run_metadata: 63129
This data as json
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| 63129 | SRR13616486 | SRX10009740 | SRS8178663 | SRP304424 | PRJNA699078 | Single cell RNA sequencing of zebrafish pancreatic cells during beta cell regeneration | GSE166052 | Transcriptome Analysis | To better understand the underlying mechanism of beta cell regeneration in adult zebrafish we performed single cell transcriptomic profiling of the pancreatic tissue using 10X Genomics at various stages post beta cell ablation. Overall design: The adult fish expressing NTR gene under the insulin promoter were treated with Mtz Sigma Aldrich M3761 dissolved at 10mM concentration in fish water. The animals were treated for 24 hours protected from light. post 24h Mtz solution was removed and the animals were placed 3 times in fresh fish water before returning them to standard maintenance conditions. Both untreated and Mtz treated animals were euthanized by an overdose of tricaine. Samples for each time point comprised of 6 animals 3 males and 3 females. Single cell suspension was prepared and 15000 live cells/per condition were FACS sorted for 10X Genomics. | pubmed:35088828 | Pancreas 7dpa | GSM5060848 | tissue:Zebrafish pancreas|strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 7 days post MTZ | Pancreas 7dpa | bcl2fastq 1: Pancreas Control Pancreas 2dpa and Pancreas 7dpa were run with bcl2fastq2 2.19.1. bcl2fastq 2: Pancreas 0dap and Pancreas 14dpa were run with bcl2fastq2 2.20.0. Reference build: Cellranger needs a reference. Here GRCz11 was used and 3 transgenic genes were added to avoid false alignments to the main references. The genes are YFP mCherry and NTR. Alignment: Processing of sequencing data was done with the cellranger pipeline cellranger 4.0.0. Genome build: GRCz11 Supplementary files format and content: Tar archives contain the cellranger filtered feature barcode folder; the 3 files per folder are explained here: https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/output/matrices | Zebrafish pancreas | Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol. | strain/background:AB|genotype/variation:Wildtype expressing NTR gene under the insulin promoter|cell type:Pancreatic cells|Sex:Pooled male and female|age:Adult|treatment:MTZ treatment for 24 hours|time point:Dissection at 7 days post MTZ | GSM5060848 | GSM5060848: Pancreas 7dpa; Danio rerio; RNA Seq | GSM5060848 | 1 | Trypsin based dissociation followed by FACS sorting of alive cells. Library prep was performed according to the 10x protocol. | GEO Accession:GSM5060848 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP304424 | L47897_Track-91889_R1.fastq.gz L47897_Track-91889_R2.fastq.gz | fastq fastq | 11982402020.0 | 98216410.0 | GSM5060848 r1 | 0:29 1:93 | A:3162707284;C:2774571882;G:2736678637;T:3307378654;N:1065563 | 29 | 93 | 3162707284 | 2774571882 | 2736678637 | 3307378654 | 1065563 | SRX10009740 | SRS8178663 | SRA1190924 | GEO | Ninov Lab, CRTD, TU Dresden | 2 | 0.01025 | 0.93044 | 0.00221 | 0.066 | 0.98938 | 0.85823 | 0.52941 | 0.62147 | 29 | 93 | T | B | sc-like readlen | illumina | novaseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2021-02-02 | Adult | Adult | Pancreas | Endocrine System |