| We differentiated human iPSCs into excitatory cortical-like neurons (igNeurons) by NGN2 induction and followed them over time. We ran three independent differentiations, recorded in the `differentiation` column as Differentiation SC1, Differentiation SC2 and Differentiation SC3, and took one RNA sample from each on days 0, 9, 15, 21, 27, 33 and 40, 21 samples in total. The day of differentiation is in the `timepoint` column (Day0, Day9, Day15, Day21, Day27, Day33, Day40); the `group` column repeats the same labels. Day0 is the undifferentiated iPSC stage, and Day9 to Day40 cover neuronal maturation. There are no treatment or control groups: this is a pure time course. | |
| Because every differentiation was sampled on every day, the samples of one differentiation are related: they come from the same starting cells and the same induction and form one series over time. Each sample was sequenced once, so there are no technical replicates. We have no record of processing or sequencing batches, and no other variable we think matters; the remaining columns are GEO annotations. | |
| The data are ribosomal-RNA-depleted bulk total RNA-seq, quantified with featureCounts as raw gene-level read counts for Ensembl genes. | |
| Our question is which genes change in expression over neuronal maturation, looking at the overall change across Day9, Day15, Day21, Day27, Day33 and Day40, with Day9 as the baseline. Only the samples whose `timepoint` is one of these six days are part of this question; the Day0 iPSC samples are not. | |