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43 rows where experiment.library_selection = "cDNA", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation = "Adipose Tissue"

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devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

  • Adipose Tissue · 43 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 43 ✖

experiment.library_selection 1

  • cDNA · 43 ✖

experiment.library_layout 1

devstage_curation_coarse 1

Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
34919 34919 SRR32390771 SRX27723138 SRS24115841 SRP564820 PRJNA1225415 Lipid metabolism studies PRJNA1225415 Other Effect of cyp27b1 knockout on gene expression in adipose tissue         cyp27b13   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month of age|dev stage:Sexual maturity|collection date:2023 06 02|geo loc name:China:Wuhan|sex:female|tissue:Adipose tissue of cyp27b1 knockout zebrafish|replicate:replicate=Biological Replicate 6|BioSampleModel:Model organism or animal                 RNA Seq of adipose tissue from wild type and cyp27b6 knockout zebrafish cyp27b13 cyp27b13 Adipose tissue of zebrafish     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP564820     L1EHF0502912--cyp27b13.R1.raw.fastq.gz L1EHF0502912--cyp27b13.R2.raw.fastq.gz fastq fastq 8920678038.0 29538669.0 L1EHF0502912 cyp27b13.R1.raw.fastq.gz 0:151 1:151 A:2272825316;C:2129553023;G:2241210697;T:2270388407;N:6700595 151 151     2272825316 2129553023 2241210697 2270388407 6700595 SRX27723138 SRS24115841 SRA2079844 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2025-02-18 Adult Adult Adipose Tissue Adipose Tissue
34920 34920 SRR32390772 SRX27723137 SRS24115840 SRP564820 PRJNA1225415 Lipid metabolism studies PRJNA1225415 Other Effect of cyp27b1 knockout on gene expression in adipose tissue         cyp27b12   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month of age|dev stage:Sexual maturity|collection date:2023 06 02|geo loc name:China:Wuhan|sex:female|tissue:Adipose tissue of cyp27b1 knockout zebrafish|replicate:replicate=Biological Replicate 5|BioSampleModel:Model organism or animal                 RNA Seq of adipose tissue from wild type and cyp27b5 knockout zebrafish cyp27b12 cyp27b12 Adipose tissue of zebrafish     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP564820     L1EHF0502911--cyp27b12.R1.raw.fastq.gz L1EHF0502911--cyp27b12.R2.raw.fastq.gz fastq fastq 6539341296.0 21653448.0 L1EHF0502911 cyp27b12.R1.raw.fastq.gz 0:151 1:151 A:1683767731;C:1537831452;G:1625315620;T:1687496025;N:4930468 151 151     1683767731 1537831452 1625315620 1687496025 4930468 SRX27723137 SRS24115840 SRA2079844 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2025-02-18 Adult Adult Adipose Tissue Adipose Tissue
34921 34921 SRR32390773 SRX27723136 SRS24115839 SRP564820 PRJNA1225415 Lipid metabolism studies PRJNA1225415 Other Effect of cyp27b1 knockout on gene expression in adipose tissue         cyp27b11   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month of age|dev stage:Sexual maturity|collection date:2023 06 02|geo loc name:China:Wuhan|sex:female|tissue:Adipose tissue of cyp27b1 knockout zebrafish|replicate:replicate=Biological Replicate 4|BioSampleModel:Model organism or animal                 RNA Seq of adipose tissue from wild type and cyp27b4 knockout zebrafish cyp27b11 cyp27b11 Adipose tissue of zebrafish     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP564820     L1EHF0502910--cyp27b11.R1.raw.fastq.gz L1EHF0502910--cyp27b11.R2.raw.fastq.gz fastq fastq 9264841466.0 30678283.0 L1EHF0502910 cyp27b11.R1.raw.fastq.gz 0:151 1:151 A:2329336084;C:2235782030;G:2356752279;T:2336076497;N:6894576 151 151     2329336084 2235782030 2356752279 2336076497 6894576 SRX27723136 SRS24115839 SRA2079844 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2025-02-18 Adult Adult Adipose Tissue Adipose Tissue
34922 34922 SRR32390774 SRX27723135 SRS24115838 SRP564820 PRJNA1225415 Lipid metabolism studies PRJNA1225415 Other Effect of cyp27b1 knockout on gene expression in adipose tissue         WT 3   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month of age|dev stage:Sexual maturity|collection date:2023 06 02|geo loc name:China:Wuhan|sex:female|tissue:Adipose tissue of wild type zebrafish|replicate:replicate=Biological Replicate 3|BioSampleModel:Model organism or animal                 RNA Seq of adipose tissue from wild type and cyp27b3 knockout zebrafish WT 3 WT 3 Adipose tissue of zebrafish     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP564820     L1EHF0502909--WT_3.R1.raw.fastq.gz L1EHF0502909--WT_3.R2.raw.fastq.gz fastq fastq 7902932904.0 26168652.0 L1EHF0502909 WT 3.R1.raw.fastq.gz 0:151 1:151 A:2042231850;C:1881707768;G:1947999179;T:2025118866;N:5875241 151 151     2042231850 1881707768 1947999179 2025118866 5875241 SRX27723135 SRS24115838 SRA2079844 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2025-02-18 Adult Adult Adipose Tissue Adipose Tissue
34923 34923 SRR32390775 SRX27723134 SRS24115837 SRP564820 PRJNA1225415 Lipid metabolism studies PRJNA1225415 Other Effect of cyp27b1 knockout on gene expression in adipose tissue         WT 2   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month of age|dev stage:Sexual maturity|collection date:2023 06 02|geo loc name:China:Wuhan|sex:female|tissue:Adipose tissue of wild type zebrafish|replicate:replicate=Biological Replicate 2|BioSampleModel:Model organism or animal                 RNA Seq of adipose tissue from wild type and cyp27b2 knockout zebrafish WT 2 WT 2 Adipose tissue of zebrafish     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP564820     L1EHF0502908_L1EHF0502908--WT_2.R1.raw.fastq.gz L1EHF0502908_L1EHF0502908--WT_2.R2.raw.fastq.gz fastq fastq 6637747392.0 21979296.0 L1EHF0502908 L1EHF0502908 WT 2.R1.raw.fastq.gz 0:151 1:151 A:1743357103;C:1532545023;G:1608580940;T:1748717704;N:4546622 151 151     1743357103 1532545023 1608580940 1748717704 4546622 SRX27723134 SRS24115837 SRA2079844 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2025-02-18 Adult Adult Adipose Tissue Adipose Tissue
