title: GSM8599025: Astro_SD_C2; Mus musculus; RNA-Seq
library_construction_protocol: Astrocytes and neuron samples were lysed using TRIzol®, and RNA was extracted with the Direct-zol™ RNA MiniPrep Kit (Zymo Research), following the manufacturer's instructions. Library preparation and RNA-sequencing Astrocytes and neuron samples were lysed using TRIzol®, and RNA was extracted with the Direct-zol™ RNA MiniPrep Kit (Zymo Research), following the manufacturer's instructions. 1μg of RNA was used to prepare total RNA libraries with the KAPA-RiboErase Hyper Prep kit, as per the manufacturer's protocol. The libraries were sequenced on an Illumina HiSeq 4000, generating 100bp pair-ended reads. The reads were aligned to the Mouse genome GRCm39 using STAR version 2.7.10a. Transcript abundance was quantified as FPKM, TPM, and counts using StringTie v2.2.1. Genes with counts below 10 in all the samples were excluded from further analysis.  Differential expression analysis was performed on the above filtered counts table using R package DESeq2 v1.44.0 to compare SD versus NS conditions. Log fold changes were adjusted using the lfcShrink function within the DESeq2 package. Genes with an FDR-adjusted p-value less than 0.05 were considered differentially expressed.