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150 rows where devstage_curation = "Undetermined" and experiment.library_selection = "Oligo-dT"

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tissue_curation >10

devstage_curation_coarse 4

technology 2

experiment.platform 2

experiment.library_source 2

experiment.library_layout 2

experiment.library_strategy 1

experiment.library_selection 1

  • Oligo-dT · 150 ✖

devstage_curation 1

  • Undetermined · 150 ✖
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
280 280 DRR161311 DRX151936 DRS095335 DRP005084 PRJDB7735 Gene expression profile in adult zebrafish liver DRP005084 Transcriptome Analysis Increasing use of zebrafish in toxicological researches requires knowledge on gene expression profile in liver that play a major role in xenobiotic metabolism. Our research provide a basal gene expression profile in adult zebrafish liver.       Transcriptome of female Danio rerio liver SAMD00153247   sample name:transcriptome zebrafish female|sex:female|strain:RIKEN WT|tissue:liver                 NextSeq 500 paired end sequencing of SAMD00153247 DRX151936 f 1 1   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP005084 NextSeq 500 paired end sequencing of SAMD00153247       2338564937.0 15498367.0 DRR161311 0:75.45 1:75.44 A:613899755;C:541756858;G:548366901;T:633083422;N:1458001 75 75     613899755 541756858 548366901 633083422 1458001 DRX151936 DRS095335 DRA007652 OBICHIKU|Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine 2 0.95814 0.96362 0.05394 0.04517 0.77932 0.7834 0.37385 0.37264 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Japan 2019-05-20 Undetermined Adult Liver Liver and Biliary System
281 281 DRR161310 DRX151935 DRS095334 DRP005084 PRJDB7735 Gene expression profile in adult zebrafish liver DRP005084 Transcriptome Analysis Increasing use of zebrafish in toxicological researches requires knowledge on gene expression profile in liver that play a major role in xenobiotic metabolism. Our research provide a basal gene expression profile in adult zebrafish liver.       Transcriptome of male Danio rerio liver SAMD00153246   sample name:transcriptome zebrafish male|sex:male|strain:RIKEN WT|tissue:liver                 NextSeq 500 paired end sequencing of SAMD00153246 DRX151935 m 1 1   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500 <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> DRP005084 NextSeq 500 paired end sequencing of SAMD00153246       2506978527.0 16611154.0 DRR161310 0:75.48 1:75.44 A:672321355;C:568289588;G:569411670;T:695545626;N:1410288 75 75     672321355 568289588 569411670 695545626 1410288 DRX151935 DRS095334 DRA007652 OBICHIKU|Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine Laboratory of Toxicology, Department of Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine 2 0.94746 0.95115 0.07899 0.06363 0.80837 0.8115 0.52008 0.58743 76 76 B B biological fallback assumption illumina nextseq unknown poly_a unknown bulk unknown unknown   Japan 2019-05-20 Undetermined Adult Liver Liver and Biliary System
8092 8092 ERR2402432 ERX2443286 ERS2295360 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Hom MO rep3 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693977 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693977|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM12|common name:zebrafish|sample name:CM12|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 12 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM12.trimmed.read_1.fastq.gz CM12.trimmed.read_2.fastq.gz fastq fastq 5384061477.0 38388598.0 ena RUN DPSQ 14 03 2018 19:09:09:420 12 0:70.70 1:69.55 A:1490429493;C:1197976503;G:1220014984;T:1475615043;N:25454 70 69     1490429493 1197976503 1220014984 1475615043 25454 ERX2443286 ERS2295360 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.92285 0.9206 0.06862 0.0688 0.73983 0.74566 0.4752 0.49125 76 75 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8093 8093 ERR2402431 ERX2443285 ERS2295359 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Hom MO rep2 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693976 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693976|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM11|common name:zebrafish|sample name:CM11|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 11 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM11.trimmed.read_1.fastq.gz CM11.trimmed.read_2.fastq.gz fastq fastq 5472085589.0 38860681.0 ena RUN DPSQ 14 03 2018 19:09:09:420 11 0:70.98 1:69.83 A:1514986213;C:1217661004;G:1240412104;T:1499000816;N:25452 70 69     1514986213 1217661004 1240412104 1499000816 25452 ERX2443285 ERS2295359 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.91987 0.91874 0.0693 0.07042 0.74042 0.74629 0.48229 0.49144 76 76 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8094 8094 ERR2402430 ERX2443284 ERS2295358 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Hom MO rep1 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693975 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693975|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM10|common name:zebrafish|sample name:CM10|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 10 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM10.trimmed.read_1.fastq.gz CM10.trimmed.read_2.fastq.gz fastq fastq 6091085806.0 43064771.0 ena RUN DPSQ 14 03 2018 19:09:09:420 10 0:71.33 1:70.11 A:1692450462;C:1348639943;G:1375433963;T:1674532019;N:29419 71 70     1692450462 1348639943 1375433963 1674532019 29419 ERX2443284 ERS2295358 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.92184 0.92064 0.0699 0.0704 0.74286 0.74874 0.48978 0.48997 75 73 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8095 8095 ERR2402429 ERX2443283 ERS2295357 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Hom uninj rep3 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693974 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693974|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM9|common name:zebrafish|sample name:CM9|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 9 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM9.trimmed.read_1.fastq.gz CM9.trimmed.read_2.fastq.gz fastq fastq 6329252570.0 45070159.0 ena RUN DPSQ 14 03 2018 19:09:09:420 9 0:70.79 1:69.64 A:1753489708;C:1407193617;G:1433449502;T:1735090181;N:29562 70 69     1753489708 1407193617 1433449502 1735090181 29562 ERX2443283 ERS2295357 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.91683 0.91616 0.06775 0.06825 0.75158 0.75737 0.49386 0.49199 76 75 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8096 8096 ERR2402428 ERX2443282 ERS2295356 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Hom uninj rep2 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693973 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693973|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM8|common name:zebrafish|sample name:CM8|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 8 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM8.trimmed.read_1.fastq.gz CM8.trimmed.read_2.fastq.gz fastq fastq 5405185494.0 38637007.0 ena RUN DPSQ 14 03 2018 19:09:09:420 8 0:70.45 1:69.44 A:1491577735;C:1206599147;G:1229354248;T:1477628006;N:26358 70 69     1491577735 1206599147 1229354248 1477628006 26358 ERX2443282 ERS2295356 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.91776 0.91567 0.07134 0.07241 0.7517 0.75716 0.47952 0.48745 73 73 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8097 8097 ERR2402427 ERX2443281 ERS2295355 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Hom uninj rep1 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693972 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693972|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM7|common name:zebrafish|sample name:CM7|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 7 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM7.trimmed.read_1.fastq.gz CM7.trimmed.read_2.fastq.gz fastq fastq 6262947202.0 44863127.0 ena RUN DPSQ 14 03 2018 19:09:09:420 7 0:70.28 1:69.32 A:1732018658;C:1394742098;G:1420957611;T:1715198292;N:30543 70 69     1732018658 1394742098 1420957611 1715198292 30543 ERX2443281 ERS2295355 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.91622 0.9144 0.0754 0.07588 0.74886 0.75371 0.48672 0.48471 76 76 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8098 8098 ERR2402426 ERX2443280 ERS2295354 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Het MO rep3 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693971 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693971|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM6|common name:zebrafish|sample name:CM6|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 6 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM6.trimmed.read_1.fastq.gz CM6.trimmed.read_2.fastq.gz fastq fastq 5819615834.0 41591499.0 ena RUN DPSQ 14 03 2018 19:09:09:420 6 0:70.47 1:69.45 A:1594833553;C:1309877713;G:1335153588;T:1579722744;N:28236 70 69     1594833553 1309877713 1335153588 1579722744 28236 ERX2443280 ERS2295354 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.92 0.9183 0.0573 0.05793 0.77362 0.778 0.47792 0.46987 76 75 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8099 8099 ERR2402425 ERX2443279 ERS2295353 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Het MO rep2 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693970 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693970|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM5|common name:zebrafish|sample name:CM5|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 5 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM5.trimmed.read_1.fastq.gz CM5.trimmed.read_2.fastq.gz fastq fastq 5573895202.0 39518227.0 ena RUN DPSQ 14 03 2018 19:09:09:420 5 0:71.02 1:70.03 A:1530297250;C:1251775796;G:1276506882;T:1515288256;N:27018 71 70     1530297250 1251775796 1276506882 1515288256 27018 ERX2443279 ERS2295353 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.92217 0.92081 0.06807 0.06843 0.76926 0.77441 0.45543 0.48098 76 75 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8100 8100 ERR2402424 ERX2443278 ERS2295352 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Het MO rep1 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693969 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693969|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM4|common name:zebrafish|sample name:CM4|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 4 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM4.trimmed.read_1.fastq.gz CM4.trimmed.read_2.fastq.gz fastq fastq 5803404091.0 41335851.0 ena RUN DPSQ 14 03 2018 19:09:09:420 4 0:70.72 1:69.67 A:1590577583;C:1305683925;G:1331895549;T:1575219146;N:27888 70 69     1590577583 1305683925 1331895549 1575219146 27888 ERX2443278 ERS2295352 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.9216 0.91971 0.05719 0.05738 0.77333 0.77761 0.47789 0.47244 76 74 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8101 8101 ERR2402423 ERX2443277 ERS2295351 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Het uninj rep3 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693968 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693968|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM3|common name:zebrafish|sample name:CM3|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 3 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM3.trimmed.read_1.fastq.gz CM3.trimmed.read_2.fastq.gz fastq fastq 5992797058.0 42390223.0 ena RUN DPSQ 14 03 2018 19:09:09:420 3 0:71.26 1:70.11 A:1639390320;C:1352082344;G:1378624207;T:1622672043;N:28144 71 70     1639390320 1352082344 1378624207 1622672043 28144 ERX2443277 ERS2295351 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.92104 0.92006 0.07044 0.07056 0.77506 0.78137 0.48154 0.46497 75 75 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8102 8102 ERR2402422 ERX2443276 ERS2295350 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Het uninj rep2 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693967 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693967|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM2|common name:zebrafish|sample name:CM2|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM2.trimmed.read_2.fastq.gz CM2.trimmed.read_1.fastq.gz fastq fastq 5611396868.0 39759688.0 ena RUN DPSQ 14 03 2018 19:09:09:420 2 0:71.11 1:70.02 A:1537234166;C:1262883447;G:1288444384;T:1522807333;N:27538 71 70     1537234166 1262883447 1288444384 1522807333 27538 ERX2443276 ERS2295350 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.91881 0.91733 0.06861 0.06958 0.77238 0.77883 0.48415 0.47367 76 73 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