34924 34924 SRR32390776 SRX27723133 SRS24115836 SRP564820 PRJNA1225415 Lipid metabolism studies PRJNA1225415 Other Effect of cyp27b1 knockout on gene expression in adipose tissue         WT 1   strain:not applicable|isolate:not applicable|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:3 month of age|dev stage:Sexual maturity|collection date:2023 06 02|geo loc name:China:Wuhan|sex:female|tissue:Adipose tissue of wild type zebrafish|replicate:replicate=Biological Replicate 1|BioSampleModel:Model organism or animal                 RNA Seq of adipose tissue from wild type and cyp27b1 knockout zebrafish WT 1 WT 1 Adipose tissue of zebrafish     RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP564820     L1EHF0502907--WT_1.R1.raw.fastq.gz L1EHF0502907--WT_1.R2.raw.fastq.gz fastq fastq 8349738884.0 27648142.0 L1EHF0502907 WT 1.R1.raw.fastq.gz 0:151 1:151 A:2031828579;C:2054226763;G:2198596210;T:2058882599;N:6204733 151 151     2031828579 2054226763 2198596210 2058882599 6204733 SRX27723133 SRS24115836 SRA2079844 Huazhong Agricultural University|College of Fisheries Huazhong Agricultural University                       B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified unknown bulk unknown unknown   China 2025-02-18 Adult Adult Adipose Tissue Adipose Tissue
53258 53258 SRR9735192 SRX6492152 SRS5140748 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose KO A13 GSM3964281   source name:Adipose|genotype:ASC 1 KO|age:6 month|tissue:Adipose Adipose KO A13 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:ASC 1 KO|age:6 month|tissue:Adipose GSM3964281 GSM3964281: Adipose KO A13; Danio rerio; RNA Seq GSM3964281   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964281 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     KO-A13_S72_R1_001.fastq KO-A13_S72_R2_001.fastq fastq fastq 5138754890.0 34082266.0 GSM3964281 r1 0:75.42 1:75.35 A:1340049186;C:1217209122;G:1186072711;T:1388580907;N:6842964 75 75     1340049186 1217209122 1186072711 1388580907 6842964 SRX6492152 SRS5140748 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.935 0.93379 0.0843 0.08471 0.64133 0.6451 0.49347 0.48752 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53259 53259 SRR9735191 SRX6492151 SRS5140747 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose KO A12 GSM3964280   source name:Adipose|genotype:ASC 1 KO|age:6 month|tissue:Adipose Adipose KO A12 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:ASC 1 KO|age:6 month|tissue:Adipose GSM3964280 GSM3964280: Adipose KO A12; Danio rerio; RNA Seq GSM3964280   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964280 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     KO-A12_S71_R1_001.fastq KO-A12_S71_R2_001.fastq fastq fastq 5247529093.0 34816716.0 GSM3964280 r1 0:75.40 1:75.32 A:1362925706;C:1248336173;G:1216659223;T:1411216050;N:8391941 75 75     1362925706 1248336173 1216659223 1411216050 8391941 SRX6492151 SRS5140747 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.9331 0.93321 0.08005 0.07957 0.63573 0.6392 0.48434 0.48612 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53260 53260 SRR9735190 SRX6492150 SRS5140746 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose KO A11 GSM3964279   source name:Adipose|genotype:ASC 1 KO|age:6 month|tissue:Adipose Adipose KO A11 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:ASC 1 KO|age:6 month|tissue:Adipose GSM3964279 GSM3964279: Adipose KO A11; Danio rerio; RNA Seq GSM3964279   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964279 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     KO-A11_S70_R1_001.fastq KO-A11_S70_R2_001.fastq fastq fastq 7278073849.0 48245295.0 GSM3964279 r1 0:75.46 1:75.39 A:1910309106;C:1710143808;G:1680260958;T:1970904301;N:6455676 75 75     1910309106 1710143808 1680260958 1970904301 6455676 SRX6492150 SRS5140746 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.93057 0.93294 0.08151 0.08126 0.64149 0.64382 0.49583 0.50069 76 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53261 53261 SRR9735189 SRX6492149 SRS5140745 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose KO A10 GSM3964278   source name:Adipose|genotype:ASC 1 KO|age:6 month|tissue:Adipose Adipose KO A10 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:ASC 1 KO|age:6 month|tissue:Adipose GSM3964278 GSM3964278: Adipose KO A10; Danio rerio; RNA Seq GSM3964278   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964278 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     KO-A10_S69_R1_001.fastq KO-A10_S69_R2_001.fastq fastq fastq 6250335404.0 41467476.0 GSM3964278 r1 0:75.40 1:75.33 A:1623367800;C:1484173582;G:1452734282;T:1680039881;N:10019859 75 75     1623367800 1484173582 1452734282 1680039881 10019859 SRX6492149 SRS5140745 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.93288 0.93316 0.07513 0.07471 0.63863 0.63926 0.49527 0.4986 76 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53262 53262 SRR9735188 SRX6492148 SRS5140744 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose KO A9 GSM3964277   source name:Adipose|genotype:ASC 1 KO|age:6 month|tissue:Adipose Adipose KO A9 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:ASC 1 KO|age:6 month|tissue:Adipose GSM3964277 GSM3964277: Adipose KO A9; Danio rerio; RNA Seq GSM3964277   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964277 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     KO-A9_S68_R1_001.fastq KO-A9_S68_R2_001.fastq fastq fastq 5146879384.0 34123155.0 GSM3964277 r1 0:75.44 1:75.40 A:1308295304;C:1251385303;G:1224804381;T:1356968336;N:5426060 75 75     1308295304 1251385303 1224804381 1356968336 5426060 SRX6492148 SRS5140744 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.93651 0.93824 0.02355 0.02291 0.72841 0.73024 0.47075 0.46919 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53263 53263 SRR9735187 SRX6492147 SRS5140743 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose KO A8 GSM3964276   source name:Adipose|genotype:ASC 1 KO|age:6 month|tissue:Adipose Adipose KO A8 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:ASC 1 KO|age:6 month|tissue:Adipose GSM3964276 GSM3964276: Adipose KO A8; Danio rerio; RNA Seq GSM3964276   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964276 