biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsMichael LovettRNA-seq of coding RNAGallus gallusGallus gallushttps://www.ebi.ac.uk/biostudies/studies/E-GEOD-56888Precise frequency discrimination is a hallmark of auditory function in birds and mammals. In the cochlea, tuning and spectral separation result from longitudinal differences in basilar membrane stiffness and numerous individual gradiations in sensory hair cell phenotypes, but it is unknown what patterns those phenotypes. Hypothesizing that morphogen levels might differ along the longitudinal axis of the developing cochlea, we sequenced the transcriptomes of the proximal, middle, and distal thirds of the chicken cochlea at E6.5, when postmitotic hair cells first form. Embryonic day 6.5 chicken cochlea were dissected. Three samples were collected from each cochlear duct by cutting the duct into three approximately equal sized pieces to produce proximal, middle, and distal pieces. Each sample contained a portion of the future tegmentum vasculosum and the basilar papilla sensory epithelium. The distal piece also contained the region fo the future lagena.biostudies-arrayexpressLibrary Construction - Chicken cochleae were dissected from E6.5 embryos. Cochlea were divided into three approximately equal sized pieces to produce proximal, middle, and distal pieces. Pieces from each region were pooled together and immediately transferred into three 1.5 mL eppendorf tubes containining 0.5 mL Tri Reagent RT (Molecular Research Center, Inc.). Samples were then stored at -20C until further processing. Samples from each section of the cochlea were then processed using Illumina mRNA-seq or TrueSeq preparation kits. Separate biological replicates were also prepared and similarly analyzed. mRNA was selected by oligo-dT magnetic beads and fragmented. First-strand cDNA was then generated using random primers. Second-strand synthesis, end repair and addition of a single A base and adaptor ligation were then performed. Each RNA-seq library was DNA-sequenced the Illumina HiSeq 2000. libraries were made using Illumina mRNA-seq or TrueSeq preparation kits.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesMichael LovettBenjamin ThiedeYena SonYuan-Chieh KuMattew KelleyZoe MannWeise ChangJeffrey CorwinData Transformation - Sequences were mapped to gga3 using Tophat v1.4.0 with default settings Alignment files (.bam) were inputed to Partek Genomics Suite v6.6 to calculate RPKM Genome_build: gga3 Supplementary_files_format_and_content: tab-delimited text file includes RPKM values of individual samplesfalseExpression data from proximal, middle, and distal segments of E6.5 chicken cochleaPrecise frequency discrimination is a hallmark of auditory function in birds and mammals. In the cochlea, tuning and spectral separation result from longitudinal differences in basilar membrane stiffness and numerous individual gradiations in sensory hair cell phenotypes, but it is unknown what patterns those phenotypes. Hypothesizing that morphogen levels might differ along the longitudinal axis of the developing cochlea, we sequenced the transcriptomes of the proximal, middle, and distal thirds of the chicken cochlea at E6.5, when postmitotic hair cells first form. Embryonic day 6.5 chicken cochlea were dissected. Three samples were collected from each cochlear duct by cutting the duct into three approximately equal sized pieces to produce proximal, middle, and distal pieces. Each sample contained a portion of the future tegmentum vasculosum and the basilar papilla sensory epithelium. The distal piece also contained the region fo the future lagena.2014-04-18T00:00:00Z2023-09-08T08:59:04.745Z2021-09-28T08:53:55ZE-GEOD-56888SRP041256EFO_0003738