run_metadata: 71091
This data as json
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| 71091 | SRR21237244 | SRX17246662 | SRS14811787 | SRP394370 | PRJNA874056 | Effect of beta cell ablation on pancreatic ductal cells in adult zebrafish | GSE212124 | Transcriptome Analysis | To determine the change at the transcriptomic level of ductal cells during beta cell regeneration we performed RNA seq on pancreatic ductal cells 3 days post beta cell destruction and compared with non ablated control Overall design: Comparative gene expression profiling analysis of RNA seq data with or without xxx cell ablation | pubmed:39383064 | MTZ1 | GSM6509760 | source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole | MTZ1 | sequenced with Illumina NextSeq500 obtained 20million 100bp paired end reads Mapped to zebrafish genome GRCz11 using STAR version 2.6.1 Gene expression levels calculated with featureCounts Assembly: GRCz11 Supplementary files format and content: tab delimited text files include TPM values for each Sample | pancreas | Adult zebrafish were treated with 10mM metronidazole and DMSO overnight. Control fish were only treated with DMSO | Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024 | tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:metronidazole | GSM6509760 | GSM6509760: MTZ1; Danio rerio; RNA Seq | GSM6509760 r1 | GSM6509760 | 1 | Lysis buffer : pure nuclease free water triton 0 28% dNTP 2 38mM oligo dT primer 2 38uM cDNA preparation with SMARTer Ultra Low RNA kit for Illumination sequencing with adaptations Picelli et.al 2014; Nextera XT DNA Library Prep Kit Illumina FC 131 1024 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP394370 | IM_2_CGTACTAG_L006_R1_001.fastq.gz IM_2_CGTACTAG_L006_R2_001.fastq.gz | fastq fastq | 17015359304.0 | 84234452.0 | GSM6509760 r1 | 0:101 1:101 | A:4643492769;C:3861165659;G:3730150815;T:4779151147;N:1398914 | 101 | 101 | 4643492769 | 3861165659 | 3730150815 | 4779151147 | 1398914 | SRX17246662 | SRS14811787 | SRA1485636 | Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège | Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège | 2 | 0.90217 | 0.90221 | 0.08047 | 0.08087 | 0.7651 | 0.76696 | 0.52075 | 0.53178 | 101 | 101 | B | B | biological fallback assumption | illumina | nextseq | full_length | poly_a | nextera | bulk | unknown | unknown | Belgium | 2022-08-26 | Adult | Adult | Pancreas | Endocrine System |