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NCBI GEO

NCBI Gene Expression Omnibus (GEO), the public archive of functional genomics data: search GEO series, curated DataSets, platforms and samples by text, organism, experiment type, platform and release date, and read a series (summary, overall design, platforms, organisms, samples, PubMed links, supplementary files), a sample (characteristics, protocols, sequencing library) or a platform. Uses NCBI E-utilities (db=gds) and the GEO accession viewer's SOFT text; no key or login.

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NCBI GEO
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1Request
string

GEO GPL accession, e.g. `GPL96` (case-insensitive). Exactly one of `accession` and `url`.

string

GEO accession viewer URL, e.g. `https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL96`. Exactly one of `accession` and `url`.

5 credits
Codefollows the fields above
const result = await firecrawl.scrape({
  alexandria: {
    provider: "geo-ncbi-nlm-nih-gov",
    capability: "datasets/platform",
    options: {
      accession: "GPL96",
    },
  },
});
2Response example

This is a sample shape. Press Run to see live data from NCBI GEO.

{
  "accession": "GPL96",
  "contact": {
    "country": "USA",
    "institute": "Affymetrix, Inc.",
    "name": "Affymetrix, Inc."
  },
  "data_row_count": 22283,
  "description": "Affymetrix submissions are typically submitted to GEO using the GEOarchive method described at http://www.ncbi.nlm.nih.gov/projects/geo/info/geo_affy.html\nJune 03, 2009: annotation table updated with netaffx build 28\nJune 08, 2012: annotation table updated with netaffx build 32\nJune 24, 2016: annotation table updated with netaffx build 35",
  "distribution": "commercial",
  "last_update_date": "2021-03-09",
  "manufacture_protocol": "see manufacturer's web site\nThe U133 set includes 2 arrays with a total of 44928 entries and was indexed 29-Jan-2002.\nThe set includes over 1,000,000 unique oligonucleotide features covering more than 39,000 transcript variants, which in turn represent greater than 33,000 of the best characterized human genes.\nSequences were selected from GenBank, dbEST, and RefSeq. Sequence clusters were created from Build 133 of UniGene (April 20, 2001) and refined by analysis and comparison with a number of other publicly available databases including the Washington University EST trace repository and the University of California, Santa Cruz golden-path human genome database (April 2001 release). In addition, ESTs were analyzed for untrimmed low-quality sequence information, correct orientation, false priming, false clustering, alternative splicing and alternative polyadenylation.",
  "manufacturer": "Affymetrix",
  "observed_at_ms": 1792446599468,
  "organisms": [
    {
      "name": "Homo sapiens",
      "taxid": "9606"
    }
  ],
  "public_date": "2002-03-11",
  "relations": [
    {
      "target": "GPL4557 (Alternative CDF)",
      "type": "Alternative to"
    },
    {
      "target": "GPL7566 (Alternative CDF)",
      "type": "Alternative to"
    },
    {
      "target": "GPL9021 (Alternative CDF)",
      "type": "Alternative to"
    },
    {
      "target": "GPL9741 (Alternative CDF)",
      "type": "Alternative to"
    },
    {
      "target": "GPL10553 (Alternative CDF: ncilpg_U133Agb)",
      "type": "Alternative to"
    },
    {
      "target": "GPL14663 (Alternative CDF)",
      "type": "Alternative to"
    },
    {
      "target": "GPL16212 (Alternative CDF)",
      "type": "Alternative to"
    },
    {
      "target": "GPL17027 (Alternative CDF)",
      "type": "Alternative to"
    },
    {
      "target": "GPL17662 (alternative CDF)",
      "type": "Alternative to"
    },
    {
      "target": "GPL19184 (CDF: v18 ENTREZG)",
      "type": "Alternative to"
    },
    {
      "target": "GPL29829 (gene name)",
      "type": "Alternative to"
    }
  ],
  "sample_count": 43657,
  "series_count": 1128,
  "status": "Public on Mar 11 2002",
  "submission_date": "2002-02-19",
  "technology": "in situ oligonucleotide",
  "terms_url": "https://www.ncbi.nlm.nih.gov/geo/info/disclaimer.html",
  "title": "[HG-U133A] Affymetrix Human Genome U133A Array",
  "url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL96",
  "web_links": [
    "http://www.affymetrix.com/support/technical/byproduct.affx?product=hgu133",
    "http://www.affymetrix.com/analysis/index.affx"
  ]
}

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