characteristics.text: 2025-04-30
characteristics.characteristic: ENA first public
characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
characteristics.characteristic: INSDC center name
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS24005450
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-15057:HB4_d13_NoMat_cDNA
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: WTC-11
characteristics.characteristic: cell line
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: For all experiments, single-cell suspensions were generated by dissociation of the organoids with a papain-based neural dissociation kit (Miltenyi Biotec, 130-092-628). Briefly, organoids were washed three times with HBSS without Ca2+ and Mg2+ (STEMCELL Technologies, 37250). Prewarmed papain solution (1-2 ml) was added to the organoids and incubated for 15 min at 37°C. The tissue pieces were triturated 5–10 times with 1000 µl wide-bore and then P1000 pipette tips. The tissue pieces were incubated twice for 10 min at 37 °C with additional trituration steps in between and after with P200 and P1000 pipette tips. Cells were filtered consecutively with a 30 or 40µm filter, centrifuged at 300g for 5 min and resuspended in cold PBS. The viability and cell count for the single cell suspensions were assessed using a Trypan Blue assay on the automated cell counter Countess (Thermo Fisher Scientific).  For the experiments with YAP activator (Fig. 6e,f, Extended Fig. 10h-l), organoids were generated using the unlabelled WTC-11 parent iPSC line. For the scRNAseq (Fig. 6e,f) organoids were cultured as described above with addition of 1:1000 DMSO in neural induction medium to control organoids on day 5 and 10µM Py-60 (MedChem Express, HY-141644) to organoids on day 5 or day 7. Media with fresh inhibitor or control media were exchanged every other day till dissociation and sequencing on day 10. For the scRNAseq (Extended Figure 9c-f; Extended Figure 10c-g), EBs were generated from 500 cells in mTSR+ (1:200 Rocki and 1:200 Pen-strep), per well of a 96 well plate and centrifuged at 200g for 5 min to generate embryoid bodies (EBs). Fresh mTSR+ with 1:200 ROCKi and 1:200 Pen-strep was exchanged on day 2 and day 4. Fresh Neural induction media was supplied on day 6 and exchanged every other day, followed by differentiation media - VitA on day 10 and differentiation media + VitA on Day 15. Organoids were given 2% matrigel, or 10µM Py-60 with 2% matrigel or no matrix on day 10. All media compositions were exchanged on day 13 followed by dissociation and sequencing on day 16. For scRNA-seq, cells were resuspended to a final concentration after counting and viability checking that enabled targeting 8,000 cells and, in case the cell numbers were not sufficient, all cells were loaded. The scRNA-seq libraries were generated using the Chromium Single Cell 3′ V3 Library & Gel Bead Kit. Single-cell encapsulation and library preparation were performed according to the manufacturer’s protocol. Single-cell encapsulation and library preparation were performed according to the manufacturer’s protocol.
characteristics.characteristic: description
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: HB4_d13_NoMat_cDNA
characteristics.characteristic: title