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
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,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,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,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,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,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,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,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,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,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,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,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
24784,SRR25502048,SRX21232930,SRS18488024,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05316 MCK mut3,GSM7678168,,tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05316 MCK mut3,Data were QC’d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+  mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf,GSM7678168,GSM7678168: Sample 15 05316 MCK mut3; Danio rerio; RNA Seq,GSM7678168 r1,GSM7678168,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05316_MCK_mut3_GTGCTT_L002_R1_001.fastq.gz 15-05316_MCK_mut3_GTGCTT_L002_R2_001.fastq.gz,fastq fastq,4329868620.0,20618422.0,GSM7678168 r1,0:105 1:105,A:1075032412;C:1077085067;G:1119735718;T:1057797736;N:217687,105,105,,,1075032412,1077085067,1119735718,1057797736,217687,SRX21232930,SRS18488024,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.78961,0.91048,0.20166,0.23232,0.81556,0.81115,0.59478,0.59379,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System
24785,SRR25502049,SRX21232929,SRS18488023,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05316 MCK mut2,GSM7678167,,tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05316 MCK mut2,Data were QC’d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+  mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf,GSM7678167,GSM7678167: Sample 15 05316 MCK mut2; Danio rerio; RNA Seq,GSM7678167 r1,GSM7678167,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05316_MCK_mut2_ACCTCA_L002_R1_001.fastq.gz 15-05316_MCK_mut2_ACCTCA_L002_R2_001.fastq.gz,fastq fastq,4444374270.0,21163687.0,GSM7678167 r1,0:105 1:105,A:1114919906;C:1098541058;G:1145427151;T:1085262902;N:223253,105,105,,,1114919906,1098541058,1145427151,1085262902,223253,SRX21232929,SRS18488023,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.74961,0.90068,0.18596,0.22057,0.81115,0.80754,0.5829,0.58615,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System
24786,SRR25502050,SRX21232928,SRS18488022,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05316 MCK mut1,GSM7678166,,tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05316 MCK mut1,Data were QC’d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+  mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+  mpx+ granulocytes|genotype:zbtb11 mutant mne|age:48 hpf,GSM7678166,GSM7678166: Sample 15 05316 MCK mut1; Danio rerio; RNA Seq,GSM7678166 r1,GSM7678166,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05316_MCK_mut1_GCACTA_L002_R1_001.fastq.gz 15-05316_MCK_mut1_GCACTA_L002_R2_001.fastq.gz,fastq fastq,4459467180.0,21235558.0,GSM7678166 r1,0:105 1:105,A:1206908747;C:1012207561;G:1060393698;T:1179731376;N:225798,105,105,,,1206908747,1012207561,1060393698,1179731376,225798,SRX21232928,SRS18488022,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.75719,0.88462,0.20719,0.24095,0.78559,0.77914,0.50538,0.55691,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System
24787,SRR25502051,SRX21232927,SRS18488021,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05315 MCK WT3,GSM7678165,,tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05315 MCK WT3,Data were QC’d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+  mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf,GSM7678165,GSM7678165: Sample 15 05315 MCK WT3; Danio rerio; RNA Seq,GSM7678165 r1,GSM7678165,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05315_MCK_WT3_AGTGAG_L002_R1_001.fastq.gz 15-05315_MCK_WT3_AGTGAG_L002_R2_001.fastq.gz,fastq fastq,3925329240.0,18692044.0,GSM7678165 r1,0:105 1:105,A:1022654212;C:930239389;G:973328942;T:998905803;N:200894,105,105,,,1022654212,930239389,973328942,998905803,200894,SRX21232927,SRS18488021,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.75647,0.89377,0.19165,0.22718,0.81057,0.80501,0.51173,0.54819,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System
24788,SRR25502052,SRX21232926,SRS18488020,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05314 MCK WT2,GSM7678164,,tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05314 MCK WT2,Data were QC’d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+  mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf,GSM7678164,GSM7678164: Sample 15 05314 MCK WT2; Danio rerio; RNA Seq,GSM7678164 r1,GSM7678164,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05314_MCK_WT2_TGGTGA_L002_R2_001.fastq.gz 15-05314_MCK_WT2_TGGTGA_L002_R1_001.fastq.gz,fastq fastq,4100489820.0,19526142.0,GSM7678164 r1,0:105 1:105,A:1022482319;C:1016090490;G:1063619365;T:998086417;N:211229,105,105,,,1022482319,1016090490,1063619365,998086417,211229,SRX21232926,SRS18488020,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.76378,0.90522,0.20093,0.23619,0.82467,0.82049,0.57261,0.562,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System
