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Items: 1 to 20 of 616

1.

Genome-wide use of high and low affinity Tbrain transcription factor binding sites during echinoderm development

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Strongylocentrotus purpuratus; Patiria miniata
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL22676 GPL20965
10 Samples
Download data: BED, BEDGRAPH, TXT
Series
Accession:
GSE89865
ID:
200089865
2.

RNA-seq assessment of morpholino knockdown of the sea star (Patiria miniata) Pm-Tbr transcription factor in early embryos

(Submitter supplied) Purpose: The Tbrain transcription factor has demonstrated an evolved preference for low-affinity, secondary site binding motifs between the sea star and sea urchin orthologs. We sought to identify targets of sea urchin and sea star orthologs of Tbr. Because less is known about the function of Tbr during sea star development, we used RNA-seq in conjuction with ChIP-seq studies (GEO:xxxx) to determine the targets of sea star Tbr in early development. more...
Organism:
Patiria miniata
Type:
Expression profiling by high throughput sequencing
Platform:
GPL22676
6 Samples
Download data: TXT
Series
Accession:
GSE89863
ID:
200089863
3.

Genome-wide detection of Tbrain binding sites during early development in both sea urchin (S. purpuratus) and sea star (P. miniata)

(Submitter supplied) Sea stars and sea urchins are model systems for interrogating the types of deep evolutionary changes that have restructured developmental gene regulatory networks (GRNs). While cis regulatory DNA evolution is likely the predominant mechanism of change, it was recently shown that Tbrain, a Tbox transcription factor protein, has evolved a changed preference for a low affinity, secondary binding motif, although the primary, high affinity motif is conserved. more...
Organism:
Strongylocentrotus purpuratus; Patiria miniata
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL20965 GPL22676
4 Samples
Download data: BED, BEDGRAPH
Series
Accession:
GSE89862
ID:
200089862
4.

Differential gene expression in the body wall of the sea cucumber (Apostichopus japonicus) under strong lighting and dark conditions

(Submitter supplied) RNA-seq provided a general overview of the gene expression profiles of the body walls of A. japonicus exposed to strong light (“light”), normal light (“control”) and fully dark (“dark”) environment.
Organism:
Apostichopus japonicus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16771
3 Samples
Download data: TXT
Series
Accession:
GSE87803
ID:
200087803
5.

Gene expression profiles of the respiratory tree of sea cucumber Apostichopus japonicus during aestivation by RNA-seq

(Submitter supplied) Sea cucumbers (Holothuroidea; Echinodermata) cycle annually between aestivation, when water temperature is above about 25°C in the summer, and active life, when temperature is below about 18°C. We used RNA-Seq to determine gene expression profiles of respiratory tree tissue of A. japonicus during non-aestivation (NA), deep-aestivation (DA), and arousal from aestivation (AA).
Organism:
Apostichopus japonicus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16771
3 Samples
Download data: TXT
Series
Accession:
GSE53815
ID:
200053815
6.

Gene expression alteration in FoxQ2 knockdown sea uchin embryos

(Submitter supplied) The transcription factor FoxQ2 is required for anterior pole neural development in S. purpuratus embryos. To understand the gene regulatory network driving neurogenesis in the anterrior pole region, it is necessary to identify genes that depend on FoxQ2. We carried out a microarray experiment to compare gene expression changes in FoxQ2 knockdown embryos.
Organism:
Strongylocentrotus purpuratus
Type:
Expression profiling by array
Platform:
GPL21701
2 Samples
Download data: PAIR, TXT
Series
Accession:
GSE80012
ID:
200080012
7.

The mid-developmental transition and the evolution of animal body plans

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Caenorhabditis elegans; Strongylocentrotus purpuratus; Danio rerio; Mnemiopsis leidyi; Nematostella vectensis; Schmidtea polychroa; Hypsibius dujardini; Platynereis dumerilii; Drosophila melanogaster; Amphimedon queenslandica
Type:
Expression profiling by high throughput sequencing
10 related Platforms
1143 Samples
Download data: PDF, XLSX
Series
Accession:
GSE70185
ID:
200070185
8.

Strongylocentrotus purpuratus high resolution developmental transcriptomic time-course

(Submitter supplied) Classical embryological studies revealed that during mid-embryogenesis vertebrates show similar morphologies. This “phylotypic stage” has recently received support from transcriptome analyses, which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. more...
Organism:
Strongylocentrotus purpuratus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19892
165 Samples
Download data: TAB
Series
Accession:
GSE70372
ID:
200070372
9.

Gene expression alterations in SoxC knockdown sea urchin embryos

(Submitter supplied) Transcription factor SoxC is required for all neural development in purple sea urchin S. purpuratus embryos. To begin to develop a gene regulatory network for neural development, we used RNA-Seq to compare transcript populations in SoxC knockdown and control embryos.
Organism:
Strongylocentrotus purpuratus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19892
2 Samples
Download data: TXT
Series
Accession:
GSE76067
ID:
200076067
10.

RNA-Seq dependent transcriptional analysis unveils adaptive mechanisms in the intestine of sea cucumber Apostichopus japonicus during aestivation

(Submitter supplied) Sea cucumbers (Holothuroidea; Echinodermata), cycle annually between aestivation when water temperature is above about 25°C in the summer and active life when temperature is below about 18°C. We used RNA-Seq to determine gene expression profiles of intestine tissue of A.japonicus during non-aestivation (NA), deep-aestivation (DA), and arousal from aestivation (AA).
Organism:
Apostichopus japonicus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16771
3 Samples
Download data: TXT
Series
Accession:
GSE51137
ID:
200051137
11.