8103 8103 ERR2402421 ERX2443275 ERS2295349 ERP107516 PRJEB25583 The transcriptome of Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos ena-STUDY-DPSQ-14-03-2018-19:09:10:340-151 Other The zebrafish gene trap line qmc551 carries a gene trap transposon in intron 1 of the gene gfi1aa which a encodes a transcriptional repressor. The presence of the transposon interferes with the transcription of the gfi1aa gene during haematopoiesis. Despite the lack of Gfi1aa expression primitive red blood cell development appears to be normal due to functional redundancy with a second gene called gfi1b. Loss of Gfi1aa and Gfi1b protein expression in embryos that are homozygous for qmc551 and injected with gfi1b morpholinos leads to maturation defects in primitive red blood cells. Here we performed an RNA sequencing experiment to study the early programming of Gfi1aa and/or Gfi1b depleted primitive red blood cells. For this purpose we made use of the gene trap's gfp reporter gene expression in the primitive red blood cells to isolate these cells by fluorescence activated cell sorting from either qmc551 heterozygous or homozygous 20 hpf embryos that were or were not injected with the gfi1b morpholinos at the one cell stage. Batches of 200 embryos were dissociated in a Liberase Blendzyme solution. GFP positive primitive red blood cells were isolated by fluorescence activated cell sorting. 3 samples of between 1700 and 4000 cells were collected per batch. Total RNA was isolated from the cells of each of the 4 x 3 samples Het1 3 HetMO1 3 Hom1 3 and HomMO1 3 and used to generate full length cDNA of polyadenylated transcripts. Following cDNA amplification and library preparation paired end 75 bp reads were generated on the Illumina NextSeq500 sequencing platform. ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 03 14   Het uninj rep1 Gfi1aa and/or Gfi1b depleted primitive red blood cells in zebrafish embryos SAMEA104693966 DPSQ ENA FIRST PUBLIC:2018 10 12T17:03:15Z|ENA LAST UPDATE:2018 03 14T19:09:14Z|External Id:SAMEA104693966|INSDC center name:DPSQ|INSDC first public:2018 10 12T17:03:15Z|INSDC last update:2018 03 14T19:09:14Z|INSDC status:public|Submitter Id:CM1|common name:zebrafish|sample name:CM1|scientific name:Danio rerio                 NextSeq 500 paired end sequencing ena EXPERIMENT DPSQ 14 03 2018 19:09:09:420 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA NextSeq 500   ERP107516 NextSeq 500 paired end sequencing ENA FIRST PUBLIC:2018 10 12|ENA LAST UPDATE:2018 11 16 CM1.trimmed.read_1.fastq.gz CM1.trimmed.read_2.fastq.gz fastq fastq 6229432533.0 44233290.0 ena RUN DPSQ 14 03 2018 19:09:09:420 1 0:70.98 1:69.85 A:1712806281;C:1395764700;G:1423415860;T:1697416127;N:29565 70 69     1712806281 1395764700 1423415860 1697416127 29565 ERX2443275 ERS2295349 ERA1246315 European Nucleotide Archive Deep Seq department, Centre for Genetics and Genomics, The University of Nottingham, United Kingdom 2 0.91818 0.9169 0.07104 0.07095 0.77585 0.78066 0.47896 0.46653 56 56 B B biological fallback assumption illumina nextseq full_length poly_a unknown bulk unknown unknown   United Kingdom 2018-03-14 Undetermined Embryo Blood Hematopoietic System
9918 9918 ERR5059480 ERX4865549 ERS5523939 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05     aAM 6h rep1 JD AD30 PRPN1970901   ENA FIRST PUBLIC:2022 07 05T12:06:33Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:33Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AD30_PRPN197090.tar.gz nanopore 3739882337.0 3148027.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 09 01 2021 19:50:56:183 1 0:1188.01 A:1054501690;C:834193435;G:847423060;T:1003764152;N:0 1188       1054501690 834193435 847423060 1003764152 0 ERX4865549 ERS5523939 ERA3206712 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       B   usable mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9920 9920 ERR4330695 ERX4277529 ERS4811113 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 2h rep1 WT 2h rep1 SAMEA7050483 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7050483|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD B2 PDBN005727|common name:zebrafish|sample name:JD B2 PDBN005727                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-B2_PDBN005727.tar.gz fastq     ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 1                       ERX4277529   ERA2767154 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                             ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9921 9921 ERR4327134 ERX4273968 ERS4808634 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 4h rep2 WT 4h rep2 SAMEA7048000 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7048000|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD AM39 PDBN042841|common name:zebrafish|sample name:JD AM39 PDBN042841                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AM39_PDBN042841.tar.gz nanopore 719646261.0 897768.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 1 0:801.59 A:210217908;C:152963718;G:157393834;T:199070801;N:0 801       210217908 152963718 157393834 199070801 0 ERX4273968 ERS4808634 ERA2764800 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9922 9922 ERR4330696 ERX4277530 ERS4811114 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 4h rep1 WT 4h rep1 JD C3 PDBN006177   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-C3_PDBN006177.tar.gz nanopore 4240799932.0 4331689.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 09 07 2020 13:48:01:100 2 0:979.02 A:1229803846;C:914476674;G:943703560;T:1152815852;N:0 979       1229803846 914476674 943703560 1152815852 0 ERX4277530 ERS4811114 ERA2767154 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       B   usable mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9923 9923 ERR4327135 ERX4273969 ERS4808635 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 6h rep1 WT 6h rep1 JD AC29 PDBN024889   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-AC29_PDBN024889.tar.gz nanopore 1900324756.0 2013035.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 16:36:02:084 2 0:944.01 A:549431032;C:411510218;G:422103800;T:517279706;N:0 944       549431032 411510218 422103800 517279706 0 ERX4273969 ERS4808635 ERA2764800 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   long read ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9924 9924 ERR4326350 ERX4273208 ERS4808398 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   430 LNA 6h rep1 430 LNA 6h rep1 SAMEA7047764 CENTER FOR GENOMIC REGULATION (CRG) ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05|External Id:SAMEA7047764|INSDC center alias:CENTER FOR GENOMIC REGULATION CRG|INSDC center name:CENTER FOR GENOMIC REGULATION CRG|INSDC first public:2022 07 05T12:06:22Z|INSDC last update:2022 07 05T12:06:22Z|INSDC status:public|Submitter Id:JD H8 PDBN059569|common name:zebrafish|sample name:JD H8 PDBN059569                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-H8_PDBN059569.tar.gz nanopore 722817654.0 657296.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 07 07 2020 10:25:22:388 1 0:1099.68 A:206996491;C:157022109;G:155085437;T:203713617;N:0 1099       206996491 157022109 155085437 203713617 0 ERX4273208 ERS4808398 ERA2764399 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9925 9925 ERR4335436 ERX4282181 ERS4818366 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 6h rep2 WT 6h rep2 JD W23 PRPN039928   ENA FIRST PUBLIC:2022 07 05T12:06:24Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:24Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 PromethION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:456 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE PromethION   ERP122761 PromethION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-W23_PRPN039928.tar.gz nanopore 1268761319.0 1385621.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 13 07 2020 18:19:23:457 1 0:915.66 A:366823862;C:275507684;G:284634548;T:341795225;N:0 915       366823862 275507684 284634548 341795225 0 ERX4282181 ERS4818366 ERA2769006 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   under 1.2% mapping rate ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
9926 9926 ERR4321680 ERX4268538 ERS4808125 ERP122761 PRJEB39265 RNA dynamics during zebrafish development ena-STUDY-CENTER FOR GENOMIC REGULATION (CRG)-06-07-2020-15:41:43:771-1183 Other RNA dynamics during early zebrafish development ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05   WT 0h rep1 WT 0h rep1 JD A1 GDDN003032   ENA FIRST PUBLIC:2022 07 05T12:06:22Z|organism:Danio rerio|ENA LAST UPDATE:2022 07 05T12:06:22Z|scientific name:Danio rerio|common name:zebrafish|ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05                 GridION sequencing ena EXPERIMENT CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1 unspecified 1     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE OXFORD_NANOPORE GridION   ERP122761 GridION sequencing ENA FIRST PUBLIC:2022 07 05|ENA LAST UPDATE:2022 07 05 JD-A1_GDDN003032.tar.gz nanopore 753417826.0 698774.0 ena RUN CENTER FOR GENOMIC REGULATION CRG 06 07 2020 17:45:26:236 1 0:1078.20 A:214525685;C:165042952;G:171160615;T:202688574;N:0 1078       214525685 165042952 171160615 202688574 0 ERX4268538 ERS4808125 ERA2763718 CENTER FOR GENOMIC REGULATION (CRG)|European Nucleotide Archive CENTER FOR GENOMIC REGULATION (CRG)                       T   long read ont ont unknown poly_a unknown bulk unknown unknown   Spain 2022-07-05 Undetermined Undetermined Undetermined Undetermined
11143 11143 ERR10034092 ERX9574496 ERS12562207 ERP140005 PRJEB55122 Danio developmental transcriptomes ca4a518e-aaf7-42d9-9758-352aac808809 Other Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08   Postmetamorphic posterior tissue including caudal fin from Danio rerio Drerio postmetamorphic 5 SAMEA110464179 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464179|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE45|collected by:Marco Podobnik|collection date:2018 07 16|common name:zebrafish|dev stage:Postmetamorphic|identified by:Marco Podobnik|sample name:SAMPLE45|sex:not provided|tissue type:posterior trunk including caudal fin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:841 19218 unspecified 1 Illumina TruSeq DNA Nano Kit   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140005 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 S879Nr45.1.fastq.gz S879Nr45.2.fastq.gz fastq fastq 31205725028.0 155856846.0 ena RUN TAB 05 08 2022 14:25:08:841 19219 0:100.11 1:100.11 A:8165930827;C:7529482042;G:7775787815;T:7734109822;N:414522 100 100     8165930827 7529482042 7775787815 7734109822 414522 ERX9574496 ERS12562207 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.97305 0.97331 0.04336 0.04353 0.73728 0.74324 0.47532 0.4806 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Multi-tissue Multi-system
