Dataset Open Access

A survey of the sorghum transcriptome using single-molecule long reads

Abdel-Ghany, Salah; Hamilton, Michael; Jacobi, Jennifer; Ngam, Peter; Devitt, Nicholas; Schilkey, Faye; Ben-Hur, Asa; Reddy, Anireddy


JSON Export

{
  "files": [
    {
      "links": {
        "self": "https://zenodo.org/api/files/a34ccc5b-de93-4960-8084-43841977f500/line21.fasta.gz"
      }, 
      "checksum": "md5:139d816318c6c7c852122a21ed09b9a6", 
      "bucket": "a34ccc5b-de93-4960-8084-43841977f500", 
      "key": "line21.fasta.gz", 
      "type": "gz", 
      "size": 489504680
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/a34ccc5b-de93-4960-8084-43841977f500/line22.fasta.gz"
      }, 
      "checksum": "md5:ffa33d0703375ce3d0259d99cac98ae5", 
      "bucket": "a34ccc5b-de93-4960-8084-43841977f500", 
      "key": "line22.fasta.gz", 
      "type": "gz", 
      "size": 409992420
    }
  ], 
  "owners": [
    21494
  ], 
  "doi": "10.5281/zenodo.49944", 
  "stats": {
    "version_unique_downloads": 90.0, 
    "unique_views": 377.0, 
    "views": 412.0, 
    "version_views": 411.0, 
    "unique_downloads": 90.0, 
    "version_unique_views": 376.0, 
    "volume": 84821051960.0, 
    "version_downloads": 184.0, 
    "downloads": 184.0, 
    "version_volume": 84821051960.0
  }, 
  "links": {
    "doi": "https://doi.org/10.5281/zenodo.49944", 
    "latest_html": "https://zenodo.org/record/49944", 
    "bucket": "https://zenodo.org/api/files/a34ccc5b-de93-4960-8084-43841977f500", 
    "badge": "https://zenodo.org/badge/doi/10.5281/zenodo.49944.svg", 
    "html": "https://zenodo.org/record/49944", 
    "latest": "https://zenodo.org/api/records/49944"
  }, 
  "created": "2016-04-27T06:42:56+00:00", 
  "updated": "2019-11-01T07:11:20.591556+00:00", 
  "conceptrecid": "632447", 
  "revision": 9, 
  "id": 49944, 
  "metadata": {
    "access_right_category": "success", 
    "doi": "10.5281/zenodo.49944", 
    "description": "<p>Alternative splicing and alternative polyadenylation (APA) of pre-mRNAs greatly contribute to transcriptome diversity, coding capacity of a genome and gene regulatory mechanisms in eukaryotes. &nbsp;Second-generation sequencing technologies have been extensively used to analyze transcriptomes. &nbsp;However, a major limitation of short-read data is that it is difficult to accurately predict full-length splice isoforms. Here we sequenced the sorghum transcriptome using Pacific Biosciences single molecule real time long-read isoform sequencing and developed a pipeline called TAPIS (Transcriptome Analysis Pipeline for Isoform Sequencing) to identify full-length splice isoforms and APA sites. Our analysis reveals transcriptome-wide full-length isoforms at an unprecedented scale with over 11,000 novel splice isoforms. &nbsp;Additionally, we uncover APA of ~11,000 expressed genes and more than 2,100 novel genes. These results greatly enhance sorghum gene annotations and aid in studying gene regulation in this important bioenergy crop. The TAPIS pipeline will serve as a useful tool to analyze Iso-Seq data from any organism.</p>", 
    "license": {
      "id": "CC0-1.0"
    }, 
    "title": "A survey of the sorghum transcriptome using single-molecule long reads", 
    "notes": "line21: control\nline22: PEG treated", 
    "relations": {
      "version": [
        {
          "count": 1, 
          "index": 0, 
          "parent": {
            "pid_type": "recid", 
            "pid_value": "632447"
          }, 
          "is_last": true, 
          "last_child": {
            "pid_type": "recid", 
            "pid_value": "49944"
          }
        }
      ]
    }, 
    "keywords": [
      "sorghum", 
      "isoseq"
    ], 
    "publication_date": "2016-04-18", 
    "creators": [
      {
        "affiliation": "Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523", 
        "name": "Abdel-Ghany, Salah"
      }, 
      {
        "affiliation": "Computer Science Department, Colorado State University, Fort Collins, CO, 80523", 
        "name": "Hamilton, Michael"
      }, 
      {
        "affiliation": "National Center for Genome Resources, 2935 Rodeo Park Dr. East, Santa Fe, NM 87505", 
        "name": "Jacobi, Jennifer"
      }, 
      {
        "affiliation": "National Center for Genome Resources, 2935 Rodeo Park Dr. East, Santa Fe, NM 87505", 
        "name": "Ngam, Peter"
      }, 
      {
        "affiliation": "National Center for Genome Resources, 2935 Rodeo Park Dr. East, Santa Fe, NM 87505", 
        "name": "Devitt, Nicholas"
      }, 
      {
        "affiliation": "National Center for Genome Resources, 2935 Rodeo Park Dr. East, Santa Fe, NM 87505", 
        "name": "Schilkey, Faye"
      }, 
      {
        "affiliation": "Computer Science Department, Colorado State University, Fort Collins, CO, 80523", 
        "name": "Ben-Hur, Asa"
      }, 
      {
        "affiliation": "Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523", 
        "name": "Reddy, Anireddy"
      }
    ], 
    "access_right": "open", 
    "resource_type": {
      "type": "dataset", 
      "title": "Dataset"
    }
  }
}
411
184
views
downloads
All versions This version
Views 411412
Downloads 184184
Data volume 84.8 GB84.8 GB
Unique views 376377
Unique downloads 9090

Share

Cite as