PacBio Iso-Seq of Atlantic cod
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB18628 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Full-Length cDNA transcriptome (Iso-Seq) data sequenced on the PacBio Sequel system using 2.1 chemistry. Multiplexed cDNA library of 12 samples (3 tissues x 4 strains). Tissues: root, embryo, endosperm. Strains: B73, Ki11, B73xKi11, Ki11xB73.
2020-02-25 | E-MTAB-7837 | biostudies-arrayexpress
Project description:A stable supply of viable eggs and embryos is crucial for successful farming of Atlantic cod. Broodstock stress can have negative effects, but little is known about the molecular mechanisms that cause abnormal development. Maternally transferred mRNAs have been shown to be essential for normal development, and stress may therefore influence their expression and the subsequent embryonic development. We investigated if mimicked stress in prespawning Atlantic cod females affects mRNA concentrations in eggs and embryos, and if this can be linked to egg/embryo viability, and if we could identify potential molecular markers for stress and egg/embryo viability. Consequently, 3 weeks prior to expected peak spawning, 20 females were intraperitoneally implanted with either cortisol-containing or cortisol-free (sham) osmotic pumps. At peak spawning all individuals were stripped and eggs were fertilized and incubated until hatching. Samples were collected from unfertilized eggs and embryos for gene expression profiling.
2012-11-01 | E-MTAB-1296 | biostudies-arrayexpress
Project description:Long-read sequencing technologies such as Iso-Seq (PacBio Inc.) generate highly accurate sequences of full-length mRNA transcript isoforms. Long-read transcriptomics may be especially useful in the context of lymphocyte functional plasticity as it relates to human health and disease. However, no long-read isoform-aware reference transcriptomes of human circulating lymphocytes seem to be publicly available despite being valuable as benchmarks in a variety of transcriptomic studies. To begin to fill this gap, we purified four lymphocyte subsets (CD4 T, CD8 T, NK, and Pan B cells) from the peripheral blood of a healthy male donor and obtained high-quality RNA (RIN>8) for PacBio Iso-Seq analysis and parallel RNA-Seq analysis.
2022-09-16 | GSE202328 | GEO
Project description:Long-read sequencing technologies such as Iso-Seq (PacBio Inc.) generate highly accurate sequences of full-length mRNA transcript isoforms. Long-read transcriptomics may be especially useful in the context of lymphocyte functional plasticity as it relates to human health and disease. However, no long-read isoform-aware reference transcriptomes of human circulating lymphocytes seem to be publicly available despite being valuable as benchmarks in a variety of transcriptomic studies. To begin to fill this gap, we purified four lymphocyte subsets (CD4 T, CD8 T, NK, and Pan B cells) from the peripheral blood of a healthy male donor and obtained high-quality RNA (RIN>8) for PacBio Iso-Seq analysis and parallel RNA-Seq analysis.
2022-09-16 | GSE202327 | GEO
Project description:STAMBPL1 plays a previously unappreciated role in post-transcriptional regulation, especially in RNA splicing pathways. Thus, PacBio long-read iso-sequencing was performed to acquire a high-precision transcription landscape after STAMBPL1 knockingdown in Huh7 cells
2024-09-11 | GSE276508 | GEO
Project description:Fish in use in aquaculture display large variation in gamete biology. To reach better understanding around this issue, this study aims at identifying if “egg life history traits” can be hidden in egg transcriptomes. To pursue this, salmon and cod eggs were selected due to their largely differencing phenotypes (size, robustness, fresh/marine). An oligo microarray analysis was performed on ovulated eggs from cod (~23 000 genes, n=8) and salmon (~44 000 genes, n=7). The arrays were normalized to a similar spectrum for both arrays. Both arrays were re-annotated based on official gene symbol to retrieve an orthologous KEGG annotation, in salmon and cod arrays this represented 14009 and 7437 genes respectively. The probe linked to the highest gene expression for that particular KEGG annotation was used to compare expression between species. Differential expression was calculated for genes that had an annotation with score > 300, resulting in a total of 2354 KEGG annotations (genes) being differently expressed between the species. The most differentially expressed genes in salmon and cod (FD≥2), were used to reveal pathways that were overrepresented in the eggs of each species. This analysis revealed that immune, signal transduction, and excretory related pathways were overrepresented in salmon compared to cod. The most overrepresented pathways in cod were related to regulation of genetic information processing and metabolism. To conclude this analysis clearly point at some distinct transcriptome repertoires for cod and salmon and that these differences may explain some of the species-specific biological features for salmon and cod eggs.
2014-08-31 | GSE59877 | GEO
Project description:Long-read sequencing technologies such as Iso-Seq (PacBio Inc.) generate highly accurate sequences of full-length mRNA transcript isoforms. Long-read transcriptomics may be especially useful in the context of T cell functional plasticity as it relates to human health and disease. However, To our knowledge, no long-read transcriptome reference exists for activated human CD4 T cells. To begin to fill this gap, we purified CD4 T cells from the peripheral blood of a healthy female donor and activated these cells with anti-CD3/CD28 beads to generate populations of early activated (4hr), mid-activated (16hr), blasting (48hr) and proliferating (120hr) CD4 T cells. From each of these time points, we obtained high-quality RNA (RIN>9) for PacBio Iso-Seq analysis and parallel RNA-Seq analysis, which we hope will serve as a reference for future transcriptomic studies of these populations. UCSC genome browser tracks for these samples can be accessed at: http://genome.ucsc.edu/cgi-bin/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=on&position=chr1:206,903,317-206,921,941&hubUrl=http://162.215.210.70/~tracks/Mitchell_IsoSeq_Stim/hub.txt
2025-02-12 | GSE229969 | GEO
Project description:Gene expression profiling of Atlantic cod (Gadus morhua) embryogenesis
2011-06-15 | E-TABM-1156 | biostudies-arrayexpress
Project description:Long-read sequencing technologies such as Iso-Seq (PacBio Inc.) generate highly accurate sequences of full-length mRNA transcript isoforms. Long-read transcriptomics may be especially useful in the context of T cell functional plasticity as it relates to human health and disease. However, To our knowledge, no long-read transcriptome reference exists for activated human CD4 T cells. To begin to fill this gap, we purified CD4 T cells from the peripheral blood of a healthy female donor and activated these cells with anti-CD3/CD28 beads to generate populations of early activated (4hr), mid-activated (16hr), blasting (48hr) and proliferating (120hr) CD4 T cells. From each of these time points, we obtained high-quality RNA (RIN>9) for PacBio Iso-Seq analysis and parallel RNA-Seq analysis, which we hope will serve as a reference for future transcriptomic studies of these populations. UCSC genome browser tracks for these samples can be accessed at: http://genome.ucsc.edu/cgi-bin/hgHubConnect?hgHub_do_redirect=on&hgHubConnect.remakeTrackHub=on&hgHub_do_firstDb=on&position=chr1:206,903,317-206,921,941&hubUrl=http://162.215.210.70/~tracks/Mitchell_IsoSeq_Stim/hub.txt
2025-02-12 | GSE229971 | GEO
Project description:Iso-Seq (PacBio) sequencing was performed to generate a reference library of H. perforatum. We generated genome-wide transcriptome data from in vitro cell suspensions and shoot cultures of H. perforatum.
2022-12-31 | E-MTAB-11423 | biostudies-arrayexpress