11144 11144 ERR10034091 ERX9574495 ERS12562206 ERP140005 PRJEB55122 Danio developmental transcriptomes ca4a518e-aaf7-42d9-9758-352aac808809 Other Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08   Postmetamorphic posterior tissue including caudal fin from Danio rerio Drerio postmetamorphic 4 SAMEA110464178 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464178|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE44|collected by:Marco Podobnik|collection date:2018 07 16|common name:zebrafish|dev stage:Postmetamorphic|identified by:Marco Podobnik|sample name:SAMPLE44|sex:not provided|tissue type:posterior trunk including caudal fin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:841 19216 unspecified 1 Illumina TruSeq DNA Nano Kit   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140005 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 S879Nr44.1.fastq.gz S879Nr44.2.fastq.gz fastq fastq 12791868714.0 63868301.0 ena RUN TAB 05 08 2022 14:25:08:841 19217 0:100.14 1:100.14 A:3327645062;C:3095411506;G:3211023712;T:3157616450;N:171984 100 100     3327645062 3095411506 3211023712 3157616450 171984 ERX9574495 ERS12562206 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.97212 0.97067 0.04428 0.04445 0.74548 0.75114 0.47785 0.49354 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Multi-tissue Multi-system
11145 11145 ERR10034090 ERX9574494 ERS12562205 ERP140005 PRJEB55122 Danio developmental transcriptomes ca4a518e-aaf7-42d9-9758-352aac808809 Other Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08   Postmetamorphic posterior tissue including caudal fin from Danio rerio Drerio postmetamorphic 3 SAMEA110464177 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464177|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE43|collected by:Marco Podobnik|collection date:2018 07 16|common name:zebrafish|dev stage:Postmetamorphic|identified by:Marco Podobnik|sample name:SAMPLE43|sex:not provided|tissue type:posterior trunk including caudal fin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:840 19214 unspecified 1 Illumina TruSeq DNA Nano Kit   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140005 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 S879Nr43.1.fastq.gz S879Nr43.2.fastq.gz fastq fastq 8220676412.0 40976395.0 ena RUN TAB 05 08 2022 14:25:08:840 19215 0:100.31 1:100.31 A:2152497687;C:1985765652;G:2020897890;T:2061403084;N:112099 100 100     2152497687 1985765652 2020897890 2061403084 112099 ERX9574494 ERS12562205 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.97126 0.97279 0.04717 0.04683 0.74223 0.74479 0.47471 0.49071 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Multi-tissue Multi-system
11146 11146 ERR10034089 ERX9574493 ERS12562204 ERP140005 PRJEB55122 Danio developmental transcriptomes ca4a518e-aaf7-42d9-9758-352aac808809 Other Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08   Postmetamorphic posterior tissue including caudal fin from Danio rerio Drerio postmetamorphic 2 SAMEA110464176 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464176|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE42|collected by:Marco Podobnik|collection date:2018 07 16|common name:zebrafish|dev stage:Postmetamorphic|identified by:Marco Podobnik|sample name:SAMPLE42|sex:not provided|tissue type:posterior trunk including caudal fin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:840 19212 unspecified 1 Illumina TruSeq DNA Nano Kit   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140005 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 S879Nr42.1.fastq.gz S879Nr42.2.fastq.gz fastq fastq 9426020714.0 47021406.0 ena RUN TAB 05 08 2022 14:25:08:840 19213 0:100.23 1:100.23 A:2487913802;C:2263414842;G:2331327650;T:2343237033;N:127387 100 100     2487913802 2263414842 2331327650 2343237033 127387 ERX9574493 ERS12562204 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.97197 0.97222 0.04546 0.04553 0.74235 0.7485 0.48841 0.48446 93 93 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Multi-tissue Multi-system
11147 11147 ERR10034088 ERX9574492 ERS12562203 ERP140005 PRJEB55122 Danio developmental transcriptomes ca4a518e-aaf7-42d9-9758-352aac808809 Other Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08   Postmetamorphic posterior tissue including caudal fin from Danio rerio Drerio postmetamorphic 1 SAMEA110464175 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464175|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE41|collected by:Marco Podobnik|collection date:2018 07 16|common name:zebrafish|dev stage:Postmetamorphic|identified by:Marco Podobnik|sample name:SAMPLE41|sex:not provided|tissue type:posterior trunk including caudal fin                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:840 19210 unspecified 1 Illumina TruSeq DNA Nano Kit   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140005 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 S879Nr41.1.fastq.gz S879Nr41.2.fastq.gz fastq fastq 10220995994.0 50953819.0 ena RUN TAB 05 08 2022 14:25:08:840 19211 0:100.30 1:100.30 A:2679378092;C:2474435843;G:2537496182;T:2529546220;N:139657 100 100     2679378092 2474435843 2537496182 2529546220 139657 ERX9574492 ERS12562203 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.97322 0.97339 0.05421 0.05374 0.73693 0.74194 0.50642 0.50631 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Multi-tissue Multi-system
11148 11148 ERR10034072 ERX9574476 ERS12562187 ERP140005 PRJEB55122 Danio developmental transcriptomes ca4a518e-aaf7-42d9-9758-352aac808809 Other Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08   Metamorphic tissue without xxx from Danio rerio Drerio metamorphic 5 SAMEA110464159 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464159|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE25|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE25|sex:not provided|tissue type:whole body without xxx                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:835 19178 unspecified 1 Illumina TruSeq DNA Nano Kit   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140005 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 S879Nr25.1.fastq.gz S879Nr25.2.fastq.gz fastq fastq 10120435126.0 50403985.0 ena RUN TAB 05 08 2022 14:25:08:835 19179 0:100.39 1:100.39 A:2679131890;C:2420708190;G:2483153503;T:2537307238;N:134305 100 100     2679131890 2420708190 2483153503 2537307238 134305 ERX9574476 ERS12562187 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.96973 0.97106 0.04979 0.04949 0.71252 0.71654 0.4806 0.49338 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Trunk Surface Structure
11149 11149 ERR10034071 ERX9574475 ERS12562186 ERP140005 PRJEB55122 Danio developmental transcriptomes ca4a518e-aaf7-42d9-9758-352aac808809 Other Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08   Metamorphic tissue without xxx from Danio rerio Drerio metamorphic 4 SAMEA110464158 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464158|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE24|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE24|sex:not provided|tissue type:whole body without xxx                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:835 19176 unspecified 1 Illumina TruSeq DNA Nano Kit   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140005 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 S879Nr24.1.fastq.gz S879Nr24.2.fastq.gz fastq fastq 7845661906.0 39121993.0 ena RUN TAB 05 08 2022 14:25:08:835 19177 0:100.27 1:100.27 A:2096079479;C:1862247618;G:1929220494;T:1958006859;N:107456 100 100     2096079479 1862247618 1929220494 1958006859 107456 ERX9574475 ERS12562186 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.96989 0.96986 0.04901 0.04902 0.71599 0.72301 0.48965 0.48827 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Trunk Surface Structure
11150 11150 ERR10034070 ERX9574474 ERS12562185 ERP140005 PRJEB55122 Danio developmental transcriptomes ca4a518e-aaf7-42d9-9758-352aac808809 Other Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08   Metamorphic tissue without xxx from Danio rerio Drerio metamorphic 3 SAMEA110464157 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464157|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE23|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE23|sex:not provided|tissue type:whole body without xxx                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:835 19174 unspecified 1 Illumina TruSeq DNA Nano Kit   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140005 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 S879Nr23.1.fastq.gz S879Nr23.2.fastq.gz fastq fastq 8270390422.0 41338131.0 ena RUN TAB 05 08 2022 14:25:08:835 19175 0:100.03 1:100.03 A:2156060704;C:1998612686;G:2055201244;T:2060404840;N:110948 100 100     2156060704 1998612686 2055201244 2060404840 110948 ERX9574474 ERS12562185 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.97085 0.97083 0.04232 0.04236 0.7219 0.72671 0.47325 0.4807 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Trunk Surface Structure
11151 11151 ERR10034069 ERX9574473 ERS12562184 ERP140005 PRJEB55122 Danio developmental transcriptomes ca4a518e-aaf7-42d9-9758-352aac808809 Other Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08   Metamorphic tissue without xxx from Danio rerio Drerio metamorphic 2 SAMEA110464156 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464156|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE22|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE22|sex:not provided|tissue type:whole body without xxx                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:834 19172 unspecified 1 Illumina TruSeq DNA Nano Kit   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140005 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 S879Nr22.1.fastq.gz S879Nr22.2.fastq.gz fastq fastq 10977356920.0 54380062.0 ena RUN TAB 05 08 2022 14:25:08:834 19173 0:100.93 1:100.93 A:2852856166;C:2671616791;G:2798184312;T:2654546853;N:152798 100 100     2852856166 2671616791 2798184312 2654546853 152798 ERX9574473 ERS12562184 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.9765 0.97629 0.03531 0.03529 0.72025 0.72705 0.47808 0.46326 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Trunk Surface Structure
