I am using the following command to retrieve GEO Datasets entries for daf-2 c. elegans that have as their experiment type High Throughpout sequencing:
esearch -db gds -query "daf-2" | efilter -query "expression profiling by high throughput sequencing [DataSet Type] AND Caenorhabditis elegans [organism]"
However, among the results that I got, I noticed that I got this:
23. Impaired Insulin-/IGF1-Signaling Extends Life Span by Promoting Mitochondrial L-Proline Catabolism to Induce a Transient ROS-Signal (Submitter supplied) Transcriptome profiling of three models with impaired insulin/IGF1 signaling. 1. Deep sequencing of endogenous mRNA from Caenorhabditis elegans N2 var. Bristol (wildtype) and daf-2(e1370) mutant; 2. Deep sequencing of endogenous mRNA from murine embryonic fibroblasts (MEF) wildtype and irs1-/- knockout; 3. Deep sequencing of endogenous mRNA from murine embryoinic fibroblast (MEF) insr+/- -lox and insr+/- knockout Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de) Organism: Mus musculus; Caenorhabditis elegans Type: Expression profiling by high throughput sequencing Platforms: GPL11002 GPL13776 14 Samples FTP download: GEO (CSV) ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE36nnn/GSE36041/ SRA Run Selector: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA151765 Series Accession: GSE36041 ID: 200036041
As you can see, in the
Organism field, there are both
Mus musculus and
Caenorhabditis elegans. How can I restrict my search so that I only get entries that exclusively work on
Caenorhabditis elegans? One naive way to do this would be to include
NOT Mus Musculus in the query, but of course that would mean that I could get something else too.
Another way I can think of solving this is just to write a script that would do the extra filtering using regexes, but I was wondering if there's a simpler solution using the e-utilities functionalities