Growth Protocol:	The hiPSC line WISCi004-B/IMR90-4 was used to differentiate BCECs. a single cell suspension of hiPSCs was prepared with Accutase. The cell suspension was centrifuged at 300 x g for 5 min and cells were seeded in mTeSRTM1 supplemented with 10 µM Y-27632 onto Matrigel-coated 6-well plates. The seeding density was optimized for each hiPSC line. For the differentiation of hiPSCs to BCECs, the neurodevelopmental process in vivo has to be recapitulated in vitro. For brain-capillary endothelial-like cells, a co-differentiation of neural and endothelial cells was initiated by treatment with so-called unconditioned medium. After 2-3 days when optimal cell densities of 2-4x104 cells/cm2 were reached, medium was switched to unconditioned medium in order to initiate co-differentiation of BCECs and neuronal cells (referred to as day 0 of differentiation throughout the manuscript). Unconditioned medium was composed of 78.5% DMEM/F12 , 20% KnockOutTM serum replacement, 1% MEM NEAA, 0.5% L-glutamine, and 0.1 mM β-mercaptoethanol. A daily change of unconditioned medium for 5 days was followed by double feeding at day 6 with endothelial cell (EC) medium supplemented with 20 ng/ml hbFGF and 10 µM retinoic acid to expand the BCECs. EC medium was composed of Human Endothelial-SFM and, if not stated otherwise, 0.5% B27 Supplement as described recently (Neal et al., 2019). After 48 h without medium change, cells were dissociated with Accutase for 30 min and seeded at a cell density of 1x106 cells/cm2 onto collagen IV/fibronectin-coated transwell insert in EC medium supplemented with 20 ng/mL hFGF and 10 µM RA. This seeding step at day 8 in combination with the collagen IV/fibronectin-coating allows for an efficient purification of BCECs. At day 9, hiPS-BCECs were adapted to EC medium without hFGF and RA (in transwell systems with 200 µl of medium apical and 800 µl basolateral) for 24 h. TEER measurements were performed to evaluate the integrity of the generated in vitro BBB to be used for further applications.
Treatment Protocol:	At day 10 of differentiation hipsc-derived BCECs were either mock infected or exposed to SARS-CoV-2. After 24 hours cells were harvested and total RNA was extracted according to the manufacturer’s instructions using the NucleoSpin® RNA Kit (#740955.250, Macherey-Nagel). RNA concentration and quality was determined using a NanoDrop™ 1000 Spectrophotometer (ThermoFisher Scientific) and samples were stored at -80 °C until further use.
Extract Protocol:	NEBNext Ultra RNA Library Prep Kit (Illumina)
Library Construction Protocol:	-

Molecule Type:	polyA(+) RNA
Library Source:
Library Layout:	PAIRED
Library Strand:	Forward
Platform:	ILLUMINA
Instrument Model:	Illumina NovaSeq 6000
Strand-Specific:	Specific

Data Resource	GEN Sample ID	GEN Dataset ID	Project ID	BioProject ID	Sample ID	Sample Name	BioSample ID	Sample Accession	Experiment Accession	Release Date	Submission Date	Update Date	Species	Race	Ethnicity	Age	Age Unit	Gender	Source Name	Tissue	Cell Type	Cell Subtype	Cell Line	Disease	Disease State	Development Stage	Mutation	Phenotype	Case Detail	Control Detail	Growth Protocol	Treatment Protocol	Extract Protocol	Library Construction Protocol	Molecule Type	Library Layout	Strand-Specific	Library Strand	Spike-In	Strategy	Platform	Instrument Model	Cell Number	Reads Number	Gbases	AvgSpotLen1	AvgSpotLen2	Uniq Mapping Rate	Multiple Mapping Rate	Coverage Rate