11152 11152 ERR10034068 ERX9574472 ERS12562183 ERP140005 PRJEB55122 Danio developmental transcriptomes ca4a518e-aaf7-42d9-9758-352aac808809 Other Transcriptomic analysis of four different developmental stages of four Danio species D. rerio D. aesculapii Danio aff. kyathit striped also known as Danio quagga and D. albolineatus. Five biological replicates were sampled for every developmental stage of a species. ENA FIRST PUBLIC:2022 08 05|ENA LAST UPDATE:2022 08 08   Metamorphic tissue without xxx from Danio rerio Drerio metamorphic 1 SAMEA110464155 max planck institute for biology ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08|External Id:SAMEA110464155|INSDC center alias:MAX PLANCK INSTITUTE FOR BIOLOGY|INSDC center name:max planck institute for biology|INSDC first public:2022 08 08T04:26:46Z|INSDC last update:2022 08 08T04:26:46Z|INSDC status:public|Submitter Id:SAMPLE21|collected by:Marco Podobnik|collection date:2018 06 27|common name:zebrafish|dev stage:Metamorphic|identified by:Marco Podobnik|sample name:SAMPLE21|sex:not provided|tissue type:whole body without xxx                 Illumina NovaSeq 6000 paired end sequencing ena EXPERIMENT TAB 05 08 2022 14:25:08:834 19170 unspecified 1 Illumina TruSeq DNA Nano Kit   RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   ERP140005 Illumina NovaSeq 6000 paired end sequencing ENA FIRST PUBLIC:2022 08 08|ENA LAST UPDATE:2022 08 08 S879Nr21.1.fastq.gz S879Nr21.2.fastq.gz fastq fastq 11346084502.0 56210802.0 ena RUN TAB 05 08 2022 14:25:08:834 19171 0:100.92 1:100.92 A:2950787998;C:2755514202;G:2902131288;T:2737495846;N:155168 100 100     2950787998 2755514202 2902131288 2737495846 155168 ERX9574472 ERS12562183 ERA16814395 max planck institute for biology|European Nucleotide Archive max planck institute for biology 2 0.9732 0.97208 0.02959 0.02983 0.72322 0.73135 0.47796 0.47326 101 101 B B biological fallback assumption illumina novaseq_era unknown poly_a trueseq bulk unknown unknown   Germany 2022-08-05 Undetermined Undetermined Trunk Surface Structure
11777 11777 ERR11758595 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S36_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S36_L001_R1_001.fastq.gz fastq fastq 211593816.0 1679316.0 E MTAB 13196:drl h2b dendra tb S36 L001 0:28 1:98 A:62689430;C:45809168;G:45709128;T:57272091;N:113999 28 98     62689430 45809168 45709128 57272091 113999 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00192 0.91331 0.00072 0.14588 0.99675 0.89292 0.51304 0.63144 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11778 11778 ERR11758629 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S37_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S37_L001_R1_001.fastq.gz fastq fastq 980164836.0 7779086.0 E MTAB 13196:drl h2b dendra tb S37 L001 0:28 1:98 A:281375011;C:216067640;G:222839674;T:259781180;N:101331 28 98     281375011 216067640 222839674 259781180 101331 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00817 0.89718 0.00237 0.12153 0.98912 0.82643 0.46403 0.64954 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11779 11779 ERR11758618 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S39_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S39_L001_R1_001.fastq.gz fastq fastq 12118302.0 96177.0 E MTAB 13196:drl h2b dendra tb S39 L001 0:28 1:98 A:3543790;C:2662872;G:2728134;T:3182383;N:1123 28 98     3543790 2662872 2728134 3182383 1123 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00786 0.88963 0.0025 0.12543 0.99403 0.88635 0.50098 0.64694 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11780 11780 ERR11758643 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S5_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S5_L005_R1_001.fastq.gz fastq fastq 2061022698.0 16357323.0 E MTAB 13196:drl h2b dendra tb S5 L005 0:28 1:98 A:587730953;C:457631700;G:470283474;T:545196979;N:179592 28 98     587730953 457631700 470283474 545196979 179592 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.01192 0.91661 0.00336 0.12397 0.98518 0.82568 0.45692 0.65555 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11781 11781 ERR11758610 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S38_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S38_L001_R1_001.fastq.gz fastq fastq 924603120.0 7338120.0 E MTAB 13196:drl h2b dendra tb S38 L001 0:28 1:98 A:265987815;C:203824483;G:210024160;T:244670646;N:96016 28 98     265987815 203824483 210024160 244670646 96016 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00773 0.89881 0.00242 0.12145 0.98944 0.82948 0.50529 0.66568 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11782 11782 ERR11758641 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S6_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S6_L005_R1_001.fastq.gz fastq fastq 1954661562.0 15513187.0 E MTAB 13196:drl h2b dendra tb S6 L005 0:28 1:98 A:558769608;C:433724557;G:445550100;T:516443984;N:173313 28 98     558769608 433724557 445550100 516443984 173313 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.0125 0.91697 0.00373 0.12359 0.98447 0.82558 0.4881 0.6456 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11783 11783 ERR11758591 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S35_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S35_L001_R1_001.fastq.gz fastq fastq 4717188.0 37438.0 E MTAB 13196:drl h2b dendra tb S35 L001 0:28 1:98 A:1419430;C:1014265;G:1016661;T:1264642;N:2190 28 98     1419430 1014265 1016661 1264642 2190 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.0012 0.65482 0.00054 0.10783 0.99953 0.97157 0.625 0.63689 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11784 11784 ERR11758606 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S34_L001_R1_001.fastq.gz drl_h2b-dendra_tb_S34_L001_R2_001.fastq.gz fastq fastq 303645636.0 2409886.0 E MTAB 13196:drl h2b dendra tb S34 L001 0:28 1:98 A:90748559;C:65369482;G:65969002;T:81405258;N:153335 28 98     90748559 65369482 65969002 81405258 153335 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00228 0.91262 0.00099 0.14666 0.99638 0.89006 0.47177 0.63109 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11785 11785 ERR11758640 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S40_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S40_L001_R1_001.fastq.gz fastq fastq 661361022.0 5248897.0 E MTAB 13196:drl h2b dendra tb S40 L001 0:28 1:98 A:190087869;C:145985661;G:150124621;T:175095762;N:67109 28 98     190087869 145985661 150124621 175095762 67109 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00785 0.89784 0.00251 0.12159 0.98948 0.83055 0.46095 0.64951 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11786 11786 ERR11758605 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S7_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S7_L005_R1_001.fastq.gz fastq fastq 25157790.0 199665.0 E MTAB 13196:drl h2b dendra tb S7 L005 0:28 1:98 A:7330053;C:5600451;G:5635840;T:6589498;N:1948 28 98     7330053 5600451 5635840 6589498 1948 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.01201 0.91385 0.00341 0.12826 0.98595 0.85161 0.49226 0.64953 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11787 11787 ERR11758600 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S8_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S8_L005_R1_001.fastq.gz fastq fastq 1422735804.0 11291554.0 E MTAB 13196:drl h2b dendra tb S8 L005 0:28 1:98 A:405788442;C:317299433;G:322206476;T:377317416;N:124037 28 98     405788442 317299433 322206476 377317416 124037 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.01226 0.91547 0.0037 0.12565 0.9849 0.83662 0.48279 0.64531 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
11788 11788 ERR11758616 ERX11157718 ERS16172936 ERP149744 PRJEB64563 Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E-MTAB-13196 Transcriptome Analysis Development of the dorsal aorta is a key step in the establishment of the adult blood forming system since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied. Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm. Here we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated by the end of gastrulation. Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation. We describe a conserved program in the zebrafish where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta. Whereas SDECs lack hematopoietic potential they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium. Thus at least three subsets of ECs contribute to the developing dorsal aorta: vascular ECs hemogenic ECs and SDECs. Taken together our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta. ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01   Protocols: Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. drl tb SAMEA114192243 Institute of Molecular Genetics of the Czech Academy of Sciences ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2                 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos E MTAB 13196:drl tb p drl tb p Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos Dechorionated embryos were collected at defined stages dissociated by pipetting centrifugation at 300g for 5 minutes washed once with PBS and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM Library & Gel Bead Kit v2 or v3 was used for library preparation.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL Oligo-dT PAIRED ILLUMINA Illumina HiSeq 2500   ERP149744 Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2 etv2:Kaede fli1:DsRed and tp1:eGFP transgenic zebrafish embryos ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01 drl_h2b-dendra_tb_S33_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S33_L001_R1_001.fastq.gz fastq fastq 328918212.0 2610462.0 E MTAB 13196:drl h2b dendra tb S33 L001 0:28 1:98 A:98036464;C:71090137;G:71650807;T:87969481;N:171323 28 98     98036464 71090137 71650807 87969481 171323 ERX11157718 ERS16172936 ERA25628220 Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive 2 0.00197 0.89969 0.00087 0.14269 0.99681 0.89134 0.49763 0.63651 28 98 T B sc-like readlen illumina hiseq_era unknown poly_a unknown sc single_cell_droplet 10x   Czech Republic 2023-08-01 Undetermined Embryo Embryo Imprecise All anatomical structures
24906 24906 SRR25532497 SRX21261798 SRS18515093 SRP453533 PRJNA1002570 MBT induced effects in zebrafish eyes PRJNA1002570 Other We intended to screen the key events in zebrafish larvae post MBT exposure.         control1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.42 E|sample type:whole organism|BioSampleModel:Model organism or animal                 RNAseq of fish S10 S10 normal RNAseq of fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453533     CK1_1.fq.gz CK1_2.fq.gz fastq fastq 6650697900.0 22168993.0 CK1 1.fq.gz 0:150 1:150 A:1918460669;C:1420936092;G:1412569553;T:1898656995;N:74591 150 150     1918460669 1420936092 1412569553 1898656995 74591 SRX21261798 SRS18515093 SRA1687160 Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES Chinese Academy of Sciences 2 0.91765 0.91694 0.15569 0.15461 0.70185 0.7027 0.47761 0.47369 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-05 Undetermined Larval Trunk Surface Structure
24907 24907 SRR25532498 SRX21261797 SRS18515092 SRP453533 PRJNA1002570 MBT induced effects in zebrafish eyes PRJNA1002570 Other We intended to screen the key events in zebrafish larvae post MBT exposure.         MBTH3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.41 E|sample type:whole organism|BioSampleModel:Model organism or animal                 RNAseq of fish S9 S9 normal RNAseq of fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453533     MBTH3_2.fq.gz MBTH3_1.fq.gz fastq fastq 6333332100.0 21111107.0 MBTH3 1.fq.gz 0:150 1:150 A:1755718187;C:1429192980;G:1420776066;T:1727550080;N:94787 150 150     1755718187 1429192980 1420776066 1727550080 94787 SRX21261797 SRS18515092 SRA1687160 Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES Chinese Academy of Sciences 2 0.93518 0.93355 0.11668 0.11602 0.67799 0.67817 0.47705 0.47875 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-05 Undetermined Larval Trunk Surface Structure
24908 24908 SRR25532499 SRX21261796 SRS18515091 SRP453533 PRJNA1002570 MBT induced effects in zebrafish eyes PRJNA1002570 Other We intended to screen the key events in zebrafish larvae post MBT exposure.         MBTH2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.40 E|sample type:whole organism|BioSampleModel:Model organism or animal                 RNAseq of fish S8 S8 normal RNAseq of fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453533     MBTH2_1.fq.gz MBTH2_2.fq.gz fastq fastq 6373733400.0 21245778.0 MBTH2 1.fq.gz 0:150 1:150 A:1775132718;C:1430955007;G:1424605018;T:1742942742;N:97915 150 150     1775132718 1430955007 1424605018 1742942742 97915 SRX21261796 SRS18515091 SRA1687160 Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES Chinese Academy of Sciences 2 0.93081 0.93016 0.12061 0.11947 0.68215 0.68172 0.47956 0.48186 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-05 Undetermined Larval Trunk Surface Structure
