run_metadata: 71092
This data as json
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| 71092 | SRR21237245 | SRX17246661 | SRS14811786 | 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 | Ductal3 | GSM6509759 | source name:pancreas|tissue:pancreas|cell type:ductal|genotype:Tgins:NTR mcherry; Tgnkx6.1:GFP|treatment:DMSO | Ductal3 | 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:DMSO | GSM6509759 | GSM6509759: Ductal3; Danio rerio; RNA Seq | GSM6509759 r1 | GSM6509759 | 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_4_CGTACTAG_L007_R2_001.fastq.gz IM_4_CGTACTAG_L007_R1_001.fastq.gz | fastq fastq | 17851670816.0 | 88374608.0 | GSM6509759 r1 | 0:101 1:101 | A:5161409723;C:3739347454;G:3476991371;T:5472775357;N:1146911 | 101 | 101 | 5161409723 | 3739347454 | 3476991371 | 5472775357 | 1146911 | SRX17246661 | SRS14811786 | SRA1485636 | Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège | Zebrafish Development and Disease Model, GIGA-Stem Cell, Université de Liège | 2 | 0.85539 | 0.85497 | 0.14301 | 0.14391 | 0.78825 | 0.79115 | 0.52575 | 0.53365 | 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 |