title: GSM6131877: E16_foxp1_cko_3; Mus musculus; RNA-Seq
library_construction_protocol: For Foxp1 bulk RNA-seq analysis, retinas were dissected freshly at e16.5. Left and right eyes were combined, and total RNA was isolated using RNeasy Plus Mini Kit (Qaigen 74134) according to manufacturer's protocol. Three biological replicates of each: Six3-Cre; Foxp1fl/fl animals and Foxp1fl/fl controls, all from the same litter, were used for RNA sequencing. Library generation, sequencing, and alignment were performed by the Huntsman Cancer Institute High-Throughput Genomics and Bioinformatics Analysis Shared Resource. Total RNA concentration and quality were measured by RNA ScreenTape Assay (Agilent Technologies, 5067-5576, 5067-5577). All samples had a RIN value of 10. Total RNA samples (5-500 ng) were hybridized with NEBNext rRNA Depletion Kit v2 (Human, Mouse, Rat) (E7400) to substantially diminish rRNA from the samples. The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L) was used to generate sequencing libraries which were qualified by D1000 ScreenTape Assay (Agilent Technologies, 5067-5582, 5067-5583) and quantified with a Kapa Library Quant Kit (Kapa Biosystems, KK4824). Samples were sequenced on an Illumina NovaSeq 6000 instrument using the NovaSeq XP workflow (20043131).  A 150 x 150 cycle paired end sequence run was performed using a NovaSeq 6000 S4 reagent Kit v1.5 (20028312).