title: GSM8584193: CHIR +Activin treated micropatterns; Homo sapiens; RNA-Seq
library_construction_protocol: The micropatterned cells were lifted off the gelled coverslips by first washing with PBS to remove debris, followed by incubating in PBS at 37°C for 5 min and then by vigorous tapping of the plate. Whole micropatterned cells floating in PBS were visualized under a microscope and approximately 10 micropatterns for each treatment were picked up with a 200µl-capacity pipette tip. Cells were dissociated with StemPro Accutase Cell Dissociation Reagent (ThermoFisher Scientific) at 37°C for 5 min. Cells were assessed for viability and concentration, before loading into a 10X Chromium Chip G (10X Genomics) for an output of 10,000 cells using single cell droplet capture performed on the Chromium Controller (10X Genomics). One channel per sample was used. After cell separation and reverse transcription reactions occurred, library preparation followed in accordance with the Chromium Next GEM Single Cell 3' v3.1 (Dual Index) protocol. Libraries were evaluated for fragment size and concentration using Agilent HSD5000 ScreenTape System (Agilent) and were sent to AGRF (https://www.agrf.org.au/) for sequencing. Samples were sequenced using paired-ended, dual indexing, using cycles 28, 10, 10, 90 (R1, i7, i5, R2), for an output of 200 million reads per sample. cDNA library preparation was performed in accordance with the Single-Cell 3' v 3.0 or v3.1 protocol. Libraries were evaluated for fragment size and concentration using Agilent HSD5000 ScreenTape System (Agilent).
identifiers.namespace: GEO
identifiers.id: GSM8584193_r1