The Rodent Research-3 (RR-3) mission was sponsored by the pharmaceutical company Eli Lilly and Co. and the Center for the Advancement of Science in Space to study the effectiveness of a potential countermeasure for the loss of muscle and bone mass that occurs during spaceflight. Twenty BALB/c, 12-weeks old female mice (ten controls and ten treated) were flown to the ISS and housed in the Rodent Habitat for 39-42 days. Twenty mice of similar age, sex and strain were used for ground controls housed in identical hardware and matching ISS environmental conditions. Basal controls were housed in standard vivarium cages. Spaceflight, ground controls and basal groups had blood collected, then were euthanized, had one hind limb removed, and finally whole carcasses were stored at -80 C until dissection. All mice in this data set received only the control/sham injection. Spatially resolved transcriptional profiles were generated from hearts from three flight and three ground control animals as follows. Hearts were cryosectioned longitudinally onto an array of capture probes that bind RNA, fixed, stained and visualized. Heart sections were then permeabilized to release RNA onto the capture probes, and cDNA synthesized on the chip so that its spatial arrangement is encoded within a set of molecular barcodes. cDNA was then released and sequenced. Four to five levels of each heart was analyzed in this manner to allow a 3D reconstruction of the transcriptome. In addition, bulk RNA-seq (ribodepleted, target depth of 60 M clusters, PE 150 bp) was performed from a pool of RNA extracted from 10-20 sections from each of 3 flight and 2 ground control samples.