24909 24909 SRR25532500 SRX21261795 SRS18515090 SRP453533 PRJNA1002570 MBT induced effects in zebrafish eyes PRJNA1002570 Other We intended to screen the key events in zebrafish larvae post MBT exposure.         MBTH1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.39 E|sample type:whole organism|BioSampleModel:Model organism or animal                 RNAseq of fish S7 S7 normal RNAseq of fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453533     MBTH1_1.fq.gz MBTH1_2.fq.gz fastq fastq 6224052600.0 20746842.0 MBTH1 1.fq.gz 0:150 1:150 A:1753175301;C:1379045823;G:1371537072;T:1720226102;N:68302 150 150     1753175301 1379045823 1371537072 1720226102 68302 SRX21261795 SRS18515090 SRA1687160 Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES Chinese Academy of Sciences 2 0.9276 0.92379 0.13642 0.13482 0.68416 0.68479 0.47638 0.47581 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-05 Undetermined Larval Trunk Surface Structure
24910 24910 SRR25532501 SRX21261794 SRS18515089 SRP453533 PRJNA1002570 MBT induced effects in zebrafish eyes PRJNA1002570 Other We intended to screen the key events in zebrafish larvae post MBT exposure.         MBTM3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.38 E|sample type:whole organism|BioSampleModel:Model organism or animal                 RNAseq of fish S6 S6 normal RNAseq of fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453533     MBTM3_2.fq.gz MBTM3_1.fq.gz fastq fastq 6885667800.0 22952226.0 MBTM3 1.fq.gz 0:150 1:150 A:1936367424;C:1526831248;G:1520656271;T:1901736749;N:76108 150 150     1936367424 1526831248 1520656271 1901736749 76108 SRX21261794 SRS18515089 SRA1687160 Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES Chinese Academy of Sciences 2 0.92736 0.92516 0.12801 0.12693 0.68982 0.69063 0.47163 0.4612 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-05 Undetermined Larval Trunk Surface Structure
24911 24911 SRR25532502 SRX21261793 SRS18515088 SRP453533 PRJNA1002570 MBT induced effects in zebrafish eyes PRJNA1002570 Other We intended to screen the key events in zebrafish larvae post MBT exposure.         MBTM2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.37 E|sample type:whole organism|BioSampleModel:Model organism or animal                 RNAseq of fish S5 S5 normal RNAseq of fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453533     MBTM2_1.fq.gz MBTM2_2.fq.gz fastq fastq 6529427400.0 21764758.0 MBTM2 1.fq.gz 0:150 1:150 A:1808908277;C:1472638598;G:1467975655;T:1779801002;N:103868 150 150     1808908277 1472638598 1467975655 1779801002 103868 SRX21261793 SRS18515088 SRA1687160 Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES Chinese Academy of Sciences 2 0.9296 0.93217 0.11772 0.11735 0.68262 0.68331 0.4724 0.4721 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-05 Undetermined Larval Trunk Surface Structure
24912 24912 SRR25532503 SRX21261792 SRS18515087 SRP453533 PRJNA1002570 MBT induced effects in zebrafish eyes PRJNA1002570 Other We intended to screen the key events in zebrafish larvae post MBT exposure.         MBTM1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.36 E|sample type:whole organism|BioSampleModel:Model organism or animal                 RNAseq of fish S4 S4 normal RNAseq of fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453533     MBTM1_2.fq.gz MBTM1_1.fq.gz fastq fastq 6733924800.0 22446416.0 MBTM1 1.fq.gz 0:150 1:150 A:1847490053;C:1535661831;G:1528806965;T:1821868439;N:97512 150 150     1847490053 1535661831 1528806965 1821868439 97512 SRX21261792 SRS18515087 SRA1687160 Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES Chinese Academy of Sciences 2 0.93177 0.93448 0.11165 0.11192 0.67722 0.67823 0.47325 0.46912 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-05 Undetermined Larval Trunk Surface Structure
24913 24913 SRR25532504 SRX21261791 SRS18515086 SRP453533 PRJNA1002570 MBT induced effects in zebrafish eyes PRJNA1002570 Other We intended to screen the key events in zebrafish larvae post MBT exposure.         MBTL3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.35 E|sample type:whole organism|BioSampleModel:Model organism or animal                 RNAseq of fish S3 S3 normal RNAseq of fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453533     MBTL3_1.fq.gz MBTL3_2.fq.gz fastq fastq 9066238500.0 30220795.0 MBTL3 1.fq.gz 0:150 1:150 A:2629692873;C:1932648084;G:1927694770;T:2576111685;N:91088 150 150     2629692873 1932648084 1927694770 2576111685 91088 SRX21261791 SRS18515086 SRA1687160 Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES Chinese Academy of Sciences 2 0.93079 0.91809 0.1476 0.14446 0.69201 0.69258 0.47663 0.47687 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-05 Undetermined Larval Trunk Surface Structure
24914 24914 SRR25532505 SRX21261790 SRS18515085 SRP453533 PRJNA1002570 MBT induced effects in zebrafish eyes PRJNA1002570 Other We intended to screen the key events in zebrafish larvae post MBT exposure.         control3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.44 E|sample type:whole organism|BioSampleModel:Model organism or animal                 RNAseq of fish S12 S12 normal RNAseq of fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453533     CK3_1.fq.gz CK3_2.fq.gz fastq fastq 6596041200.0 21986804.0 CK3 1.fq.gz 0:150 1:150 A:1886076947;C:1431757712;G:1423068767;T:1855067482;N:70292 150 150     1886076947 1431757712 1423068767 1855067482 70292 SRX21261790 SRS18515085 SRA1687160 Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES Chinese Academy of Sciences 2 0.92168 0.92147 0.14797 0.14768 0.68962 0.68935 0.47874 0.48307 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-05 Undetermined Larval Trunk Surface Structure
24915 24915 SRR25532506 SRX21261789 SRS18515084 SRP453533 PRJNA1002570 MBT induced effects in zebrafish eyes PRJNA1002570 Other We intended to screen the key events in zebrafish larvae post MBT exposure.         control2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.43 E|sample type:whole organism|BioSampleModel:Model organism or animal                 RNAseq of fish S11 S11 normal RNAseq of fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453533     CK2_1.fq.gz CK2_2.fq.gz fastq fastq 6749651400.0 22498838.0 CK2 1.fq.gz 0:150 1:150 A:1934306700;C:1451979582;G:1445551014;T:1917740723;N:73381 150 150     1934306700 1451979582 1445551014 1917740723 73381 SRX21261789 SRS18515084 SRA1687160 Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES Chinese Academy of Sciences 2 0.92261 0.92062 0.15096 0.14969 0.69783 0.69702 0.48303 0.49016 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-05 Undetermined Larval Trunk Surface Structure
24916 24916 SRR25532507 SRX21261788 SRS18515083 SRP453533 PRJNA1002570 MBT induced effects in zebrafish eyes PRJNA1002570 Other We intended to screen the key events in zebrafish larvae post MBT exposure.         MBTL2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.34 E|sample type:whole organism|BioSampleModel:Model organism or animal                 RNAseq of fish S2 S2 normal RNAseq of fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453533     MBTL2_1.fq.gz MBTL2_2.fq.gz fastq fastq 6868354800.0 22894516.0 MBTL2 1.fq.gz 0:150 1:150 A:1956017484;C:1493585329;G:1486220640;T:1932456728;N:74619 150 150     1956017484 1493585329 1486220640 1932456728 74619 SRX21261788 SRS18515083 SRA1687160 Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES Chinese Academy of Sciences 2 0.92126 0.91908 0.14701 0.14525 0.69394 0.69363 0.47281 0.47636 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-05 Undetermined Larval Trunk Surface Structure
24917 24917 SRR25532508 SRX21261787 SRS18515082 SRP453533 PRJNA1002570 MBT induced effects in zebrafish eyes PRJNA1002570 Other We intended to screen the key events in zebrafish larvae post MBT exposure.         MBTL1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|collection date:2022 11|geo loc name:China: Beijing|sex:not applicable|tissue:whole body|lat lon:39.9 N 116.33 E|sample type:whole organism|BioSampleModel:Model organism or animal                 RNAseq of fish S1 S1 normal RNAseq of fish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP453533     MBTL1_1.fq.gz MBTL1_2.fq.gz fastq fastq 6305127900.0 21017093.0 MBTL1 1.fq.gz 0:150 1:150 A:1797030982;C:1364002775;G:1357954929;T:1786051425;N:87789 150 150     1797030982 1364002775 1357954929 1786051425 87789 SRX21261787 SRS18515082 SRA1687160 Chinese Academy of Sciences|RESEARCH CENTER FOR ECO-ENVIRONMENTAL SCIENCES Chinese Academy of Sciences 2 0.92195 0.92138 0.14404 0.1433 0.69656 0.69623 0.47185 0.46936 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-05 Undetermined Larval Trunk Surface Structure
24918 24918 SRR25594442 SRX21322829 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome Z 2 1.fq Z 2 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     Z-2_2.fq.gz Z-2_1.fq.gz fastq fastq 5621492400.0 18738308.0 Z 2 1.fq.gz 0:150 1:150 A:1483421677;C:1306378425;G:1338052121;T:1493618330;N:21847 150 150     1483421677 1306378425 1338052121 1493618330 21847 SRX21322829 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94389 0.93819 0.03702 0.03621 0.71758 0.72423 0.43774 0.4558 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24919 24919 SRR25594443 SRX21322828 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome Z 1 1.fq Z 1 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     Z-1_2.fq.gz Z-1_1.fq.gz fastq fastq 6301274700.0 21004249.0 Z 1 1.fq.gz 0:150 1:150 A:1671253253;C:1458678359;G:1491311308;T:1680006330;N:25450 150 150     1671253253 1458678359 1491311308 1680006330 25450 SRX21322828 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94339 0.93817 0.03831 0.03813 0.71752 0.72293 0.42611 0.43548 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24920 24920 SRR25594444 SRX21322827 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome K 3 1.fq K 3 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     K-3_2.fq.gz K-3_1.fq.gz fastq fastq 5519682000.0 18398940.0 K 3 1.fq.gz 0:150 1:150 A:1469946965;C:1270791684;G:1304075220;T:1474846842;N:21289 150 150     1469946965 1270791684 1304075220 1474846842 21289 SRX21322827 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94356 0.93561 0.03986 0.03923 0.71877 0.72697 0.44771 0.44936 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24921 24921 SRR25594445 SRX21322826 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome K 2 1.fq K 2 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     K-2_1.fq.gz K-2_2.fq.gz fastq fastq 5808261300.0 19360871.0 K 2 1.fq.gz 0:150 1:150 A:1538012312;C:1343217111;G:1375887577;T:1551118640;N:25660 150 150     1538012312 1343217111 1375887577 1551118640 25660 SRX21322826 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94469 0.94137 0.03929 0.03857 0.7175 0.71946 0.44395 0.44354 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24922 24922 SRR25594446 SRX21322825 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome ZP 3 1.fq ZP 3 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     ZP-3_1.fq.gz ZP-3_2.fq.gz fastq fastq 5397938100.0 17993127.0 ZP 3 1.fq.gz 0:150 1:150 A:1438191584;C:1244532731;G:1271700792;T:1443491138;N:21855 150 150     1438191584 1244532731 1271700792 1443491138 