{"database": "metadata", "table": "run_metadata", "rows": [[30746, "SRR28348607", "SRX23954674", "SRS20755104", "SRP495302", "PRJNA1088122", "Decoding the molecular  cellular  and functional heterogeneity of zebrafish intracardiac nervous system", "GSE261619", "Transcriptome Analysis", "In this project  we present a comprehensive taxonomy of the intracardiac nervous system IcNS  utilizing single cell RNA sequencing  anatomical studies  and electrophysiological techniques. Overall design: For single cell sequencing experiments  25 Tgelavl3:eGFP previously known as HuC:GFP of 5 mpf animal were used from both sexes for the first set and 25 Tgelavl3:eGFP of 11 mpf  and 10 Tgnbt:DsRed of 22 mpf animals from both sexes were used for the second set. Cells were dissociated sorted by FACS as described Cosacak et al. 2019. The single cell encapsulation and cDNA synthesis done by following 10X Genomics' workflows. The reads were aligned to zebrafish genome GRChZ 11  v 105 was used for gene annotation and assigning reads to genes. Cellranger software version 6.1.2 was used to process the data.", null, "pubmed:39632839", null, "Tgelavl3:eGFP  Tgnbt:DsRed", "GSM8147512", null, "source name:atrium|tissue:atrium|genotype:Tgelavl3:eGFP  Tgnbt:DsRed|geo loc name:missing|collection date:missing", "Tgelavl3:eGFP  Tgnbt:DsRed", "The demultiplexing  barcoded processing  gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/metrics The fastq files were aligned to zebrafish genome GRCz11 and ensemble transcripts from Ensembl Release 105 by using STAR. The BAM files were as input for Cell Ranger 10X genomics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Assembly: GRCz11 Supplementary files format and content: filtered bc matrix outputs from Cell Ranger", "atrium", null, "Cells from zebrafish heart were dissociated. In addition to GFP and DsRed in the genome of the fish  viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol. 10X genomics", "Zebrafish were kept in the re circulating system on a 14/10 h light/dark cycle  pH7.5  at 28\u00b0C \u00b11\u00b0C in groups of 20 animals per 2.8L.", "tissue:atrium|genotype:Tgelavl3:eGFP  Tgnbt:DsRed", "GSM8147512", "GSM8147512: Tgelavl3:eGFP  Tgnbt:DsRed; Danio rerio; RNA Seq", "GSM8147512 r1", "GSM8147512", "1", "Cells from zebrafish heart were dissociated. In addition to GFP and DsRed in the genome of the fish  viability indicator dyes Sytox Blue Invitrogen  Cat No. S34857 and Dycle Ruby Invitrogen  Cat. No. V10309 were used to sort the cells by FACS. 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