biostudies-arrayexpressMaria ZappiaDrosophila melanogasterhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-9444Our study focuses on understanding the early transcriptional changes taking place during the divergence of the adult muscle precursors that give rise to indirect flight muscles and direct flight muscles in Drosophila. We analyzed the heterogenous cell population of the adult muscle precursors by scRNA-seq and build an integrated single-cell reference atlas. We addressed the differences among muscle-type and different cell state during myoblast differentiation. Also, our dataset includes the transcriptional profile of the epithelial cells localized in the presumptive hinge and notum of third instar larval wing discs. In addition we studied the functional relevance of Amalgam in flight muscle development by depleting Ama expression specifically in the adult muscle precursors. We determined the transcriptional changes and perturbations in AMP cell identity upon Ama knockdown.biostudies-arrayexpressSequencing - Tagmented DNA was sequenced using NextSeq 500 - paired endLibrary Construction - Library construction was performed as written in the Drop-seq protocol. 1) RNA was reverse transcribed. 2) cDNA was PCR amplified. 3) tagmentation was done using Nextera XT kitGrowth Protocol - Flies were kept at 25 °C in vials containing standard cornmeal- agar medium.Sample Collection - Wandering third instar larvae were selected once outside the foodNucleic Acid Extraction - Third instar larva were collected, wing discs were dissected, pouch was manually removed using a microblade. Tissue was dissociated into single-cell suspension using a combination of Trypsin and Collagenase. Then Drop-seq was performed on the single cell suspension. Libraries were made and sequenced.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Illumina paired end raw FastQ file were processed for read alignment and gene expression. Drop-seq single-cell data was analyzed using the data anlysis protocol described in Drop-seq cook-book (Macosko et al. 2015)(http://mccarrolllab.com/dropseq/) and used the Drop-seq_tools-1.13. We used STAR aligner to align the reads against Drosophila melanogaster genome version BDGP6 (From Ensembl) and corresponding gene model is extracted from Ensembl version 90.Data Transformation - To create processed data matrix file, Digital Gene Expression (DGE) data obtained from an aligned library is done using the Drop­seq program DigitalExpression (integrated in Drop-seq_tools). Number of cells that were extracted from aligned BAM file is based on knee plot which extracts the number of reads per cell, then plot the cumulative distribution of reads and select the “knee” of the distribution.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 500RNA-seq of coding RNA from single cellsDrosophila melanogasterMaria ZappiafalseSingle cell transcriptional profile of third instar larval wing discs in DrosophilaOur study focuses on understanding the early transcriptional changes taking place during the divergence of the adult muscle precursors that give rise to indirect flight muscles and direct flight muscles in Drosophila. We analyzed the heterogenous cell population of the adult muscle precursors by scRNA-seq and build an integrated single-cell reference atlas. We addressed the differences among muscle-type and different cell state during myoblast differentiation. Also, our dataset includes the transcriptional profile of the epithelial cells localized in the presumptive hinge and notum of third instar larval wing discs. In addition we studied the functional relevance of Amalgam in flight muscle development by depleting Ama expression specifically in the adult muscle precursors. We determined the transcriptional changes and perturbations in AMP cell identity upon Ama knockdown.2020-08-31T00:00:00Z2024-01-13T19:02:46.662Z2022-02-02T19:11:09.517ZE-MTAB-9444ERP123521EFO_0002944EFO_0004170EFO_0003789EFO_0005684EFO_0004917EFO_0005518EFO_0003816EFO_0004184