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.
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 |