21855 SRX21322825 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94839 0.94406 0.04345 0.04279 0.71719 0.72362 0.42772 0.4311 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24923 24923 SRR25594447 SRX21322824 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome ZP 2 1.fq ZP 2 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     ZP-2_1.fq.gz ZP-2_2.fq.gz fastq fastq 6062424900.0 20208083.0 ZP 2 1.fq.gz 0:150 1:150 A:1612595576;C:1398589726;G:1427536119;T:1623678727;N:24752 150 150     1612595576 1398589726 1427536119 1623678727 24752 SRX21322824 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.95013 0.94657 0.04364 0.04342 0.71565 0.71908 0.44652 0.44832 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24924 24924 SRR25594448 SRX21322823 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome ZP 1 1.fq ZP 1 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     ZP-1_2.fq.gz ZP-1_1.fq.gz fastq fastq 6487607100.0 21625357.0 ZP 1 1.fq.gz 0:150 1:150 A:1728514584;C:1494175744;G:1521726756;T:1743164500;N:25516 150 150     1728514584 1494175744 1521726756 1743164500 25516 SRX21322823 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94867 0.94432 0.04535 0.0449 0.71926 0.72348 0.43747 0.44661 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24925 24925 SRR25594449 SRX21322822 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome Z 3 1.fq Z 3 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     Z-3_1.fq.gz Z-3_2.fq.gz fastq fastq 8111204700.0 27037349.0 Z 3 1.fq.gz 0:150 1:150 A:2143712842;C:1879826122;G:1918517283;T:2169119328;N:29125 150 150     2143712842 1879826122 1918517283 2169119328 29125 SRX21322822 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94485 0.94083 0.03886 0.03798 0.71362 0.71768 0.44066 0.44713 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
24926 24926 SRR25594450 SRX21322821 SRS18569855 SRP454395 PRJNA1002816 Danio rerio Raw sequence reads PRJNA1002816 Whole Genome Sequencing Zebrafish Transcriptome         Zebrafish intestine   strain:Not Applicable|isolate:Not Applicable|breed:Not Applicable|cultivar:Not Applicable|ecotype:Not Applicable|age:Not Applicable|dev stage:Not Applicable|collection date:Not Applicable|geo loc name:Not Applicable|sex:Not Applicable|tissue:intestine|BioSampleModel:Model organism or animal                 Zebrafish Intestinal Transcriptome K 1 1.fq K 1 1.fq Intestinal Transcriptome     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP454395     K-1_1.fq.gz K-1_2.fq.gz fastq fastq 7164142200.0 23880474.0 K 1 1.fq.gz 0:150 1:150 A:1896647470;C:1661542391;G:1700422400;T:1905500150;N:29789 150 150     1896647470 1661542391 1700422400 1905500150 29789 SRX21322821 SRS18569855 SRA1689922 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences|fish Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences 2 0.94635 0.94209 0.03738 0.03664 0.71961 0.72571 0.45014 0.44857 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-08-10 Undetermined Undetermined Gut Digestive System
28458 28458 SRR26265233 SRX21974767 SRS19050630 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         IFN4 2   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 10|BioSampleModel:Model organism or animal                 RNAseq of zebrafish IFND2 IFND2 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     IFN4-2.R2.fq.gz IFN4-2.R1.fq.gz fastq fastq 6934783900.0 23533465.0 IFN4 2.R1.fq.gz 0:147.35 1:147.33 A:1868083790;C:1590902416;G:1598661179;T:1876555558;N:580957 147 147     1868083790 1590902416 1598661179 1876555558 580957 SRX21974767 SRS19050630 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95226 0.95256 0.09237 0.09199 0.73403 0.73472 0.50112 0.4946 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28459 28459 SRR26265234 SRX21974766 SRS19050629 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         IFN4 1   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 9|BioSampleModel:Model organism or animal                 RNAseq of zebrafish IFND1 IFND1 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     IFN4-1.R2.fq.gz IFN4-1.R1.fq.gz fastq fastq 6955503146.0 23557276.0 IFN4 1.R1.fq.gz 0:147.65 1:147.61 A:1873984869;C:1595727817;G:1603714470;T:1881209728;N:866262 147 147     1873984869 1595727817 1603714470 1881209728 866262 SRX21974766 SRS19050629 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95329 0.95472 0.09371 0.09311 0.73535 0.7362 0.49542 0.49872 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28460 28460 SRR26265235 SRX21974765 SRS19050628 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         IFN1 4   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 8|BioSampleModel:Model organism or animal                 RNAseq of zebrafish IFNA4 IFNA4 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     IFN1-4.R1.fq.gz IFN1-4.R2.fq.gz fastq fastq 6497442039.0 22025966.0 IFN1 4.R1.fq.gz 0:147.50 1:147.49 A:1752434033;C:1488528327;G:1495225910;T:1760699235;N:554534 147 147     1752434033 1488528327 1495225910 1760699235 554534 SRX21974765 SRS19050628 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95168 0.95288 0.09073 0.09058 0.73691 0.73697 0.49659 0.49706 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28461 28461 SRR26265236 SRX21974764 SRS19050627 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         IFN1 3   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 7|BioSampleModel:Model organism or animal                 RNAseq of zebrafish IFNA3 IFNA3 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     IFN1-3.R1.fq.gz IFN1-3.R2.fq.gz fastq fastq 6258791362.0 21164255.0 IFN1 3.R1.fq.gz 0:147.88 1:147.85 A:1687323085;C:1434335716;G:1441365307;T:1695236268;N:530986 147 147     1687323085 1434335716 1441365307 1695236268 530986 SRX21974764 SRS19050627 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95206 0.95262 0.09255 0.09194 0.73549 0.73503 0.49685 0.50433 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28462 28462 SRR26265237 SRX21974763 SRS19050626 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         IFN1 2   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 6|BioSampleModel:Model organism or animal                 RNAseq of zebrafish IFNA2 IFNA2 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     IFN1-2.R1.fq.gz IFN1-2.R2.fq.gz fastq fastq 5566110483.0 18875664.0 IFN1 2.R1.fq.gz 0:147.46 1:147.43 A:1498457518;C:1278011392;G:1284254482;T:1504942516;N:444575 147 147     1498457518 1278011392 1284254482 1504942516 444575 SRX21974763 SRS19050626 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95197 0.9524 0.09035 0.08962 0.73606 0.73634 0.50146 0.49994 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28463 28463 SRR26265238 SRX21974762 SRS19050625 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         IFN1 1   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 5|BioSampleModel:Model organism or animal                 RNAseq of zebrafish IFNA1 IFNA1 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     IFN1-1.R1.fq.gz IFN1-1.R2.fq.gz fastq fastq 6919610192.0 23425305.0 IFN1 1.R1.fq.gz 0:147.71 1:147.68 A:1863998722;C:1587286271;G:1595557648;T:1872190552;N:576999 147 147     1863998722 1587286271 1595557648 1872190552 576999 SRX21974762 SRS19050625 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95297 0.95392 0.08926 0.0886 0.73744 0.73716 0.48737 0.49536 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28464 28464 SRR26265239 SRX21974761 SRS19050624 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         Control 4   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 4|BioSampleModel:Model organism or animal                 RNAseq of zebrafish C4 C4 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     Control-4.R1.fq.gz Control-4.R2.fq.gz fastq fastq 7048754711.0 23843338.0 Control 4.R1.fq.gz 0:147.83 1:147.80 A:1886695953;C:1629137936;G:1637672845;T:1894536437;N:711540 147 147     1886695953 1629137936 1637672845 1894536437 711540 SRX21974761 SRS19050624 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.9556 0.95723 0.09014 0.08984 0.73533 0.73643 0.50146 0.50134 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28465 28465 SRR26265240 SRX21974760 SRS19050623 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         Control 3   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 RNAseq of zebrafish C3 C3 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     Control-3.R1.fq.gz Control-3.R2.fq.gz fastq fastq 6936430397.0 23495179.0 Control 3.R1.fq.gz 0:147.63 1:147.60 A:1861679698;C:1598594022;G:1606747561;T:1868699697;N:709419 147 147     1861679698 1598594022 1606747561 1868699697 709419 SRX21974760 SRS19050623 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95496 0.95472 0.09092 0.08958 0.73505 0.73586 0.50541 0.50256 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28466 28466 SRR26265241 SRX21974759 SRS19050622 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         IFN4 4   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 12|BioSampleModel:Model organism or animal                 RNAseq of zebrafish IFND4 IFND4 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     IFN4-4.R1.fq.gz IFN4-4.R2.fq.gz fastq fastq 6904025687.0 23391394.0 IFN4 4.R1.fq.gz 0:147.59 1:147.56 A:1858866141;C:1585020535;G:1592940944;T:1866550686;N:647381 147 147     1858866141 1585020535 1592940944 1866550686 647381 SRX21974759 SRS19050622 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95345 0.95394 0.08901 0.08834 0.73537 0.73596 0.50012 0.49674 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28467 28467 SRR26265242 SRX21974758 SRS19050621 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         IFN4 3   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 11|BioSampleModel:Model organism or animal                 RNAseq of zebrafish IFND3 IFND3 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     IFN4-3.R1.fq.gz IFN4-3.R2.fq.gz fastq fastq 6983243474.0 23627912.0 IFN4 3.R1.fq.gz 0:147.80 1:147.75 A:1880838380;C:1603492441;G:1611871993;T:1885974103;N:1066557 147 147     1880838380 1603492441 1611871993 1885974103 1066557 SRX21974758 SRS19050621 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95262 0.95399 0.09442 0.09269 0.73586 0.73519 0.50113 0.49912 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28468 28468 SRR26265243 SRX21974757 SRS19050620 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         Control 2   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNAseq of zebrafish C2 C2 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     Control-2.R1.fq.gz Control-2.R2.fq.gz fastq fastq 7064416471.0 23901145.0 Control 2.R1.fq.gz 0:147.80 1:147.77 A:1896430007;C:1626943513;G:1635235356;T:1905174563;N:633032 147 147     1896430007 1626943513 1635235356 1905174563 633032 SRX21974757 SRS19050620 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95546 0.95678 0.08984 0.08994 0.73535 0.73565 0.49891 0.49705 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
