Permafrost soils are often frozen since millennia and with that lock enormous amounts of carbon as well as viable cold-adapted microorganisms. We sampled a thermal erosion site, where the soil surface collapsed due to melting of ground ice - this process deepened the seasonal active layer from 40cm down to 90cm, former 26500-year-old permafrost. This data set includes 30 triplicates from 10cm horizons down to the still intact permafrost at 90-100cm depth. These raw reads are totalRNA shotgun Illumina NextSeq paired reads.