Dataset Search tutorial
Introduction to Siftome Dataset Search for non-biologists
How to use Dataset Search
Describe your question. Enter a disease or condition, choose where the samples came from, and select the comparison you need, such as disease versus healthy control, tumor versus normal, or treatment versus control.
Add filters when they are relevant. You can narrow the search by organism, assay type, minimum sample count, and processed-data availability.
Review the results. Read why each dataset matches, check the likely case and control groups, and note any metadata warnings. Before using a dataset in an analysis, open its details and confirm the information against the original GEO record.
Three guided searches from the landing page
Each example below gives every value to enter or select. “Any” means keep the default option, and “leave blank” means do not enter text. Set the fields and checkboxes on the Siftome landing page, then select Search datasets. You can also use the link after each recipe to submit the same landing-page search directly.
1. Prostate-cancer cell-line drug versus vehicle RNA-seq
Use this search to find human prostate-cancer cell-line studies comparing drug treatment with vehicle or untreated controls.
Disease/condition: prostate cancer
Anatomical source: Any anatomical source
Specimen material: Any specimen material
Cell population: Any cell population
Comparison type: Treatment vs control
Organism: Homo sapiens
Assay type: bulk RNA-seq
Minimum samples: 6
Experimental model: Cell line
Check: Require processed data.
Leave unchecked: Exclude cell lines; GEO only; recount3 available; Expression Atlas available.
Open the completed prostate-cancer search
2. Hepatocellular-carcinoma serum extracellular RNA or miRNA versus healthy control
Use this search to find human serum studies comparing hepatocellular carcinoma with healthy controls.
Disease/condition: hepatocellular carcinoma
Anatomical source: Any anatomical source
Specimen material: Serum
Cell population: Any cell population
Comparison type: Disease vs healthy control
Organism: Homo sapiens
Assay type: Any assay
Minimum samples: 12
Experimental model: Any model
Check: Require processed data.
Leave unchecked: Exclude cell lines; GEO only; recount3 available; Expression Atlas available.
Open the completed hepatocellular-carcinoma search
3. Liver-organoid treatment versus control RNA-seq
Use this search to find human liver-organoid experiments comparing treated or stimulated organoids with matched controls.
Disease/condition: leave blank
Anatomical source: Liver
Specimen material: Any specimen material
Cell population: Any cell population
Comparison type: Treatment vs control
Organism: Homo sapiens
Assay type: bulk RNA-seq
Minimum samples: 6
Experimental model: Organoid
Check: Require processed data.
Leave unchecked: Exclude cell lines; GEO only; recount3 available; Expression Atlas available.
Search-terms to improve
We are continuing to improve the quality and coverage of searches such as “COVID-19 whole blood healthy control RNA-seq” and “pancreatic cancer serum healthy control extracellular RNA or miRNA.” These examples help guide our ongoing work to make relevant datasets easier to find and evaluate.