Evolutionary comparison reveals that diverging CCCTC-binding factor (CTCF) sites are signatures of ancestral topological associating domains borders

(Submitter supplied) Comparison of conserved TAD boundaries reveals that diverging CTCF sites is an evolutionary conserved signature associated with TAD borders
Organism:
Strongylocentrotus purpuratus; Mus musculus; Danio rerio
Type:
Other
Platforms:
GPL19892 GPL14875 GPL13112
63 Samples
Download data: BEDGRAPH
12.

NA-Seq reveals dynamic changes of gene expression in key stages of intestine regeneration in the sea cucumber Apostichopus japonicus.

(Submitter supplied) Sea cucumbers (Holothuroidea; Echinodermata) have the capacity to regenerate lost tissues and organs.We used RNA-Seq to determine gene expression profiles associated with intestinal regeneration in A. japonicus at 3, 7, 14 and 21 days post evisceration (dpe)
Organism:
Apostichopus japonicus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16771
5 Samples
Download data: FNA, TXT
Series
Accession:
GSE44995
ID:
200044995
13.

Large-scale identification and comparative analysis of miRNA expression profile in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Apostichopus japonicus
Type:
Non-coding RNA profiling by array; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL16771 GPL17445
8 Samples
Download data: TXT
Series
Accession:
GSE52226
ID:
200052226
14.

Large-scale identification and comparative analysis of miRNA expression profile in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation (part 2)

(Submitter supplied) The sea cucumber Apostichopus japonicus withstands high water temperatures in the summer by suppressing metabolic rate and entering a state of aestivation. We hypothesized that changes in the expression of miRNAs could provide important post-transcriptional regulation of gene expression during hypometabolism via control over mRNA translation. The present study analyzed profiles of miRNA expression in the sea cucumber respiratory tree using Solexa deep sequencing technology. more...
Organism:
Apostichopus japonicus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL16771
2 Samples
Download data: TXT
Series
Accession:
GSE52225
ID:
200052225
15.

Large-scale identification and comparative analysis of miRNA expression profile in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation (part 1)

(Submitter supplied) The sea cucumber Apostichopus japonicus withstands high water temperatures in the summer by suppressing metabolic rate and entering a state of aestivation. We hypothesized that changes in the expression of miRNAs could provide important post-transcriptional regulation of gene expression during hypometabolism via control over mRNA translation. The present study analyzed profiles of miRNA expression in the sea cucumber respiratory tree using Solexa deep sequencing technology. more...
Organism:
Apostichopus japonicus
Type:
Non-coding RNA profiling by array
Platform:
GPL17445
6 Samples
Download data: TXT
Series
Accession:
GSE52224
ID:
200052224
16.

High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Apostichopus japonicus
Type:
Non-coding RNA profiling by high throughput sequencing; Non-coding RNA profiling by array
Platforms:
GPL16771 GPL17445
8 Samples
Download data: TXT
Series
Accession:
GSE48869
ID:
200048869
17.

High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation [microarray]

(Submitter supplied) The regulatory role of miRNA in gene expression is an emerging hot new topic in the control of hypometabolism. Sea cucumber aestivation is a complicated physiological process that includes obvious hypometabolism as evidenced by a decrease in the rates of oxygen consumption and ammonia nitrogen excretion, as well as a serious degeneration of the intestine into a very tiny filament. To determine whether miRNAs play an important regulatory roles in this process, the present study analyzed profiles of miRNA expression in the intestine of sea cucumber (Apostichopus japonicus), using Solexa deep sequencing technology. more...
Organism:
Apostichopus japonicus
Type:
Non-coding RNA profiling by array
Platform:
GPL17445
6 Samples
Download data: TXT
Series
Accession:
GSE48868
ID:
200048868
18.

High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation [miRNA-Seq]

(Submitter supplied) The regulatory role of miRNA in gene expression is an emerging hot new topic in the control of hypometabolism. Sea cucumber aestivation is a complicated physiological process that includes obvious hypometabolism as evidenced by a decrease in the rates of oxygen consumption and ammonia nitrogen excretion, as well as a serious degeneration of the intestine into a very tiny filament. To determine whether miRNAs play an important regulatory roles in this process, the present study analyzed profiles of miRNA expression in the intestine of sea cucumber (Apostichopus japonicus), using Solexa deep sequencing technology. more...
Organism:
Apostichopus japonicus
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL16771
2 Samples
Download data: TXT
Series
Accession:
GSE48867
ID:
200048867
19.

Synergistic effects of temperature and pCO2 on growth, development and gene expression of Strongylocentrotus purpuratus larvae

(Submitter supplied) Transcriptional profiling of purple sea urchin (Strongylocentrotus purpuratus) larvae cultured under four different seawater conditions: (i)13°C/400 µatm pCO2, (ii)13°C/1100 µatm pCO2, (iii)18°C/400 µatm pCO2 (iv)18°C/1100 µatm pCO2. The goal was to determine the effects of temperature and CO2, both important climate change variables, on gene expression
Organism:
Strongylocentrotus purpuratus
Type:
Expression profiling by array
Platform:
GPL15767
12 Samples
Download data: TXT
Series
Accession:
GSE39125
ID:
200039125
20.

Response to elevated pCO2 in Strongylocentrotus purpuratus larvae

(Submitter supplied) Transcriptional profiling of purple sea urchin (Strongylocentrotus purpuratus) larvae cultured under three different seawater CO2 concentrations 400, 800, 1200 µatm. The goal was to determine the effects of CO2, an important climate change variable, on global gene expression
Organism:
Strongylocentrotus purpuratus
Type:
Expression profiling by array
Platform:
GPL15767
24 Samples
Download data: TXT
Series
Accession:
GSE37522
ID:
200037522
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