title: GSM4411416: RNAseq; Fibroblast; 0dpa; uninjured; batch 3; rep1; Danio rerio; RNA-Seq
library_construction_protocol: For RNA-seq, biological triplicate D. rerio caudal fin clip  pools were collected at 0 dpa, 1 dpa, or 4 dpa time points via razor blade (VWR) from 15 fish aged between 3-12 months. Homozygous evx1 knockout fish were used for evx1 knockout libraries. Fin tissue was collected in Tri-Reagent (Sigma) and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit-5 (Zymo). For ATAC-seq libraries, biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa, 1 dpa, or 4 dpa time points via razor blade (VWR) from 15 fish aged 3-12 months. Homozygous Evx1 knockout fish (screened visually by jointless phenotype) (Borday et al., 2001) were used for Evx1 knockout libraries. Cells were dissociated using 1.18 U/mL Liberase DH (Roche) in Hank's Balanced Salt Solution (Gibco) stirring at 37°C for 2 hours, collected in 15 minute increments, then strained through a 70 μm nylon cell strainer (Corning). Samples were quantitated for 100K live cells using the Countess Automated Cell Counter (Thermo Fisher Scientific).Fibroblast samples were sorted for 100K mCherry+ fluorescent cells on a B-C Astrios cell sorter insead of quaitized for 100K live cells on a Contess SCell Conter. RNA-seq libraries were prepared using a Stranded mRNA-seq Kit (KAPA). ATAC-seq library preparation was performed as detailed in (Buenrostro et al., 2013).
attributes.tag: GEO Accession
attributes.value: GSM4411416