text: user4121: AIM: Download "Unique Identifier List" for the following query from GEO DataSets.
  Query: ("Expression profiling by high throughput sequencing"[DataSet Type] AND ("Homo sapiens"[Organism] OR "Mus musculus"[Organism] OR "rattus norvegicus"[Organism])) AND ("2020/01/01"[PDAT] : "3000"[PDAT])
  which means, all RNASeq studies deposited on GEO in the year 2020 for humans, mice or rat.
  Problem: I need the GSE ID list for ~9k datasets, but while trying to download the list of ids, it loads to a blank page and nothing happens. Also, clicking on "Next Page" gives error.
  I have been trying for the last 3-4 days but it doesn't work.
  Steps to generate file:
  "Send To" -> "File" -> "Format" (Unique Identifier List) -> "Sort By" (Default Order) -> "Create File"
  
  user3577: You can use Entrez Direct for this. The following returns Unique Identifiers which are just bare integers.
  $ geo_query='"Expression profiling by high throughput sequencing"[DataSet Type] AND ("Homo sapiens"[Organism] OR "Mus musculus"[Organism] OR "rattus norvegicus"[Organism]) AND ("2020/01/01"[PDAT] : "3000"[PDAT])'
  $ esearch -db gds -query "$geo_query" | efetch -format uid > gds_results.txt 
  $ wc -l gds_results.txt 
  9981 gds_results.txt
  $ head -n2 gds_results.txt 
  200134092
  200120931
  
  Instead, if you are looking for a way to get the GSE accessions, you can use the built-in xtract command to parse the XML returned by esummary as follows:
  $ esearch -db gds -query "$geo_query" | esummary | xtract -pattern DocumentSummary -first Accession > gse_accs.txt > gse_accs.txt
  $ wc -l gse_accs.txt 
  9981 gse_accs.txt
  $ head -n2 gse_accs.txt 
  GSE165829
  GSE165824
  
  
original_text: 4121: <p><strong>AIM:</strong> Download &quot;Unique Identifier List&quot; for the following query from <a href="https://www-ncbi-nlm-nih-gov.ezproxy.u-pec.fr/gds" rel="nofollow noreferrer">GEO DataSets</a>.</p>
  <p><strong>Query:</strong> <em>(&quot;Expression profiling by high throughput sequencing&quot;[DataSet Type] AND (&quot;Homo sapiens&quot;[Organism] OR &quot;Mus musculus&quot;[Organism] OR &quot;rattus norvegicus&quot;[Organism])) AND (&quot;2020/01/01&quot;[PDAT] : &quot;3000&quot;[PDAT])</em></p>
  <p>which means, all RNASeq studies deposited on GEO in the year 2020 for humans, mice or rat.</p>
  <p>Problem: I need the GSE ID list for ~9k datasets, but while trying to download the list of ids, it loads to a blank page and nothing happens. Also, clicking on &quot;Next Page&quot; gives error.
  I have been trying for the last 3-4 days but it doesn't work.</p>
  <p><strong>Steps to generate file:</strong></p>
  <p><em>&quot;Send To&quot; -&gt; &quot;File&quot; -&gt; &quot;Format&quot; (Unique Identifier List) -&gt; &quot;Sort By&quot; (Default Order) -&gt; &quot;Create File&quot;</em></p>
   3577: <p>You can use <a href="https://www.ncbi.nlm.nih.gov/books/NBK179288/" rel="nofollow noreferrer">Entrez Direct</a> for this. The following returns Unique Identifiers which are just bare integers.</p>
  <pre><code>$ geo_query='&quot;Expression profiling by high throughput sequencing&quot;[DataSet Type] AND (&quot;Homo sapiens&quot;[Organism] OR &quot;Mus musculus&quot;[Organism] OR &quot;rattus norvegicus&quot;[Organism]) AND (&quot;2020/01/01&quot;[PDAT] : &quot;3000&quot;[PDAT])'
  $ esearch -db gds -query &quot;$geo_query&quot; | efetch -format uid &gt; gds_results.txt 
  $ wc -l gds_results.txt 
  9981 gds_results.txt
  $ head -n2 gds_results.txt 
  200134092
  200120931
  </code></pre>
  <p>Instead, if you are looking for a way to get the GSE accessions, you can use the built-in <code>xtract</code> command to parse the XML returned by <code>esummary</code> as follows:</p>
  <pre><code>$ esearch -db gds -query &quot;$geo_query&quot; | esummary | xtract -pattern DocumentSummary -first Accession &gt; gse_accs.txt &gt; gse_accs.txt
  $ wc -l gse_accs.txt 
  9981 gse_accs.txt
  $ head -n2 gse_accs.txt 
  GSE165829
  GSE165824
  </code></pre>
  