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     KO-A8_S67_R1_001.fastq KO-A8_S67_R2_001.fastq fastq fastq 6451988817.0 42793124.0 GSM3964276 r1 0:75.42 1:75.35 A:1683086295;C:1528898615;G:1498099595;T:1733026886;N:8877426 75 75     1683086295 1528898615 1498099595 1733026886 8877426 SRX6492147 SRS5140743 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.93365 0.93498 0.07705 0.0772 0.64305 0.64695 0.48242 0.49262 76 74 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53264 53264 SRR9735186 SRX6492146 SRS5140742 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose KO A7 GSM3964275   source name:Adipose|genotype:ASC 1 KO|age:6 month|tissue:Adipose Adipose KO A7 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:ASC 1 KO|age:6 month|tissue:Adipose GSM3964275 GSM3964275: Adipose KO A7; Danio rerio; RNA Seq GSM3964275   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964275 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     KO-A7_S66_R1_001.fastq KO-A7_S66_R2_001.fastq fastq fastq 5216519024.0 34658426.0 GSM3964275 r1 0:75.29 1:75.22 A:1355357386;C:1236474760;G:1213941961;T:1396130960;N:14613957 75 75     1355357386 1236474760 1213941961 1396130960 14613957 SRX6492146 SRS5140742 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.93221 0.93203 0.08221 0.08139 0.63678 0.63958 0.48897 0.49047 76 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53265 53265 SRR9735185 SRX6492145 SRS5140741 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose KO A6 GSM3964274   source name:Adipose|genotype:ASC 1 KO|age:6 month|tissue:Adipose Adipose KO A6 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:ASC 1 KO|age:6 month|tissue:Adipose GSM3964274 GSM3964274: Adipose KO A6; Danio rerio; RNA Seq GSM3964274   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964274 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     KO-A6_S60_R1_001.fastq KO-A6_S60_R2_001.fastq fastq fastq 5029559020.0 33338985.0 GSM3964274 r1 0:75.47 1:75.39 A:1315693469;C:1191236029;G:1161411700;T:1356918715;N:4299107 75 75     1315693469 1191236029 1161411700 1356918715 4299107 SRX6492145 SRS5140741 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.93307 0.93431 0.0803 0.07962 0.63556 0.63842 0.48626 0.48677 75 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53266 53266 SRR9735184 SRX6492144 SRS5140740 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose KO A5 GSM3964273   source name:Adipose|genotype:ASC 1 KO|age:6 month|tissue:Adipose Adipose KO A5 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:ASC 1 KO|age:6 month|tissue:Adipose GSM3964273 GSM3964273: Adipose KO A5; Danio rerio; RNA Seq GSM3964273   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964273 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     KO-A5_S59_R1_001.fastq KO-A5_S59_R2_001.fastq fastq fastq 4248040067.0 28185659.0 GSM3964273 r1 0:75.40 1:75.32 A:1109513588;C:1005952629;G:981560840;T:1144059315;N:6953695 75 75     1109513588 1005952629 981560840 1144059315 6953695 SRX6492144 SRS5140740 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.93233 0.9341 0.07965 0.07934 0.64145 0.64331 0.4856 0.4902 75 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53267 53267 SRR9735183 SRX6492143 SRS5140739 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose KO A4 GSM3964272   source name:Adipose|genotype:ASC 1 KO|age:6 month|tissue:Adipose Adipose KO A4 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:ASC 1 KO|age:6 month|tissue:Adipose GSM3964272 GSM3964272: Adipose KO A4; Danio rerio; RNA Seq GSM3964272   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964272 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     KO-A4_S58_R1_001.fastq KO-A4_S58_R2_001.fastq fastq fastq 6392993509.0 42397316.0 GSM3964272 r1 0:75.43 1:75.36 A:1675757830;C:1504320009;G:1478667713;T:1726331052;N:7916905 75 75     1675757830 1504320009 1478667713 1726331052 7916905 SRX6492143 SRS5140739 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.93219 0.93293 0.07772 0.07734 0.63782 0.64193 0.4886 0.49125 75 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53268 53268 SRR9735182 SRX6492142 SRS5140738 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose KO A3 GSM3964271   source name:Adipose|genotype:ASC 1 KO|age:6 month|tissue:Adipose Adipose KO A3 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:ASC 1 KO|age:6 month|tissue:Adipose GSM3964271 GSM3964271: Adipose KO A3; Danio rerio; RNA Seq GSM3964271   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964271 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     KO-A3_S57_R1_001.fastq KO-A3_S57_R2_001.fastq fastq fastq 6746800381.0 44738574.0 GSM3964271 r1 0:75.43 1:75.37 A:1761609432;C:1594754083;G:1559830166;T:1823605880;N:7000820 75 75     1761609432 1594754083 1559830166 1823605880 7000820 SRX6492142 SRS5140738 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.93115 0.9313 0.07704 0.07567 0.63767 0.63844 0.49601 0.5018 75 74 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53269 53269 SRR9735181 SRX6492141 SRS5140737 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose KO A2 GSM3964270   source name:Adipose|genotype:ASC 1 KO|age:6 month|tissue:Adipose Adipose KO A2 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:ASC 1 KO|age:6 month|tissue:Adipose GSM3964270 GSM3964270: Adipose KO A2; Danio rerio; RNA Seq GSM3964270   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964270 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     KO-A2_S56_R1_001.fastq KO-A2_S56_R2_001.fastq fastq fastq 5178912160.0 34352174.0 GSM3964270 r1 0:75.42 1:75.34 A:1355500844;C:1221527452;G:1199707224;T:1395740755;N:6435885 75 75     1355500844 1221527452 1199707224 1395740755 6435885 SRX6492141 SRS5140737 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.93426 0.93454 0.07738 0.07682 0.64212 0.6464 0.48878 0.49331 73 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53270 53270 SRR9735180 SRX6492140 SRS5140736 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose KO A1 GSM3964269   source name:Adipose|genotype:ASC 1 KO|age:6 month|tissue:Adipose Adipose KO A1 