Holothuria glaberrima
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ABSTRACT:
PROVIDER: PRJNA115073 | ENA |
REPOSITORIES: ENA
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Project description:We assembled and annotated a de novo transcriptome using RNA-seq data consisting of regenerating and non-regenerating intestinal tissues from the sea cucumber Holothuria glaberrima. Analysis of differential expression revealed a large number of differentially expressed transcripts associated with transcription factors with diverse expression patterns. Activity involving developmental and cancer-related events found in the analysis could be related to the regenerative process. Our study demonstrates the broad and diversified gene expression profile during the early stages of the process using the mesentery as the focal point of intestinal regeneration. It also establishes the genes that are the most important candidates in the cellular processes that underlie regenerative responses.
2020-10-29 | GSE160340 | GEO
Project description:Regenerating intestine tissues were compared with normal (non-regenerating tissues) to determine the gene expression profile at early stages of regeneration (3, 7 and 14 days post- evisceration (dpe)). Immuno activated tissues with LPS were compared with Normal (non-regenerating tissues) and regenerating tissues (3 and 7 dpe) to determine the gene expression of immune related genes in the sea cucumber and it's expression during early stages of regeneration.
2009-05-21 | GSE16182 | GEO
Project description:Regenerating intestine tissues were compared with normal (non-regenerating tissues) to determine the gene expression profile at early stages of regeneration (3, 7 and 14 days post- evisceration (dpe)). Immuno activated tissues with LPS were compared with Normal (non-regenerating tissues) and regenerating tissues (3 and 7 dpe) to determine the gene expression of immune related genes in the sea cucumber and it's expression during early stages of regeneration. 16 Total arrays. 8 comparisons with 8 dye swap replicates. Normal Vs. (3, 7 and 14 days of regeneration), and Vs. (LPS) 2 microarray slides used. Each slide with 8 Arrays (8 x 15k). 15,744 probes printed per array. (all 16 arrays are identically printed). 7,209 ESTs from Normal, 3 dpe and 7 dpe tissues were used to design the probes. Two probes per EST from diferent regions of the sequence (as a technical replicate). 536 technical controls and more than 600 internal biological controls (from different species).
2010-05-18 | E-GEOD-16182 | biostudies-arrayexpress
Project description:Holothuria glaberrima Transcriptome or Gene expression
| PRJNA158511 | ENA
Project description: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. We identified 309 sea cucumber miRNAs, including 19 novel miRNAs specific to sea cucumber. Animals sampled during deep aestivation (DA) after at least 15 days of continuous torpor, were compared with animals from a non-aestivation (NA) state (animals that had passed through aestivation and returned to an active state). We identified 42 differentially expressed miRNAs (RPM (reads per million) >10, |FC| (|fold change|) ≥1, FDR<0.01) during aestivation, which were validated by two other miRNA profiling methods: miRNA microarray and real-time PCR. Among the most prominent miRNA species, miR-200-3p, miR-2004, miR-2010, miR-22, miR-252a, miR-252a-3p and miR-92 were significantly over-expressed during deep aestivation compared with non-aestivation animals. Preliminary analyses of their putative target genes suggest that these miRNAs could play important roles in global transcriptional depression during aestivation. analyze the global profile of small RNAs in non-aestivation (NA) and deep aestivation (DA) sea cucumbers' intestine using Solexa sequencing technology
2014-06-06 | E-GEOD-48867 | biostudies-arrayexpress
Project description: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. We identified 309 sea cucumber miRNAs, including 19 novel miRNAs specific to sea cucumber. Animals sampled during deep aestivation (DA) after at least 15 days of continuous torpor, were compared with animals from a non-aestivation (NA) state (animals that had passed through aestivation and returned to an active state). We identified 42 differentially expressed miRNAs (RPM (reads per million) >10, |FC| (|fold change|) M-bM-^IM-%1, FDR<0.01) during aestivation, which were validated by two other miRNA profiling methods: miRNA microarray and real-time PCR. Among the most prominent miRNA species, miR-200-3p, miR-2004, miR-2010, miR-22, miR-252a, miR-252a-3p and miR-92 were significantly over-expressed during deep aestivation compared with non-aestivation animals. Preliminary analyses of their putative target genes suggest that these miRNAs could play important roles in global transcriptional depression during aestivation. In the present study,we present for the first time, using Solexa sequencing technology, an analysis of the global profile of small RNAs in non-aestivation (NA) and deep aestivation (DA) sea cucumbers. We focus on intestine in the present study because it is the major site responsible for the strong metabolic rate depression seen under deep aestivating conditions and the global expression profile of mRNA from the this organ has also been constructed applying RNA-seq technology in our previous study (Zhao and Chen, unpublished data). A preliminary analysis of the functional relevance of miRNA expression in relation to hypometabolism during aestivation is presented. A miRNA microarray and RT-qPCR were both used to supplement and confirm differentially expressed miRNAs. Our findings provide important new insights into the molecular mechanisms of sea cucumber aestivation.
2014-06-06 | E-GEOD-48868 | biostudies-arrayexpress
Project description:RNAseq of sea cucumber Holothuria leucospilota embryos
| PRJDB3196 | ENA
Project description:Oryza glaberrima Transcriptome or Gene expression
| PRJNA313017 | ENA