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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"

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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
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I think I would just try to do this with GEOquery.

https://bioconductor.org/packages/release/bioc/html/GEOquery.html

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  • $\begingroup$ GEOquery would download datasets for a given accession ID. R provides a library 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. $\endgroup$ Jan 2 at 5:17
  • $\begingroup$ 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 $\endgroup$
    – k1sauce
    Jan 6 at 0:03

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