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:ASC 1 KO|age:6 month|tissue:Adipose GSM3964269 GSM3964269: Adipose KO A1; Danio rerio; RNA Seq GSM3964269   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964269 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     KO-A1_S55_R1_001.fastq KO-A1_S55_R2_001.fastq fastq fastq 5542839857.0 36746361.0 GSM3964269 r1 0:75.44 1:75.40 A:1446459244;C:1311682387;G:1288685673;T:1491071107;N:4941446 75 75     1446459244 1311682387 1288685673 1491071107 4941446 SRX6492140 SRS5140736 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.93776 0.93895 0.04491 0.04446 0.67675 0.67872 0.41719 0.42005 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53271 53271 SRR9735179 SRX6492139 SRS5140735 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose WT A11 GSM3964268   source name:Adipose|genotype:WT|age:6 month|tissue:Adipose Adipose WT A11 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:WT|age:6 month|tissue:Adipose GSM3964268 GSM3964268: Adipose WT A11; Danio rerio; RNA Seq GSM3964268   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964268 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     WT-A11_S65_R1_001.fastq WT-A11_S65_R2_001.fastq fastq fastq 5857223474.0 38844475.0 GSM3964268 r1 0:75.43 1:75.36 A:1521095503;C:1393796570;G:1358405170;T:1576525007;N:7401224 75 75     1521095503 1393796570 1358405170 1576525007 7401224 SRX6492139 SRS5140735 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.9333 0.93417 0.07614 0.07626 0.64076 0.64325 0.49571 0.49874 76 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53272 53272 SRR9735178 SRX6492138 SRS5140734 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose WT A10 GSM3964267   source name:Adipose|genotype:WT|age:6 month|tissue:Adipose Adipose WT A10 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:WT|age:6 month|tissue:Adipose GSM3964267 GSM3964267: Adipose WT A10; Danio rerio; RNA Seq GSM3964267   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964267 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     WT-A10_S64_R1_001.fastq WT-A10_S64_R2_001.fastq fastq fastq 5309702286.0 35198072.0 GSM3964267 r1 0:75.46 1:75.39 A:1388459753;C:1253922327;G:1230145617;T:1432366497;N:4808092 75 75     1388459753 1253922327 1230145617 1432366497 4808092 SRX6492138 SRS5140734 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.9317 0.93346 0.08434 0.0851 0.63984 0.64425 0.48934 0.49315 76 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53273 53273 SRR9735177 SRX6492137 SRS5140733 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose WT A9 GSM3964266   source name:Adipose|genotype:WT|age:6 month|tissue:Adipose Adipose WT A9 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:WT|age:6 month|tissue:Adipose GSM3964266 GSM3964266: Adipose WT A9; Danio rerio; RNA Seq GSM3964266   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964266 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     WT-A9_S63_R1_001.fastq WT-A9_S63_R2_001.fastq fastq fastq 4236242483.0 28084714.0 GSM3964266 r1 0:75.45 1:75.38 A:1109376701;C:1000854007;G:974810548;T:1146740655;N:4460572 75 75     1109376701 1000854007 974810548 1146740655 4460572 SRX6492137 SRS5140733 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.9309 0.93204 0.08077 0.0797 0.63591 0.63696 0.48176 0.4882 75 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53274 53274 SRR9735176 SRX6492136 SRS5140732 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose WT A8 GSM3964265   source name:Adipose|genotype:WT|age:6 month|tissue:Adipose Adipose WT A8 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:WT|age:6 month|tissue:Adipose GSM3964265 GSM3964265: Adipose WT A8; Danio rerio; RNA Seq GSM3964265   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964265 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     WT-A8_S62_R1_001.fastq WT-A8_S62_R2_001.fastq fastq fastq 4940494520.0 32753328.0 GSM3964265 r1 0:75.46 1:75.38 A:1295977907;C:1165807642;G:1138647407;T:1335314520;N:4747044 75 75     1295977907 1165807642 1138647407 1335314520 4747044 SRX6492136 SRS5140732 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.93086 0.93278 0.08264 0.08266 0.63577 0.6383 0.49385 0.48993 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53275 53275 SRR9735175 SRX6492135 SRS5140731 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose WT A7 GSM3964264   source name:Adipose|genotype:WT|age:6 month|tissue:Adipose Adipose WT A7 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:WT|age:6 month|tissue:Adipose GSM3964264 GSM3964264: Adipose WT A7; Danio rerio; RNA Seq GSM3964264   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964264 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     WT-A7_S61_R1_001.fastq WT-A7_S61_R2_001.fastq fastq fastq 5512616919.0 36544990.0 GSM3964264 r1 0:75.45 1:75.39 A:1452114567;C:1290637600;G:1266464795;T:1497383449;N:6016508 75 75     1452114567 1290637600 1266464795 1497383449 6016508 SRX6492135 SRS5140731 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.93121 0.93118 0.09277 0.09194 0.62591 0.63023 0.49799 0.50579 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53276 53276 SRR9735174 SRX6492134 SRS5140730 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose WT A6 GSM3964263   source name:Adipose|genotype:WT|age:6 month|tissue:Adipose Adipose WT A6 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:WT|age:6 month|tissue:Adipose GSM3964263 GSM3964263: Adipose WT A6; Danio rerio; RNA Seq GSM3964263   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964263 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     WT-A6_S54_R1_001.fastq WT-A6_S54_R2_001.fastq fastq fastq 5724404718.0 37976322.0 GSM3964263 r1 0:75.40 1:75.34 A:1494251238;C:1350286944;G:1328643993;T:1541931890;N:9290653 75 75     1494251238 1350286944 1328643993 1541931890 9290653 SRX6492134 SRS5140730 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.93006 0.93284 0.08404 0.08457 0.63471 0.63851 0.49167 0.49936 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53277 53277 SRR9735173 SRX6492133 SRS5140729 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose WT A5 GSM3964262   source