For the buds samples (samples 1-8): buds were microdissected along with their surrounding tunic and some ampullae and washed twice in in calcium- and magnesium-free artificial sea water (CMFASW; 31g/L NaCl, 0.8g/L KCl, 0.29g/L NaHCO3, 1.6g/L Na2SO4, pH 8.0) with 40U/ml RNAsin Plus (Promega). Buds were then detunicated and dissociated by pipetting in 0.2µm-filtered 1% Trypsin (m./v.) in CMFASW with 40 U/ml RNAsin Plus for 20-30 min. Cell suspensions with over 85% cell viability were fixed in ACME (10% acetic acid, 15% methanol, 10% glycerol in molecular grade water) with 40U/ml RNAsin Plus for 1h on ice, gently shaking, then stored at -20°C for up to a few days. Fixative was removed from cell suspensions by washing and centrifugating cells in 0.2µm-filtered 1% BSA in PBS, then stored at -80°C with 10% (v./v.)  DMSO. On the day of library preparation, cryopreserved samples were slowly thawed on ice, centrifuged and  resuspended in 1% BSA-PBS with 40U/ml RNAsin Plus. They were then filtered with 40µm cell strainer to remove largest aggregates, stained with Draq5 and sorted by FACS to select only single cells. For the circulating cells samples (sample 9-10): colonies were cleaned a couple hours before dissections and kept in 0.22µm filtered ASW until blood collection. At collection time, colonies were dried gently with a Kim wipe, then 100-200 µL of PBS-M-DTT (0.7M D-mannitol in 1X PBS with 0.01 M dithiothreitol, added fresh each day) was added on top. Blood was extracted by making multiple cuts in vascularized regions of the colony, and gently pressing on it. The PBS-M-DTT with suspended blood cells was collected and kept in a microcentrifuge tube on ice. Blood cells from several colonies at the same stage were pooled. Each cell suspension was filtered through a 40µm strainer into a microcentrifuge tube which had been coated with 10% (v./v.) bovine serum albumin in Dulbecco's phosphate-buffered saline and washed by centrifugation before resuspension in PBS-M-DTT. The cell viability prior to encapsulation was 79% (Sample 9 -A1) and 80% (Sample 10 - B2). Cell encapsulation, RT, cDNA amplification, and library preparation were carried out using the Chromium Next GEM Single Cell 3′ v3.1 Kits (10X Genomics 1000123, 1000127, and 1000190). For the buds samples (samples 1-8): The manufacturer's guidelines were followed. The libraries were then sequenced (paired-end) on an Illumina NextSeq2000. When necessary, resequencing was performed to achieve a sequencing saturation of approximately 40% or higher. FASTQ files in this archive contain the concatenated reads from all sequencing of the same library. For the circulating cells samples (sample 9-10): The manufacturer's guidelines were followed except for one step. To prepare the RT mix prior to cell encapsulation, the manufacturer protocol instructs to add nuclease-free water, then to add the cell suspension; we added PBS-M instead of nuclease-free water to adjust for live cells osmolarity.