28469 28469 SRR26265244 SRX21974756 SRS19050619 SRP464312 PRJNA1022576 Danio rerio Raw sequence reads PRJNA1022576 Whole Genome Sequencing In teleost type I IFNs are categorized into 2 subgroups containing one or two pairs of disulphide bond. However their functional differences have not been fully unveiled. It has been shown that IFN1 can be induced by viruses and trigger strong antiviral response in inducing hundreds of IFN stimulated genes conferring cell resistance to viruses. However the antiviral functions of IFN4 have been debated. To investigate the genes modulated by IFN1 and IFN4 ZF4 cells were stimulated with recombinant IFN1 and IFN4 and were performed transcriptome analysis.         Control 1   strain:not collected|age:not collected|collection date:2023 08 20|geo loc name:not collected|sex:not collected|tissue:not collected|cell line:ZF4|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNAseq of zebrafish C1 C1 normal RNA seq of zebrafish     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP464312     Control-1.R1.fq.gz Control-1.R2.fq.gz fastq fastq 7005585889.0 23733330.0 Control 1.R1.fq.gz 0:147.61 1:147.57 A:1874251473;C:1620035540;G:1628125464;T:1882607735;N:565677 147 147     1874251473 1620035540 1628125464 1882607735 565677 SRX21974756 SRS19050619 SRA1725060 Shanghai Ocean University|College of Fisheries and Life Science Shanghai Ocean University 2 0.95539 0.95612 0.08699 0.08663 0.73777 0.73833 0.49693 0.49816 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2023-10-03 Undetermined Undetermined Cell Line Cell Line
29719 29719 SRR27485664 SRX23156885 SRS20107306 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           eggs R3   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|replicate:3|BioSampleModel:Model organism or animal                 mRNA seq of zebrafish: eggs rep4 EV06009 EV06009 RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP482074     EV06009.R1.fastq.gz fastq 809138488.0 10734286.0 EV06009.R1.fastq.gz 0:75.38 A:236901398;C:156814193;G:179647937;T:235732894;N:42066 75       236901398 156814193 179647937 235732894 42066 SRX23156885 SRS20107306 SRA1783314 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.92159   0.07516   0.837   0.7566   69   B   usable mapping rate illumina nextseq 3prime poly_a lexogen bulk unknown unknown   Austria 2024-01-11 Undetermined Embryo Undetermined Embryo Imprecise
29730 29730 SRR27485675 SRX23156874 SRS20107295 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           eggs R2   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|replicate:2|BioSampleModel:Model organism or animal                 mRNA seq of zebrafish: eggs rep4 EV06002 EV06002 RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP482074     EV06002.R1.fastq.gz fastq 632849068.0 8404028.0 EV06002.R1.fastq.gz 0:75.30 A:194183801;C:123105421;G:139266843;T:176255048;N:37955 75       194183801 123105421 139266843 176255048 37955 SRX23156874 SRS20107295 SRA1783314 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.88896   0.09385   0.81864   0.73385   75   B   usable mapping rate illumina nextseq 3prime poly_a lexogen bulk unknown unknown   Austria 2024-01-11 Undetermined Embryo Undetermined Embryo Imprecise
29737 29737 SRR27477297 SRX23148650 SRS20099368 SRP482074 PRJNA1061456 tRAM seq: tRNA abundance and modification analysis during zebrafish embryo development PRJNA1061456 Other           eggs R4   strain:TLAB fish|isolate:NA|breed:cross of zebrafish AB and the natural variant TL Tupfel Longfin|cultivar:NA|ecotype:NA|dev stage:activated eggs|collection date:2022|geo loc name:Austria|sex:mixed|tissue:activated eggs|replicate:4|BioSampleModel:Model organism or animal                 mRNA seq of zebrafish: eggs rep4 EV09002 EV09002 RNA was extracted with Trizol and processed with QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen. 500 ng total RNA per sample. Single indexed QuantSeq libraries were QC checked on a Bioanalyzer 2100 Agilent using a High Sensitivity DNA Kit for correct insert size and quantified using Qubit dsDNA HS Assay Invitrogen. Pooled libraries were sequenced on a NextSeq500 instrument Illumina in 1x75bp single end sequencing mode     RNA-Seq TRANSCRIPTOMIC Oligo-dT SINGLE ILLUMINA NextSeq 500   SRP482074     EV09002.R1.fastq.gz fastq 546999929.0 7270092.0 EV09002.R1.fastq.gz 0:75.24 A:165415993;C:110874896;G:124384517;T:146294099;N:30424 75       165415993 110874896 124384517 146294099 30424 SRX23148650 SRS20099368 SRA1782413 Medical University of Vienna|Cell and Developmental Biology Medical University of Vienna 1 0.9065   0.11883   0.82231   0.74466   75   B   usable mapping rate illumina nextseq 3prime poly_a lexogen bulk unknown unknown   Austria 2024-01-10 Undetermined Embryo Undetermined Embryo Imprecise
67836 67836 SRR17386276 SRX13560365 SRS11453104 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         G7 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 9|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S131 S131 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_7dpi3_Clean_Data1.fq.gz Gill_7dpi3_Clean_Data2.fq.gz fastq fastq 6714068679.0 23990941.0 Gill 7dpi3 Clean Data1.fq.gz 0:139.94 1:139.92 A:1763959035;C:1585978862;G:1593569642;T:1770413859;N:147281 139 139     1763959035 1585978862 1593569642 1770413859 147281 SRX13560365 SRS11453104 SRA1350370 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.9346 0.93604 0.05602 0.05525 0.69877 0.69761 0.5006 0.50091 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
67837 67837 SRR17386277 SRX13560364 SRS11453103 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         G7 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 8|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S130 S130 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_7dpi2_Clean_Data1.fq.gz Gill_7dpi2_Clean_Data2.fq.gz fastq fastq 6651799504.0 23755238.0 Gill 7dpi2 Clean Data1.fq.gz 0:140.01 1:140.00 A:1739818732;C:1574969869;G:1589121073;T:1747742026;N:147804 140 140     1739818732 1574969869 1589121073 1747742026 147804 SRX13560364 SRS11453103 SRA1350370 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.93216 0.93204 0.05441 0.05411 0.70021 0.70017 0.49971 0.50022 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
67838 67838 SRR17386278 SRX13560363 SRS11453102 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         G7 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 7|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S129 S129 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_7dpi1_Clean_Data1.fq.gz Gill_7dpi1_Clean_Data2.fq.gz fastq fastq 4992822830.0 17852500.0 Gill 7dpi1 Clean Data1.fq.gz 0:139.84 1:139.83 A:1332570758;C:1157260526;G:1174499594;T:1328481612;N:10340 139 139     1332570758 1157260526 1174499594 1328481612 10340 SRX13560363 SRS11453102 SRA1350370 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.9281 0.93065 0.06937 0.06833 0.69033 0.68893 0.50068 0.50026 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
67839 67839 SRR17386279 SRX13560362 SRS11453101 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         G3 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 6|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S128 S128 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_3dpi3_Clean_Data1.fq.gz Gill_3dpi3_Clean_Data2.fq.gz fastq fastq 6997831816.0 24954040.0 Gill 3dpi3 Clean Data1.fq.gz 0:140.22 1:140.21 A:1830864881;C:1655547632;G:1672630082;T:1838637853;N:151368 140 140     1830864881 1655547632 1672630082 1838637853 151368 SRX13560362 SRS11453101 SRA1350370 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.93226 0.93407 0.04804 0.04727 0.71981 0.71881 0.48198 0.48333 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
67840 67840 SRR17386280 SRX13560361 SRS11453100 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         G3 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 5|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S127 S127 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_3dpi2_Clean_Data1.fq.gz Gill_3dpi2_Clean_Data2.fq.gz fastq fastq 7042078942.0 25114470.0 Gill 3dpi2 Clean Data1.fq.gz 0:140.21 1:140.19 A:1839895370;C:1667692247;G:1684937624;T:1849401074;N:152627 140 140     1839895370 1667692247 1684937624 1849401074 152627 SRX13560361 SRS11453100 SRA1350370 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.93037 0.93106 0.04787 0.04704 0.71956 0.71833 0.4789 0.48397 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
67841 67841 SRR17386281 SRX13560360 SRS11453099 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         G3 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 4|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S126 S126 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_3dpi1_Clean_Data1.fq.gz Gill_3dpi1_Clean_Data2.fq.gz fastq fastq 6795179593.0 24546282.0 Gill 3dpi1 Clean Data1.fq.gz 0:138.41 1:138.42 A:1740617128;C:1653484959;G:1667383107;T:1733667548;N:26851 138 138     1740617128 1653484959 1667383107 1733667548 26851 SRX13560360 SRS11453099 SRA1350370 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.93975 0.93965 0.04328 0.04269 0.71908 0.72032 0.47917 0.47612 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
67842 67842 SRR17386282 SRX13560359 SRS11453098 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         ck 3   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 3|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S125 S125 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_con3_Clean_Data1.fq.gz Gill_con3_Clean_Data2.fq.gz fastq fastq 6532623508.0 23299642.0 Gill con3 Clean Data1.fq.gz 0:140.19 1:140.18 A:1719338437;C:1532877064;G:1551680948;T:1728585867;N:141192 140 140     1719338437 1532877064 1551680948 1728585867 141192 SRX13560359 SRS11453098 SRA1350370 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.93634 0.93701 0.0531 0.05253 0.72936 0.72977 0.48876 0.49167 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
67843 67843 SRR17386283 SRX13560358 SRS11453097 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         ck 2   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 2|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S124 S124 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_con2_Clean_Data1.fq.gz Gill_con2_Clean_Data2.fq.gz fastq fastq 5961805472.0 21275022.0 Gill con2 Clean Data1.fq.gz 0:140.12 1:140.11 A:1562509100;C:1405898016;G:1423494829;T:1569772023;N:131504 140 140     1562509100 1405898016 1423494829 1569772023 131504 SRX13560358 SRS11453097 SRA1350370 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.93445 0.93628 0.04993 0.04957 0.73182 0.73077 0.48248 0.49573 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
67844 67844 SRR17386284 SRX13560357 SRS11453096 SRP352979 PRJNA793147 Danio rerio Raw sequence reads PRJNA793147 Whole Genome Sequencing normal RNA seq of Danio rerio         ck 1   strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:not collected|sex:not determined|tissue:Gill|replicate:replicate=biological replicate 1|BioSampleModel:Model organism or animal                 RNAseq of Danio rerio S123 S123 normal RNA seq of Danio rerio     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP352979     Gill_con1_Clean_Data1.fq.gz Gill_con1_Clean_Data2.fq.gz fastq fastq 5140938459.0 18343430.0 Gill con1 Clean Data1.fq.gz 0:140.14 1:140.12 A:1372431897;C:1190016635;G:1209788123;T:1368690050;N:11754 140 140     1372431897 1190016635 1209788123 1368690050 11754 SRX13560357 SRS11453096 SRA1350370 Northwest A&amp;F University|College of Animal Science and Technology Northwest A&F University 2 0.92642 0.93067 0.06487 0.06429 0.72529 0.72403 0.51099 0.51071 141 141 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2021-12-30 Undetermined Undetermined Gill Respiratory System
