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
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,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,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,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,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,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,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,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,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,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,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,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