name:Adipose|genotype:WT|age:6 month|tissue:Adipose Adipose WT A5 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:WT|age:6 month|tissue:Adipose GSM3964262 GSM3964262: Adipose WT A5; Danio rerio; RNA Seq GSM3964262   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964262 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     WT-A5_S53_R1_001.fastq WT-A5_S53_R2_001.fastq fastq fastq 4659158769.0 30909376.0 GSM3964262 r1 0:75.40 1:75.33 A:1221375603;C:1098925945;G:1074577334;T:1257075301;N:7204586 75 75     1221375603 1098925945 1074577334 1257075301 7204586 SRX6492133 SRS5140729 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.93225 0.93214 0.08272 0.082 0.63617 0.63993 0.49384 0.49616 74 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53278 53278 SRR9735172 SRX6492132 SRS5140728 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose WT A4 GSM3964261   source name:Adipose|genotype:WT|age:6 month|tissue:Adipose Adipose WT A4 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:WT|age:6 month|tissue:Adipose GSM3964261 GSM3964261: Adipose WT A4; Danio rerio; RNA Seq GSM3964261   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964261 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     WT-A4_S52_R1_001.fastq WT-A4_S52_R2_001.fastq fastq fastq 7788950127.0 51651988.0 GSM3964261 r1 0:75.43 1:75.36 A:2051073731;C:1826674351;G:1787914965;T:2114738619;N:8548461 75 75     2051073731 1826674351 1787914965 2114738619 8548461 SRX6492132 SRS5140728 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.92964 0.92925 0.09108 0.09118 0.63287 0.63721 0.48738 0.49099 76 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53279 53279 SRR9735171 SRX6492131 SRS5140727 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose WT A3 GSM3964260   source name:Adipose|genotype:WT|age:6 month|tissue:Adipose Adipose WT A3 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:WT|age:6 month|tissue:Adipose GSM3964260 GSM3964260: Adipose WT A3; Danio rerio; RNA Seq GSM3964260   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964260 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     WT-A3_S51_R1_001.fastq WT-A3_S51_R2_001.fastq fastq fastq 5588378020.0 37052916.0 GSM3964260 r1 0:75.45 1:75.37 A:1469832305;C:1313012667;G:1286542723;T:1514017333;N:4972992 75 75     1469832305 1313012667 1286542723 1514017333 4972992 SRX6492131 SRS5140727 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.92914 0.92954 0.08888 0.08846 0.6336 0.63573 0.48669 0.49048 75 75 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53280 53280 SRR9735170 SRX6492130 SRS5140726 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose WT A2 GSM3964259   source name:Adipose|genotype:WT|age:6 month|tissue:Adipose Adipose WT A2 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:WT|age:6 month|tissue:Adipose GSM3964259 GSM3964259: Adipose WT A2; Danio rerio; RNA Seq GSM3964259   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964259 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     WT-A2_S50_R1_001.fastq WT-A2_S50_R2_001.fastq fastq fastq 5155694538.0 34195331.0 GSM3964259 r1 0:75.42 1:75.35 A:1348612302;C:1218323703;G:1189107260;T:1393758155;N:5893118 75 75     1348612302 1218323703 1189107260 1393758155 5893118 SRX6492130 SRS5140726 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.92918 0.92952 0.08351 0.08186 0.62832 0.63027 0.48677 0.49178 75 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
53281 53281 SRR9735169 SRX6492129 SRS5140725 SRP216059 PRJNA556239 Adipocyte serine uptake curbs ROS generation and visceral adiposity [Zebrafish] GSE134733 Transcriptome Analysis Obesity and visceral adiposity in particular increases the risk of common metabolic diseases including type 2 diabetes cardiovascular disease and several forms of cancer. However the molecular mechanisms responsible for regional fat storage remain poorly characterized preventing therapeutic innovation. We here applied a systematic genome wide screen and translational approach and discovered a novel role for the adipocyte expressed neutral amino acid transporter SLC7A10/ASC 1 in the regulation of visceral adiposity. Among 65 genes showing both adipose depot dependent and fat loss dependent expression 27 genes further showed significant correlations with waist to hip WHR ratio adjusted for BMI. Among these ASC 1 was expressed at the highest level in isolated visceral adipocytes. Further we found decreased ASC 1 mRNA in visceral and not subcutaneous adipose tissue in carriers of the KLF14 type 2 diabetes risk allele compared to the protective allele. By profiling amino acid fluxes during adipocyte differentiation in vitro we found that ASC 1 inhibition by a selective inhibitor decreased adipocyte uptake particularly of serine in mature adipocytes. Interestingly radiometric amino acid uptake assays showed ASC 1 dependent uptake of the serine D enantiomere. Using primary human and murine adipocyte models we uncovered marked effects of inhibiting ASC 1 on mitochondrial respiratory capacity within hours and lipid accumulation within days. Finally Asc 1 knockout KO zebrafish had increased body weight and adipocyte enlargement upon eight week overfeeding compared to wild type WT fish. RNA sequencing data from zebrafish adipose tissue showed up regulation of genes involved in fatty acid and lipid metabolism in the ASC 1 KOs consistent with the increased lipid accumulation in the inhibitor treated cell models. Additionally duox an enzyme involved in ROS generation showed higher expression in the KOs compared to the WTs. Importantly we confirmed increased reactive oxygen species ROS generation within min… parent bioproject:PRJNA557596     Adipose WT A1 GSM3964258   source name:Adipose|genotype:WT|age:6 month|tissue:Adipose Adipose WT A1 Illumina Casava v1.8 Reads were aligned to the Zebrafish reference genome GRCz10 using HiSat Version 2.05 with options “hisat2 align s wrapper basic 0 p 140” Aligned reads were then put into featureCounts Version 1.5.2 with options “featureCounts T 64 p t exon g gene id” Differential expression analysis was performed via DESeq2 Version 1.14.1 Genome build: GRCz10 Supplementary files format and content: tab delimited text files include DESeq2 normalised counts for each Sample ... Adipose Individuals were overfed for a period of 2 month on GEMMA Micro 500 Skretting USA 3 times per day and given 3 drops of freshly hatched Artemia once per day. Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols Zebrafish were housed in 3 litre tanks for a period of 4 month and subsequently housed for a further 2 month in 1.5 litre tanks with 3 individuals per tank. genotype:WT|age:6 month|tissue:Adipose GSM3964258 GSM3964258: Adipose WT A1; Danio rerio; RNA Seq GSM3964258   1 Tissue biopsies from three fish in each tank were pooled together snap frozen and processed for kit based extraction of RNA using the RNeasy kit QIAGEN and quality checked via spectrophotometer. RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM3964258 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 4000   SRP216059     WT-A1_S49_R1_001.fastq WT-A1_S49_R2_001.fastq fastq fastq 4250306891.0 28182505.0 GSM3964258 r1 0:75.44 1:75.37 A:1119067057;C:999399803;G:974466658;T:1152728469;N:4644904 75 75     1119067057 999399803 974466658 1152728469 4644904 SRX6492129 SRS5140725 SRA925242 GEO Hormone Laboratory, Clinical Institute, University of Bergen 2 0.92921 0.93037 0.08377 0.08425 0.63727 0.64122 0.48849 0.49306 75 76 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Norway 2019-07-23 Adult Adult Adipose Tissue Adipose Tissue
70104 70104 SRR19548855 SRX15600909 SRS13301859 SRP378691 PRJNA846095 Transcriptomic evolution across bilaterian tissues GSE205498 Other We investigate tissue transcriptomic evolution across bilaterian animals by analyzing RNA seq data from eight different tissues across twenty species. Overall design: Characterization of ancestral and novel tissue gene expression patterns throughout bilaterian evolution.   pubmed:35801824;pubmed:38622362;pubmed:39933573   RNA seq of adult Danio rerio adipose tissue [Dre Adipose a] GSM6213744   source name:Adult adipose tissue|tissue:Adipose|genome build:danRer10|gtf:danRer10 GTF enriched from Ensembl v80 RNA seq of adult Danio rerio adipose tissue [Dre Adipose a] Estimated counts and TPMs were computed by Kallisto v0.44.0 Supplementary files format and content: Tab delimited file with length effective length estimated counts and transcript per million TPM for all species protein coding genes in the relative GTF Adult adipose tissue   Rneasy plus Mini Kit Qiagen polyA selected stranded RNA seq; RNA libraries were prepared for sequencing using standard Illumina protocols   tissue:Adipose|genome build:danRer10|gtf:danRer10 GTF enriched from Ensembl v80 GSM6213744 GSM6213744: RNA seq of adult Danio rerio adipose tissue [Dre Adipose a]; Danio rerio; RNA Seq GSM6213744 r1 GSM6213744 1 Rneasy plus Mini Kit Qiagen polyA selected stranded RNA seq; RNA libraries were prepared for sequencing using standard Illumina protocols   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2500   SRP378691     Dre_Adipose_a_R1-125.fq.gz Dre_Adipose_a_R2-125.fq.gz fastq fastq 19085464750.0 76341859.0 GSM6213744 r1 0:125 1:125 A:4736764645;C:4749222175;G:4787002077;T:4805028216;N:7447637 125 125     4736764645 4749222175 4787002077 4805028216 7447637 SRX15600909 SRS13301859 SRA1432871 CRG CRG 2 0.97251 0.97417 0.02687 0.02652 0.72823 0.72987 0.55308 0.53025 125 125 B B biological fallback assumption illumina hiseq_era unknown poly_a unknown bulk unknown unknown   Unknown 2022-06-05 Adult Adult Adipose Tissue Adipose Tissue
74641 74641 SRR26902472 SRX22596599 SRS19602930 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   cold eAT epicardial fat 6 GSM7912825   source name:adipose tissue|tissue:adipose tissue|cell line:epicardial fat|Sex:female|geo loc name:missing|collection date:missing cold eAT epicardial fat 6 RNA seq data were processed and analyzed using pseudo mapping to the zebrafish transcriptome GRCz11 Ensembl and unique transcript counts were performed using Kallisto v0.46.1. Transcript level counts were summarized into gene counts using Tximport v1.22.0 and genes with over 10 counts were maintained. Read count normalization and downstream analysis of differential gene expression was carried out using DESeq2 R package version 1.34.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values of DESeq2 normalized counts for cold treated eAT and control temperature epicardial adipocytes 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|cell line:epicardial fat|Sex:female GSM7912825 GSM7912825: cold eAT epicardial fat 6; Danio rerio; RNA Seq GSM7912825 r1 GSM7912825 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 18_EAT_3_S61_L003_R1_001.fastq.gz 18_EAT_3_S61_L003_R2_001.fastq.gz fastq fastq 36579991200.0 182899956.0 GSM7912825 r1 0:100 1:100 A:8145461331;C:10304868211;G:10196177152;T:7931483805;N:2000701 100 100     8145461331 10304868211 10196177152 7931483805 2000701 SRX22596599 SRS19602930 SRA1755255 AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin 2 0.95229 0.89455 0.06603 0.06146 0.9347 0.94028 0.89248 0.89618 100 100 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Germany 2023-11-21 Undetermined Adult Adipose Tissue Adipose Tissue
74642 74642 SRR26902473 SRX22596598 SRS19602928 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   cold eAT epicardial fat 5 GSM7912824   source name:adipose tissue|tissue:adipose tissue|cell line:epicardial fat|Sex:female|geo loc name:missing|collection date:missing cold eAT epicardial fat 5 RNA seq data were processed and analyzed using pseudo mapping to the zebrafish transcriptome GRCz11 Ensembl and unique transcript counts were performed using Kallisto v0.46.1. Transcript level counts were summarized into gene counts using Tximport v1.22.0 and genes with over 10 counts were maintained. Read count normalization and downstream analysis of differential gene expression was carried out using DESeq2 R package version 1.34.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values of DESeq2 normalized counts for cold treated eAT and control temperature epicardial adipocytes 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|cell line:epicardial fat|Sex:female GSM7912824 GSM7912824: cold eAT epicardial fat 5; Danio rerio; RNA Seq GSM7912824 r1 GSM7912824 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 18_EAT_2_S60_L003_R1_001.fastq.gz 18_EAT_2_S60_L003_R2_001.fastq.gz fastq fastq 44027178200.0 220135891.0 GSM7912824 r1 0:100 1:100 A:9589007843;C:12544005309;G:12515602341;T:9376136142;N:2426565 100 100     9589007843 12544005309 12515602341 9376136142 2426565 SRX22596598 SRS19602928 SRA1755255 AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin 2 0.93679 0.87737 0.08679 0.08125 0.9151 0.92263 0.87011 0.8743 100 100 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Germany 2023-11-21 Undetermined Adult Adipose Tissue Adipose Tissue