70225 70225 SRR19627917 SRX15678474 SRS13376477 SRP379658 PRJNA848069 Transcriptome analysis of ZFL cells PRJNA848069 Other the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress         9 FAC hypoxia   isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:3 0.1% O2 with FAC supplementation|BioSampleModel:Model organism or animal                 FAC hypoxia 3 FAC hypoxia 3 FAC hypoxia 3 supplemrntation with FAC and hypoxia for 5d     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379658     FAC_hypoxia-3.R1.fastq.gz FAC_hypoxia-3.R2.fastq.gz fastq fastq 6380199000.0 21267330.0 FAC hypoxia 3.R1.fastq.gz 0:150 1:150 A:1671433136;C:1499373647;G:1576679120;T:1632651556;N:61541 150 150     1671433136 1499373647 1576679120 1632651556 61541 SRX15678474 SRS13376477 SRA1435736 SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science SHANGHAI OCEAN UNIVERSITY 2 0.95363 0.95459 0.05881 0.05873 0.76631 0.76577 0.53835 0.52835 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-11 Undetermined Undetermined Liver Liver and Biliary System
70226 70226 SRR19627918 SRX15678473 SRS13376476 SRP379658 PRJNA848069 Transcriptome analysis of ZFL cells PRJNA848069 Other the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress         8 FAC hypoxia   isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:2 0.1% O2 with FAC supplementation|BioSampleModel:Model organism or animal                 FAC hypoxia 2 FAC hypoxia 2 FAC hypoxia 2 supplemrntation with FAC and hypoxia for 4d     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379658     FAC_hypoxia-2.R1.fastq.gz FAC_hypoxia-2.R2.fastq.gz fastq fastq 6101829600.0 20339432.0 FAC hypoxia 2.R1.fastq.gz 0:150 1:150 A:1574893595;C:1454868394;G:1547239872;T:1524768201;N:59538 150 150     1574893595 1454868394 1547239872 1524768201 59538 SRX15678473 SRS13376476 SRA1435736 SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science SHANGHAI OCEAN UNIVERSITY 2 0.95634 0.95739 0.05342 0.05362 0.76881 0.76749 0.53034 0.53011 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-11 Undetermined Undetermined Liver Liver and Biliary System
70227 70227 SRR19627919 SRX15678472 SRS13376475 SRP379658 PRJNA848069 Transcriptome analysis of ZFL cells PRJNA848069 Other the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress         7 FAC hypoxia   isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:1 0.1% O2 with FAC supplementation|BioSampleModel:Model organism or animal                 FAC hypoxia 1 FAC hypoxia 1 FAC hypoxia 1 supplemrntation with FAC and hypoxia for 3d     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379658     FAC_hypoxia-1.R1.fastq.gz FAC_hypoxia-1.R2.fastq.gz fastq fastq 6414187800.0 21380626.0 FAC hypoxia 1.R1.fastq.gz 0:150 1:150 A:1641953069;C:1546854359;G:1629263103;T:1596055004;N:62265 150 150     1641953069 1546854359 1629263103 1596055004 62265 SRX15678472 SRS13376475 SRA1435736 SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science SHANGHAI OCEAN UNIVERSITY 2 0.95903 0.9597 0.0736 0.0737 0.7723 0.77045 0.54827 0.55406 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-11 Undetermined Undetermined Liver Liver and Biliary System
70228 70228 SRR19627920 SRX15678471 SRS13376474 SRP379658 PRJNA848069 Transcriptome analysis of ZFL cells PRJNA848069 Other the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress         6 WT hypoxia   isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:3 0.1% O2|BioSampleModel:Model organism or animal                 WT hypoxia 3 WT hypoxia 3 WT hypoxia 3 hypoxia for 3d     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379658     WT_hypoxia-3.R1.fastq.gz WT_hypoxia-3.R2.fastq.gz fastq fastq 6841301400.0 22804338.0 WT hypoxia 3.R1.fastq.gz 0:150 1:150 A:1750979097;C:1640750395;G:1756510566;T:1692995648;N:65694 150 150     1750979097 1640750395 1756510566 1692995648 65694 SRX15678471 SRS13376474 SRA1435736 SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science SHANGHAI OCEAN UNIVERSITY 2 0.95521 0.95574 0.05844 0.05863 0.76889 0.76745 0.52412 0.5208 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-11 Undetermined Undetermined Liver Liver and Biliary System
70229 70229 SRR19627921 SRX15678470 SRS13376473 SRP379658 PRJNA848069 Transcriptome analysis of ZFL cells PRJNA848069 Other the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress         5 WT hypoxia   isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:2 0.1% O2|BioSampleModel:Model organism or animal                 WT hypoxia 2 WT hypoxia 2 WT hypoxia 2 hypoxia for 3d     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379658     WT_hypoxia-2.R1.fastq.gz WT_hypoxia-2.R2.fastq.gz fastq fastq 7296870000.0 24322900.0 WT hypoxia 2.R1.fastq.gz 0:150 1:150 A:1872215969;C:1749380281;G:1856930287;T:1818277482;N:65981 150 150     1872215969 1749380281 1856930287 1818277482 65981 SRX15678470 SRS13376473 SRA1435736 SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science SHANGHAI OCEAN UNIVERSITY 2 0.95541 0.95711 0.05508 0.05529 0.77528 0.77498 0.52698 0.52686 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-11 Undetermined Undetermined Liver Liver and Biliary System
70230 70230 SRR19627922 SRX15678469 SRS13376472 SRP379658 PRJNA848069 Transcriptome analysis of ZFL cells PRJNA848069 Other the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress         4 WT hypoxia   isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:1 0.1% O2|BioSampleModel:Model organism or animal                 WT hypoxia 1 WT hypoxia 1 WT hypoxia 1 hypoxia for 3d     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379658     WT_hypoxia-1.R1.fastq.gz WT_hypoxia-1.R2.fastq.gz fastq fastq 6122333700.0 20407779.0 WT hypoxia 1.R1.fastq.gz 0:150 1:150 A:1596743120;C:1445830065;G:1529572290;T:1550128482;N:59743 150 150     1596743120 1445830065 1529572290 1550128482 59743 SRX15678469 SRS13376472 SRA1435736 SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science SHANGHAI OCEAN UNIVERSITY 2 0.9487 0.94932 0.06381 0.0636 0.75883 0.75856 0.52097 0.52495 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-11 Undetermined Undetermined Liver Liver and Biliary System
70231 70231 SRR19627923 SRX15678468 SRS13376471 SRP379658 PRJNA848069 Transcriptome analysis of ZFL cells PRJNA848069 Other the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress         3 WT normoxia   isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:3 21% O2|BioSampleModel:Model organism or animal                 WT normoxia 3 WT normoxia 3 WT normoxia 3 normoxia for 3d     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379658     WT_normoxia-3.R1.fastq.gz WT_normoxia-3.R2.fastq.gz fastq fastq 6129969300.0 20433231.0 WT normoxia 3.R1.fastq.gz 0:150 1:150 A:1603815001;C:1446155900;G:1518644535;T:1561242175;N:111689 150 150     1603815001 1446155900 1518644535 1561242175 111689 SRX15678468 SRS13376471 SRA1435736 SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science SHANGHAI OCEAN UNIVERSITY 2 0.9511 0.94975 0.06489 0.06398 0.75653 0.75832 0.5219 0.51649 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-11 Undetermined Undetermined Liver Liver and Biliary System
70232 70232 SRR19627924 SRX15678467 SRS13376470 SRP379658 PRJNA848069 Transcriptome analysis of ZFL cells PRJNA848069 Other the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress         2 WT normoxia   isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:2 21% O2|BioSampleModel:Model organism or animal                 WT normoxia 2 WT normoxia 2 WT normoxia 2 normoxia for 3d     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379658     WT_normoxia-2.R1.fastq.gz WT_normoxia-2.R2.fastq.gz fastq fastq 6477041700.0 21590139.0 WT normoxia 2.R1.fastq.gz 0:150 1:150 A:1689277340;C:1533072440;G:1600344997;T:1654227811;N:119112 150 150     1689277340 1533072440 1600344997 1654227811 119112 SRX15678467 SRS13376470 SRA1435736 SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science SHANGHAI OCEAN UNIVERSITY 2 0.95025 0.9486 0.06318 0.06262 0.75816 0.75933 0.49794 0.50063 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-11 Undetermined Undetermined Liver Liver and Biliary System
70233 70233 SRR19627925 SRX15678466 SRS13376469 SRP379658 PRJNA848069 Transcriptome analysis of ZFL cells PRJNA848069 Other the transcriptome analysis of ZFL zebrafish liver cells under hypoxia stress         1 WT normoxia   isolate:liver cell|dev stage:mature|sex:pooled male and female|tissue:liver|cell line:ZFL|sample type:cell culture|treatment:1 21% O2|BioSampleModel:Model organism or animal                 WT normoxia 1 WT normoxia 1 WT normoxia 1 normoxia for 3d     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina NovaSeq 6000   SRP379658     WT_normoxia-1.R1.fastq.gz WT_normoxia-1.R2.fastq.gz fastq fastq 7612447200.0 25374824.0 WT normoxia 1.R1.fastq.gz 0:150 1:150 A:1995483560;C:1776838669;G:1907898454;T:1932088660;N:137857 150 150     1995483560 1776838669 1907898454 1932088660 137857 SRX15678466 SRS13376469 SRA1435736 SHANGHAI OCEAN UNIVERSITY|College of Fisheries and Life Science SHANGHAI OCEAN UNIVERSITY 2 0.94638 0.94688 0.06242 0.06151 0.76506 0.76524 0.53233 0.53157 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a unknown bulk unknown unknown   China 2022-06-11 Undetermined Undetermined Liver Liver and Biliary System
70307 70307 SRR19661767 SRX15711495 SRS13405890 SRP381845 PRJNA849172 Danio rerio Raw sequence reads PRJNA849172 Other Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf.         96h3 S3 L004 R1   strain:not collected|isolate:71|age:not collected|dev stage:function|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal                 71 96h3 S3 L004 R1 96h3 S3 L004 R1 sorting     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina Genome Analyzer IIx   SRP381845     96h3_S3_L004_R1_001.fastq.gz 96h3_S3_L004_R2_001.fastq.gz fastq fastq 724691152.0 3367984.0 96h3 S3 L004 R1 001.fastq.gz 0:107.15 1:108.02 A:197062569;C:164860065;G:168446417;T:193112518;N:1209583 107 108     197062569 164860065 168446417 193112518 1209583 SRX15711495 SRS13405890 SRA1437609 Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat Institute of Hydrobiology, Chinese Academy of Sciences 2 0.74397 0.74651 0.05835 0.05714 0.92417 0.92638 0.5822 0.56964 151 151 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   China 2022-06-15 Undetermined Undetermined Liver Liver and Biliary System
70308 70308 SRR19661768 SRX15711494 SRS13405889 SRP381845 PRJNA849172 Danio rerio Raw sequence reads PRJNA849172 Other Liver is an essential organ with multiple biological functions including metabolism detoxification digestion and homeostasis in vertebrates. Zebrafish Danio rerio is an excellent genetic model system to study both processes of liver development and liver regeneration while the molecular mechanism of zebrafish early liver development remain unclear. In this study we performed comparative transcriptome analysis of liver cells which were sorting by flow cytometry in different time points i.e. 60 hpf 72 hpf or 96 hpf.         96h3 S3 L002 R1   strain:not collected|isolate:67|age:not collected|dev stage:function|sex:not determined|tissue:liver|BioSampleModel:Model organism or animal                 67 96h3 S3 L002 R1 96h3 S3 L002 R1 sorting     RNA-Seq TRANSCRIPTOMIC Oligo-dT PAIRED ILLUMINA Illumina Genome Analyzer IIx   SRP381845     96h3_S3_L002_R1_001.fastq.gz 96h3_S3_L002_R2_001.fastq.gz fastq fastq 727527211.0 3371310.0 96h3 S3 L002 R1 001.fastq.gz 0:107.54 1:108.26 A:197175975;C:166079247;G:169466504;T:193755887;N:1049598 107 108     197175975 166079247 169466504 193755887 1049598 SRX15711494 SRS13405889 SRA1437609 Institute of Hydrobiology, Chinese Academy of Sciences|Center for Molecular and Cellular Biology of Aquat Institute of Hydrobiology, Chinese Academy of Sciences 2 0.74895 0.75162 0.05798 0.05783 0.92437 0.92624 0.5779 0.58024 151 151 B B biological fallback assumption illumina early_illumina unknown poly_a unknown bulk unknown unknown   China 2022-06-15 Undetermined Undetermined Liver Liver and Biliary System

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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");;