run_metadata: 74648
This data as json
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| 74648 | SRR23908259 | SRX19719739 | SRS17086855 | SRP428087 | PRJNA946307 | The zebrafish heart harbors a thermogenic beige fat depot analog of human epicardial adipose tissue | GSE227670 | Other | The main goal of this study was to examine the presence and specific transcriptomic profile of epicardial adipose tissue eAT in zebrafish. We assessed how cold treatment affects the epicardial adipose tissue. Additional we provided some key differences between human mouse and zebrafish epicardial adipose tissue. Overall design: We compared the transcriptomes of zebrafish eAT epicardial adipose tissue and vAT visceral adipose tissue using RNA sequencing RNA Seq from adult female zebrafish. Adult zebrafish were acclimated from 27°C control temperature to 18°C by gradual reduction of tank water at the rate of 1 °C/h with an external water chiller. Cold acclimated fish were maintained at 18±1°C for 24h while control fish were maintained at 27±1°C. Hearts were isolated to harvest eAT for RNA sequencing | pubmed:38507414 | vAT visceral fat 2 | GSM7104993 | source name:adipose tissue|tissue:adipose tissue|tissue subtype:Viscerlal fat|Sex:female|geo loc name:missing|collection date:missing | vAT visceral fat 2 | RNA seq data were processed and analyzed using the PiGx RNAseq pipeline version 0.0.19 The raw reads were mapped to the zebrafish genome using STAR aligner version 2.7.3a Read count normalization and downstream analysis of differential gene expression was carried out using DESeq2 R package version 1.32.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values of DESeq2 normalized counts for eAT and vAT | adipose tissue | Adipocytes were collected for RNA extraction. Total RNA was prepared using TRIzol Life Technologies 15596026 Libraries were prepared using SMARTer Stranded Total RNA Seq Kit v3 TaKaRa 634487 following manufacturer's protocols. | tissue:adipose tissue|tissue subtype:Viscerlal fat|Sex:female | GSM7104993 | GSM7104993: vAT visceral fat 2; Danio rerio; RNA Seq | GSM7104993 r1 | GSM7104993 | 1 | Adipocytes were collected for RNA extraction. Total RNA was prepared using TRIzol Life Technologies 15596026 Libraries were prepared using SMARTer Stranded Total RNA Seq Kit v3 TaKaRa 634487 following manufacturer's protocols. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP428087 | loader:fastq load.py | vAT2_L001_R1.fastq.gz vAT2_L001_R2.fastq.gz | fastq fastq | 9570642032.0 | 47379416.0 | GSM7104993 r1 | 0:101 1:101 | A:1723773940;C:3093746894;G:3053200070;T:1695451865;N:4469263 | 101 | 101 | 1723773940 | 3093746894 | 3053200070 | 1695451865 | 4469263 | SRX19719739 | SRS17086855 | SRA1606837 | AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin | AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin | 2 | 0.93262 | 0.87031 | 0.18134 | 0.17953 | 0.95345 | 0.95775 | 0.75307 | 0.78294 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | full_length | cdna_unspecified | smarter | bulk | unknown | unknown | Germany | 2023-03-19 | Undetermined | Adult | Adipose Tissue | Adipose Tissue |