74643 74643 SRR26902474 SRX22596597 SRS19602929 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   cold eAT epicardial fat 4 GSM7912823   source name:adipose tissue|tissue:adipose tissue|cell line:epicardial fat|Sex:female|geo loc name:missing|collection date:missing cold eAT epicardial fat 4 RNA seq data were processed and analyzed using pseudo mapping to the zebrafish transcriptome GRCz11 Ensembl and unique transcript counts were performed using Kallisto v0.46.1. Transcript level counts were summarized into gene counts using Tximport v1.22.0 and genes with over 10 counts were maintained. Read count normalization and downstream analysis of differential gene expression was carried out using DESeq2 R package version 1.34.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values of DESeq2 normalized counts for cold treated eAT and control temperature epicardial adipocytes 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|cell line:epicardial fat|Sex:female GSM7912823 GSM7912823: cold eAT epicardial fat 4; Danio rerio; RNA Seq GSM7912823 r1 GSM7912823 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 18_EAT_1_S59_L003_R1_001.fastq.gz 18_EAT_1_S59_L003_R2_001.fastq.gz fastq fastq 41270229600.0 206351148.0 GSM7912823 r1 0:100 1:100 A:9105294909;C:11691383796;G:11565493480;T:8905831583;N:2225832 100 100     9105294909 11691383796 11565493480 8905831583 2225832 SRX22596597 SRS19602929 SRA1755255 AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin 2 0.93662 0.87723 0.0769 0.07242 0.91952 0.92579 0.88027 0.89176 100 100 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Germany 2023-11-21 Undetermined Adult Adipose Tissue Adipose Tissue
74644 74644 SRR26902475 SRX22596596 SRS19602927 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   control eAT epicardial fat 3 GSM7912822   source name:adipose tissue|tissue:adipose tissue|cell line:epicardial fat|Sex:female|geo loc name:missing|collection date:missing control eAT epicardial fat 3 RNA seq data were processed and analyzed using pseudo mapping to the zebrafish transcriptome GRCz11 Ensembl and unique transcript counts were performed using Kallisto v0.46.1. Transcript level counts were summarized into gene counts using Tximport v1.22.0 and genes with over 10 counts were maintained. Read count normalization and downstream analysis of differential gene expression was carried out using DESeq2 R package version 1.34.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values of DESeq2 normalized counts for cold treated eAT and control temperature epicardial adipocytes 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|cell line:epicardial fat|Sex:female GSM7912822 GSM7912822: control eAT epicardial fat 3; Danio rerio; RNA Seq GSM7912822 r1 GSM7912822 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 27_EAT_3_S58_L003_R1_001.fastq.gz 27_EAT_3_S58_L003_R2_001.fastq.gz fastq fastq 43010873200.0 215054366.0 GSM7912822 r1 0:100 1:100 A:10273902176;C:11407089868;G:11344047061;T:9983469034;N:2365061 100 100     10273902176 11407089868 11344047061 9983469034 2365061 SRX22596596 SRS19602927 SRA1755255 AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin 2 0.95205 0.89769 0.06386 0.06145 0.92947 0.93549 0.90926 0.91366 100 100 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Germany 2023-11-21 Undetermined Adult Adipose Tissue Adipose Tissue
74645 74645 SRR26902476 SRX22596595 SRS19602926 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   control eAT epicardial fat 2 GSM7912821   source name:adipose tissue|tissue:adipose tissue|cell line:epicardial fat|Sex:female|geo loc name:missing|collection date:missing control eAT epicardial fat 2 RNA seq data were processed and analyzed using pseudo mapping to the zebrafish transcriptome GRCz11 Ensembl and unique transcript counts were performed using Kallisto v0.46.1. Transcript level counts were summarized into gene counts using Tximport v1.22.0 and genes with over 10 counts were maintained. Read count normalization and downstream analysis of differential gene expression was carried out using DESeq2 R package version 1.34.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values of DESeq2 normalized counts for cold treated eAT and control temperature epicardial adipocytes 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|cell line:epicardial fat|Sex:female GSM7912821 GSM7912821: control eAT epicardial fat 2; Danio rerio; RNA Seq GSM7912821 r1 GSM7912821 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 27_EAT_2_S57_L003_R2_001.fastq.gz 27_EAT_2_S57_L003_R1_001.fastq.gz fastq fastq 38133432200.0 190667161.0 GSM7912821 r1 0:100 1:100 A:9220777607;C:9949450800;G:9982624020;T:8978518929;N:2060844 100 100     9220777607 9949450800 9982624020 8978518929 2060844 SRX22596595 SRS19602926 SRA1755255 AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin 2 0.96342 0.9072 0.06324 0.06041 0.92717 0.93318 0.91146 0.90224 100 100 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Germany 2023-11-21 Undetermined Adult Adipose Tissue Adipose Tissue
