLSX

(Submitter supplied) ChIP-seq was used to generate chromatin state maps, profile binding patterns of key architectural proteins and locate putative enhancer regions in the early development (TB stage) and developing gonads of the marine chrodate Oikopleura dioica.

Organism:

Oikopleura dioica

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL28972

47 Samples

Download data: BW

(Submitter supplied) ATAC-seq was used to locate putative enhancer regions in the early development (tailbud stage), developing male and female gonads of the marine chrodate Oikopleura dioica.

Organism:

Oikopleura dioica

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL28972

6 Samples

Download data: BW

(Submitter supplied) Under crowded, nutrient-limiting conditions, growth in the marine chordate O. dioica arrests until favorable conditions return. We profiled translation genome-wide using ribosome profiling in O. dioica during growth arrest and growth arrest recovery. We found that initial recovery is independent of nutrient-responsive, trans-spliced genes, suggesting that animal density is the primary trigger for the resumption of development in this species.

Organism:

Oikopleura dioica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25139

8 Samples

Download data: TXT

(Submitter supplied) Protein synthesis is an energy-demanding process essential for cell proliferation and survival. Balancing the cost of protein synthesis with available resources has driven the evolution of its nutrient-dependent regulation. A central mechanism in this regulation is the repression of translation of the protein synthesis machinery during unfavorable growth conditions. This is mediated via mammalian target of rapamycin (mTOR), a master regulator of growth conserved from yeast to human. more...

Organism:

Oikopleura dioica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21546

12 Samples

Download data: GFF, TXT

(Submitter supplied) The selection and activity of transcription start sites (TSSs) are central to gene regulation and depend on sequence and chromatin features within a core promoter region. We present, at single-bp resolution, the TSS landscape of Oikopleura dioica, a marine chordate in the sister group to vertebrates and relate dynamics of promoter usage, and their architectures, across its life cycle, to chromatin features. more...

Organism:

Oikopleura dioica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17726

6 Samples

Download data: TXT

(Submitter supplied) In multicellular organisms, histone posttranslational modifications plays roles in transitions associated with the cell cycle, development, germline specification, gametogenesis and inheritance. Here we defined adaptations of an epigenome in tunicates, sister group to vertebrates, to strong secondary genome compaction in the larvacean, Oikopleura dioica, that has separate sexes and male heterogamy. We profiled 19 histone post-translational modifications in homogeneous ovary and testis samples and used the combinatorics of these marks to define chromatin states. We supplemented these with profiles of RNA polymerase II, CTCF and p300 binding sites and integrated existing annotation and expression data to characterize distinct epigenomic landscapes of the ovary and testis.

Organism:

Oikopleura dioica

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL15837

116 Samples

Download data: BEDGRAPH, PAIR

(Submitter supplied) The appendicularian, Oikopleura dioica, is a marine or planktonic tunicate that has a swimming tadpole shape through its entire life. For several reasons, this animal possesses advantages as a model organisms: (1) It has a short life cycle (about 5 days at 20℃); (2) Its development is rapid and it completes organogenesis within 10 hour of post-fertilization to form functional body; (3) its morphogenesis and cell linages are well-described; (4) live imaging of embryos by introducing fluorescent protein mRNAs is feasible; (5) RNAi method is available for knockdown of zygotic mRNA as well as maternal mRNAs in the ovary and eggs. more...

Organism:

Oikopleura dioica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19577

2 Samples

Download data: FASTA, TXT

(Submitter supplied) Polycistronic mRNAs transcribed from operons are resolved via the trans-splicing of a spliced leader (SL) RNA. The SL is also frequently trans-spliced to monocistronic transcripts. Using a modified cap analysis of gene expression (CAGE) protocol we mapped sites of SL trans-splicing genome-wide in the marine chordate Oikopleura dioica and find evidence for proposed functions of SL-trans-splicing. A recent hypothesis postulates that operons facilitate recovery from growth arrested states in metazoans. more...

Organism:

Oikopleura dioica

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17726

1 Sample

Download data: TXT

(Submitter supplied) Polycistronic mRNAs transcribed from operons are resolved via the trans-splicing of a spliced leader (SL) RNA. The SL is also frequently trans-spliced to monocistronic transcripts. Using a modified cap analysis of gene expression (CAGE) protocol we mapped sites of SL trans-splicing genome-wide in the marine chordate Oikopleura dioica and find evidence for proposed functions of SL-trans-splicing. A recent hypothesis postulates that operons facilitate recovery from growth arrested states in metazoans. more...

Organism:

Oikopleura dioica

Type:

Expression profiling by genome tiling array

Platform:

GPL15837

8 Samples

Download data: PAIR

(Submitter supplied) Animals have developed extensive mechanisms of response to xenobiotic chemical attacks. Although recent genome surveys have suggested a broad conservation of the chemical defensome across metazoans, global gene expression responses to xenobiotics are not known in most invertebrates. Here, using high density tiling arrays with over 2 million probes, we explored genome-wide gene expression in the tunicate Oikopleura dioica in response to two model xenobiotic chemicals – the carcinogenic polycyclic aromatic hydrocarbon benzo[a]pyrene (BaP) the pharmaceutical compound Clofibrate (Clo). more...

Organism:

Oikopleura dioica

Type:

Expression profiling by genome tiling array

Platform:

GPL14906

8 Samples

Download data: PAIR

(Submitter supplied) The developmental transcriptomics of every significant developmental stage of O. dioica at ultra-high resolution.

Organism:

Oikopleura dioica

Type:

Expression profiling by genome tiling array

Platform:

GPL15837

18 Samples

Download data: PAIR