run_metadata: 74691
This data as json
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| 74691 | SRR23948529 | SRX19757598 | SRS17122788 | SRP428929 | PRJNA947958 | Transcriptome profiling Zebrafish Sap130a gene mutations in embryogenesis | GSE228057 | Transcriptome Analysis | This study profiled the transcriptome of zebrafish embryos harboring mutation in the Sin3A associated Protein 130a sap130a gene at 36 hpf. The sap130a mutant was generated via Cas9 mediated gene editing. Zebrafish sap130a mutants are viable presumable due to the presence of maternal RNA. Generation of maternal zygotic MZ mutants resulted in an incomplete penetrance of heart ventricle defects that were visible as early as 36 hpf. In this experiment the MZsap130a mutant embryos were further sorted for embryos with smaller ventricle SV vs normal size ventricle NV. To extend on this study and to specifically analyze the heart sap130a mutant and WT hearts at 48 hpf were extracted for RNA seq analysis. Overall design: Total RNA was extracted from embryos at 36 hpf from wildetype MZsap130a mutants. | parent bioproject:PRJNA949794 | pubmed:37711853 | WT1 heart | GSM7113341 | source name:heart|tissue:heart|genotype:AB*|geo loc name:missing|collection date:missing | WT1 heart | fastq files were analyzed using CLC genomics workbench 20.0 sequence reads were mapped onto Danio rerio GRC.z11 EDGE test was performed using CLC genomics workbench Assembly: Danio rerio GRC.z11 Supplementary files format and content: .xlsx files. Data shows expression counts TPM and RKPM. | heart | embryos were kept at 28.5C temperature in standard egg water | Zebrafish embryos at 36hpf were sorted based on genotype and heart ventricle size for one study. The other study isolated heart tissue from embryos at 48hpf. RNA was harvested using Trizol reagent and Quiagen RNeasy micro kit Cat# 74004. | Zebrafish emrbyos were obtained from natural mating | tissue:heart|genotype:AB* | GSM7113341 | GSM7113341: WT1 heart; Danio rerio; RNA Seq | GSM7113341 r1 | GSM7113341 | 1 | Zebrafish embryos at 36hpf were sorted based on genotype and heart ventricle size for one study. The other study isolated heart tissue from embryos at 48hpf. RNA was harvested using Trizol reagent and Quiagen RNeasy micro kit Cat# 74004. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP428929 | loader:fastq load.py | WT_S13_R1_001.fastq.gz WT_S13_R2_001.fastq.gz | fastq fastq | 5820973044.0 | 30368728.0 | GSM7113341 r1 | 0:95.83 1:95.85 | A:1551155828;C:1325329152;G:1347896806;T:1526993048;N:69598210 | 95 | 95 | 1551155828 | 1325329152 | 1347896806 | 1526993048 | 69598210 | SRX19757598 | SRS17122788 | SRA1609766 | Developmental Biology, University of Pittsburgh | Developmental Biology, University of Pittsburgh | 2 | 0.77225 | 0.77451 | 0.09591 | 0.09552 | 0.71496 | 0.71518 | 0.47489 | 0.47506 | 101 | 101 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United States | 2023-03-23 | Multi-stage | Embryo | Heart | Cardiovascular System |