Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-01-31T01:56:28.673Z
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Answers.UserDisplayName: vkkodali
Answers.Body: <p>I think I would just try to do this with GEOquery.</p>
  <p><a href="https://bioconductor.org/packages/release/bioc/html/GEOquery.html" rel="nofollow noreferrer">https://bioconductor.org/packages/release/bioc/html/GEOquery.html</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
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Answers.Text: GEOquery would download datasets for a given accession ID. R provides a library https://www.bioconductor.org/packages/release/bioc/html/GEOmetadb.html which contains metadata for microarray studies. I couldn't find anything similar to this for RNASeq studies so had to resort to the GUI.
Answers.UserDisplayName: Pawan Verma
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Answers.Text: Oh you're right, I did something similar before, i though it was GEOquery but i guess i don't remember... Ok, can you download the text file like:
  "Send To" -> "File" -> "Format" Summary (text)
  
  And then do something like:
  
  cat gds_result.txt | grep 'Accession: GSE' | cut -f 3 | cut -f 2 -d ' ' | sort > gse.txt
Answers.UserDisplayName: k1sauce
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Answers.UserDisplayName: k1sauce
Body: <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>
  
Tags: <phylogenetics><geo>
Title: Getting Unique Identifier List for GEO Datasets NCBI
ThreadText: # Getting Unique Identifier List for GEO Datasets NCBI
  
  (Asked by: username_0 on 2020-12-31)
  
  **AIM:** Download "Unique Identifier List" for the following query from [GEO DataSets](https://www-ncbi-nlm-nih-gov.ezproxy.u-pec.fr/gds).
  
  **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"*
  
  **Tags:** phylogenetics, geo
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2021-01-31. Score: 1 | Accepted answer
  
  You can use [Entrez Direct](https://www.ncbi.nlm.nih.gov/books/NBK179288/) 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
  
  ```
  
  
  ---
  
  ### Answer by username_2 on 2020-12-31. Score: 0
  
  I think I would just try to do this with GEOquery.
  
  <https://bioconductor.org/packages/release/bioc/html/GEOquery.html>
  
  > **Comments:**
  > **username_0**: GEOquery would download datasets for a given accession ID. R provides a library https://www.bioconductor.org/packages/release/bioc/html/GEOmetadb.html which contains metadata for microarray studies. I couldn't find anything similar to this for RNASeq studies so had to resort to the GUI.  
  > **username_2**: Oh you're right, I did something similar before, i though it was GEOquery but i guess i don't remember... Ok, can you download the text file like: "Send To" -> "File" -> "Format" Summary (text)  And then do something like:  cat gds_result.txt | grep 'Accession: GSE' | cut -f 3 | cut -f 2 -d ' ' | sort > gse.txt  
  
  ---
  
  