Zhang CSE FASTQ - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001015356 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:We used PacBio data to identify more reliable transcripts from hESC, based on which we can estimate gene/transcript abundance better from Illumina data. PacBio long reads and Illumina short reads were generated from the same hESC cell line H1. PacBio reads were error-corrected by Illumina reads to identify transcripts. rSeq is used to estimate gene/transcript abundance of the identified transcriptome.
2013-10-30 | E-GEOD-51861 | biostudies-arrayexpress
Project description:We consturcted a full-length transcript reference of CD4SP and CD8SP T cells using TGS (PacBio) data. We then used SGS (Illumina) CD4SP and CD8SP data to quantify isoform expressions and study alternative splicing patterns against the full-length transcript reference between CD4SP and CD8SP cells.
2021-10-13 | GSE159290 | GEO
Project description:Genome-wide association studies (GWASs) have revealed thousands of associations in many complex traits and diseases. Previous studies suggest that a subset of associations are due to alterations in splicing; however, interpreting the effects of splicing on protein isoforms is hindered by limitations in defining full-length transcript isoforms using short-read RNA-seq data. Long-read RNA-seq represents a powerful approach to define and quantify transcript isoforms. In this study, we developed a novel approach that integrates information from GWAS, splicing QTL (sQTL), and PacBio long-read RNA-seq in a disease relevant model to infer the effects of sQTL on the ultimate protein isoform products they encode. Such information enables identification of genes potentially responsible for GWAS associations. As a proof-of-concept, we generated deep coverage (N=~22 million full-length reads) PacBio long-read RNAseq data on human fetal osteoblasts (hFOBs), a cell-line of relevance to the regulation of bone mineral density (BMD). We identified 68,326 protein-coding isoforms, including 17,375 (25%) which were novel. Next, we used Bayesian colocalization to identify 1,863 sQTLs from the Genotype-Tissue Expression (GTEx) project in 732 protein-coding genes which colocalized with BMD associations (H4PP > 0.75). A total of 836 junctions with colocalizing sQTLs in 459 (of the 732) genes were expressed in hFOB long-read RNA-seq data. With these data, we formulated hypotheses regarding the potential mechanism of action of each sQTL. For example, we identified 7 junctions with colocalizing sQTLs (maximum H4PP = 0.98-0.99) in TPM2 for splice junctions between two nearly mutually exclusive exons, and two different transcript termination sites, making it impossible to interpret without long-read RNA-seq data. siRNA mediated knockdown in hFOBs showed two TPM2 isoforms with opposing effects on mineralization. Our results suggest that splicing is a major mechanism underlying GWAS associations and long-read proteogenomics data is critical to precisely define the protein isoforms that are produced from splicing alterations.
2023-03-01 | GSE224588 | GEO
Project description:Deregulated gene expression is a hallmark of cancer, however most studies to date have analyzed short-read RNA-sequencing data with inherent limitations. Here, we combine PacBio long-read isoform sequencing (Iso-Seq) and Illumina paired-end short read RNA sequencing to comprehensively survey the transcriptome of gastric cancer (GC), a leading cause of global cancer mortality. We performed full-length transcriptome analysis across 10 GC cell lines covering four major GC molecular subtypes (chromosomal unstable, Epstein-Barr positive, genome stable and microsatellite unstable). We identify 60,239 non-redundant full-length transcripts, of which >66% are novel compared to current transcriptome databases. Novel isoforms are more likely to be cell-line and subtype specific, expressed at lower levels with larger number of exons, with longer isoform/coding sequence lengths. Most novel isoforms utilize an alternate first exon, and compared to other alternative splicing categories are expressed at higher levels and exhibit higher variability. Collectively, we observe alternate promoter usage in 25% of detected genes, with the majority (84.2%) of known/novel promoter pairs exhibiting potential changes in their coding sequences. Mapping these alternate promoters to TCGA GC samples, we identify several cancer-associated isoforms, including novel variants of oncogenes. Tumor-specific transcript isoforms tend to alter protein coding sequences to a larger extent than other isoforms. Analysis of outcome data suggests that novel isoforms may impart additional prognostic information. Our results provide a rich resource of full-length transcriptome data for deeper studies of GC and other gastrointestinal malignancies.
2021-02-02 | PXD023373 | Pride
Project description:We used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi-C matrices from these two new assemblies with D. melanogaster with respect to synteny blocks and dosage compensation as a chromosome-wide gene-regulatory mechanism.
2019-10-14 | GSE120751 | GEO
Project description:We used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi-C matrices from these two new assemblies with D. melanogaster with respect to synteny blocks and dosage compensation as a chromosome-wide gene-regulatory mechanism.
2019-10-14 | GSE120750 | 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 | 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:Long non-coding RNAs are often not conserved and their specific functions remain enigmatic. Our studies identify independent and opposing roles for two neural-specific and differentially expressed non-coding RNAs derived from the same locus: the evolutionarily conserved lncRNA Rncr3 and the embedded microRNA miR124a-1. In this study, we found that Rncr3 is expressed in and necessary for embryonic neuroepithelial progenitor proliferation and survival whereas miR124a expression initiates at the onset of and promotes neuronal differentiation. Exons 2 and 3 are also highly conserved between mouse lncRncr3 and human RNCR3. We used CRISPR/Cas9 gene editing of NE-4C cells, a neuroepithelial progenitor cell line from cerebral vesicles of embryonic day 9 (E9) mouse embryos, to create full-length deletion of the Rncr3-miR124a locus (exons 1-4) and specifically delete conserved exons 2 and 3. Both knock-out (KO) and exon2/3 deletion reduced proliferation and increased apoptosis. To comprehensively evaluate the effects of full-length Rncr3-miR124a KO and exons 2/3 deletion, we performed RNA-seq. Genes whose expression was consistently up- or down-regulated in full-length KO and exons 2/3 deletion clones relative to wildtype were aimed. Gene ontology (GO) functional annotation showed enrichment for negative regulation of cell proliferation; cell fate commitment; cell cycle arrest; negative regulation of apoptotic process. We also found that expression of miR124a encoded in exon 4 is limited by Rncr3 conserved exons 2 and 3. The RNA-seq data showed that the GO Biological Process (BP) enrichment of genes significantly upregulated in exons 2/3 deletion cells but not significantly changed in full-length deletion cells (where miR124a is deleted, and hence more similar to wildtype proliferating NPCs with very low miR124a expression) are associated with neuronal differentiation, consistent with miR124a function in differentiation. Our studies illustrate that two non-coding RNAs, Rncr3 and miR124a, are differentially generated from the same primary transcript and have opposing functions in NPC maintenance versus promotion of neuronal differentiation.
2024-04-16 | GSE191133 | GEO
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