74646 74646 SRR26902477 SRX22596594 SRS19602925 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   control eAT epicardial fat 1 GSM7912820   source name:adipose tissue|tissue:adipose tissue|cell line:epicardial fat|Sex:female|geo loc name:missing|collection date:missing control eAT epicardial fat 1 RNA seq data were processed and analyzed using pseudo mapping to the zebrafish transcriptome GRCz11 Ensembl and unique transcript counts were performed using Kallisto v0.46.1. Transcript level counts were summarized into gene counts using Tximport v1.22.0 and genes with over 10 counts were maintained. Read count normalization and downstream analysis of differential gene expression was carried out using DESeq2 R package version 1.34.0 Assembly: GRCz11 Supplementary files format and content: Tab separated values of DESeq2 normalized counts for cold treated eAT and control temperature epicardial adipocytes 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|cell line:epicardial fat|Sex:female GSM7912820 GSM7912820: control eAT epicardial fat 1; Danio rerio; RNA Seq GSM7912820 r1 GSM7912820 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 27_EAT_1_S56_L003_R1_001.fastq.gz 27_EAT_1_S56_L003_R2_001.fastq.gz fastq fastq 39974303600.0 199871518.0 GSM7912820 r1 0:100 1:100 A:10036716123;C:10114630248;G:10121937185;T:9698802482;N:2217562 100 100     10036716123 10114630248 10121937185 9698802482 2217562 SRX22596594 SRS19602925 SRA1755255 AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin 2 0.95488 0.8982 0.04392 0.04158 0.94663 0.95128 0.93292 0.93141 100 100 B B biological fallback assumption illumina novaseq_era full_length cdna_unspecified smarter bulk unknown unknown   Germany 2023-11-21 Undetermined Adult Adipose Tissue Adipose Tissue
74647 74647 SRR23908258 SRX19719740 SRS17086856 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 3 GSM7104994   source name:adipose tissue|tissue:adipose tissue|tissue subtype:Viscerlal fat|Sex:female|geo loc name:missing|collection date:missing vAT visceral fat 3 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 GSM7104994 GSM7104994: vAT visceral fat 3; Danio rerio; RNA Seq GSM7104994 r1 GSM7104994 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 vAT3_L001_R1.fastq.gz vAT3_L001_R2.fastq.gz fastq fastq 10565948148.0 52306674.0 GSM7104994 r1 0:101 1:101 A:1907534975;C:3416174946;G:3360188823;T:1877111445;N:4937959 101 101     1907534975 3416174946 3360188823 1877111445 4937959 SRX19719740 SRS17086856 SRA1606837 AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin 2 0.95152 0.88467 0.18636 0.18241 0.93221 0.93835 0.76503 0.78028 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
74648 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
74649 74649 SRR23908260 SRX19719738 SRS17086854 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 1 GSM7104992   source name:adipose tissue|tissue:adipose tissue|tissue subtype:Viscerlal fat|Sex:female|geo loc name:missing|collection date:missing vAT visceral fat 1 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 GSM7104992 GSM7104992: vAT visceral fat 1; Danio rerio; RNA Seq GSM7104992 r1 GSM7104992 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 vAT1_L001_R1.fastq.gz vAT1_L001_R2.fastq.gz fastq fastq 8935423338.0 44234769.0 GSM7104992 r1 0:101 1:101 A:1612234838;C:2880684382;G:2851082026;T:1587227700;N:4194392 101 101     1612234838 2880684382 2851082026 1587227700 4194392 SRX19719738 SRS17086854 SRA1606837 AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin 2 0.92901 0.87214 0.18482 0.18116 0.95272 0.957 0.76369 0.77972 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
74650 74650 SRR23908261 SRX19719737 SRS17086853 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   eAT epicardial fat 3 GSM7104991   source name:adipose tissue|tissue:adipose tissue|tissue subtype:epicardial fat|Sex:female|geo loc name:missing|collection date:missing eAT epicardial fat 3 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:epicardial fat|Sex:female GSM7104991 GSM7104991: eAT epicardial fat 3; Danio rerio; RNA Seq GSM7104991 r1 GSM7104991 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 eAT3_L001_R1.fastq.gz eAT3_L001_R2.fastq.gz fastq fastq 9377159968.0 46421584.0 GSM7104991 r1 0:101 1:101 A:2098439200;C:2609083252;G:2593459500;T:2071786259;N:4391757 101 101     2098439200 2609083252 2593459500 2071786259 4391757 SRX19719737 SRS17086853 SRA1606837 AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin 2 0.93545 0.8537 0.11651 0.10971 0.87468 0.88605 0.81242 0.83864 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
74651 74651 SRR23908262 SRX19719736 SRS17086852 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   eAT epicardial fat 2 GSM7104990   source name:adipose tissue|tissue:adipose tissue|tissue subtype:epicardial fat|Sex:female|geo loc name:missing|collection date:missing eAT epicardial 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:epicardial fat|Sex:female GSM7104990 GSM7104990: eAT epicardial fat 2; Danio rerio; RNA Seq GSM7104990 r1 GSM7104990 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 eAT2_L001_R1.fastq.gz eAT2_L001_R2.fastq.gz fastq fastq 9217906400.0 45633200.0 GSM7104990 r1 0:101 1:101 A:2095369950;C:2541400234;G:2516772463;T:2060018641;N:4345112 101 101     2095369950 2541400234 2516772463 2060018641 4345112 SRX19719736 SRS17086852 SRA1606837 AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin 2 0.94554 0.86763 0.10304 0.0988 0.89079 0.90035 0.84365 0.84363 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
74652 74652 SRR23908263 SRX19719735 SRS17086851 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   eAT epicardial fat 1 GSM7104989   source name:adipose tissue|tissue:adipose tissue|tissue subtype:epicardial fat|Sex:female|geo loc name:missing|collection date:missing eAT epicardial fat 1 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:epicardial fat|Sex:female GSM7104989 GSM7104989: eAT epicardial fat 1; Danio rerio; RNA Seq GSM7104989 r1 GSM7104989 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 eAT1_L001_R1.fastq.gz eAT1_L001_R2.fastq.gz fastq fastq 13621771828.0 67434514.0 GSM7104989 r1 0:101 1:101 A:3232962486;C:3590754208;G:3575836334;T:3215920897;N:6297903 101 101     3232962486 3590754208 3575836334 3215920897 6297903 SRX19719735 SRS17086851 SRA1606837 AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin AG Sawamiphak, Max-Delbrück-Centrum für Molekulare Medizin 2 0.90965 0.81819 0.20716 0.17706 0.84386 0.85742 0.76749 0.76572 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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;