I wrote a R script to query the NCBI-GEO datasets to see whether microarrays are still been used for several species. I also query the sequencing datasets.

This is not a perfect search as I only queried the GEO. Many sequencing libraries are only at SRA. Also, some early day microarray data is probably not on GEO. Besides, I only counted the number of datasets, not the samples within the datasets.

With that being said, I’m likely underestimate the sequencing data.

A while back, I also wrote some Python code to query the number of DNA and RNA sequencing libraries on SRA. See SRA_search.ipynb. I wrote a R version before, but I can’t find the script.

Link to Github

I got all the possible query terms for Dataset Type from NCBI-GEO-Advanced Search.

Here are the results for the Human. The sequencing is totally taken up the GEO, only a small portion of array assays.

Here are all the possible Dataset Type

Number DataSet Type
1 expression profiling by array
2 expression profiling by genome tiling array
3 expression profiling by snp array
4 genome binding/occupancy profiling by array
5 genome binding/occupancy profiling by genome tiling array
6 genome binding/occupancy profiling by snp array
7 genome variation profiling by array
8 genome variation profiling by genome tiling array
9 genome variation profiling by snp array
10 methylation profiling by array
11 methylation profiling by genome tiling array
12 methylation profiling by snp array
13 non coding rna profiling by array
14 non coding rna profiling by genome tiling array
15 protein profiling by protein array
16 snp genotyping by snp array
20 expression profiling by high throughput sequencing
21 genome binding/occupancy profiling by high throughput sequencing
22 genome variation profiling by high throughput sequencing
23 methylation profiling by high throughput sequencing
24 non coding rna profiling by high throughput sequencing
26 protein profiling by mass spec
27 third party reanalysis
17 expression profiling by mpss
18 expression profiling by rt pcr
19 expression profiling by sage
25 other