24789,SRR25502053,SRX21232925,SRS18488019,SRP453114,PRJNA1001808,The Pu.1 target gene Zbtb11 regulates neutrophil development through its integrase like HHCC zinc finger,GSE239949,Transcriptome Analysis,From a forward genetic screen in zebrafish  we identified the transcription factor  ZBTB11  as critical for basal and emergency granulopoiesis and showed that ZBTB11 sits in a pathway directly downstream of master myeloid regulators including PU.1  GFI1 and CEBPa. To better understand target genes regulated by Zbtb11  RNAseq profiling was performed in neutrophils from WT and Zbtb11 mutant zebrafish. Overall design: At 48 hpf  single cell suspensions were prepared from either pooled WT embryos or from pooled phenotype sorted zbtb11 mutant embryos. Neutrophils were FACS sorted on the basis of bright fluorescence for the transgenic neutrophil markers mpx:EGFP or lyz:dsRed into RNALater. N=3 biologically independent pools of neutrophils were obtained from WT and from zbtb11 mutant embryos and used for preparation of RNA and sequencing libraries.,,pubmed:28382966,,Sample 15 05313 MCK WT1,GSM7678163,,tissue:lyz+  mpx+ granulocytes|cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf|geo loc name:missing|collection date:missing,Sample 15 05313 MCK WT1,Data were QC’d using FastQC  ends trimmed using Trimgalore and trimmed sequence aligned to the zebrafish genome GRCz10 using STAR. Counts were derived using HTseq count and differentially expressed genes determined using limma + voom using Degust v0.21 David R. Powell  Victorian Bioinformatics Consortium  Australia. Assembly: genome GRCz10 Supplementary files format and content: Excel spreadsheet includes HT Seq counts for each sample,lyz+  mpx+ granulocytes,,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,cell type:lyz+  mpx+ granulocytes|genotype:wild type|age:48 hpf,GSM7678163,GSM7678163: Sample 15 05313 MCK WT1; Danio rerio; RNA Seq,GSM7678163 r1,GSM7678163,1,RNA was extracted from sorted cells using RNeasy Micro Qiagen. Unstranded barcoded libraries were prepared using total RNA and Nugen Ovation RNA Seq system V2 for amplification and cDNA generation  followed by Ovation Ultralow System V2 for library preparation.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 1500,,SRP453114,,,15-05313_MCK_WT1_AACCAG_L002_R1_001.fastq.gz 15-05313_MCK_WT1_AACCAG_L002_R2_001.fastq.gz,fastq fastq,4135721100.0,19693910.0,GSM7678163 r1,0:105 1:105,A:1048700719;C:1014162128;G:1070155053;T:1002495763;N:207437,105,105,,,1048700719,1014162128,1070155053,1002495763,207437,SRX21232925,SRS18488019,SRA1685493,"Rural Clinical Sciences, La Trobe University","Rural Clinical Sciences, La Trobe University",2,0.70974,0.9073,0.1771,0.22534,0.82483,0.81625,0.56311,0.55183,105,105,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Australia,2023-08-03,Hatching,Embryo,Blood,Hematopoietic System
30066,SRR27676305,SRX23343658,SRS20205511,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;CUT TAG,,,,,smart seq of setdb1b mt 2,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 2|id</u><u>:9</u><u>|BioSampleModel:Model organism or animal,,,,,,,,,smart seq of setdb1b mt 2,smart seq of setdb1b mt 2,smart seq of setdb1b mt 2,smart seq of setdb1b mt of replicate 2,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485121,,,smart-seq of setdb1b mt_2_R2.fastq.gz.gz smart-seq of setdb1b mt_2_R1.fastq.gz.gz,fastq fastq,11957458200.0,39858194.0,smart seq of setdb1b mt 2 R1.fastq.gz.gz,0:150 1:150,A:3692371435;C:1893324720;G:2810967928;T:3560751613;N:42504,150,150,,,3692371435,1893324720,2810967928,3560751613,42504,SRX23343658,SRS20205511,SRA1789215,East China Normal University|Institute of Biomedical Sciences,East China Normal University,2,0.76332,0.82639,0.22191,0.23939,0.87093,0.87117,0.59757,0.60008,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-01-22,Larval,Larval,Blood,Hematopoietic System
30067,SRR27676306,SRX23343657,SRS20205510,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;CUT TAG,,,,,smart seq of setdb1b mt 1,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 1|id</u><u>:8</u><u>|BioSampleModel:Model organism or animal,,,,,,,,,smart seq of setdb1b mt 1,smart seq of setdb1b mt 1,smart seq of setdb1b mt 1,smart seq of setdb1b mt of replicate 1,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485121,,,smart-seq of setdb1b mt_1_R1.fastq.gz.gz smart-seq of setdb1b mt_1_R2.fastq.gz.gz,fastq fastq,9537788700.0,31792629.0,smart seq of setdb1b mt 1 R1.fastq.gz.gz,0:150 1:150,A:3044433376;C:1450924984;G:2142347814;T:2900047705;N:34821,150,150,,,3044433376,1450924984,2142347814,2900047705,34821,SRX23343657,SRS20205510,SRA1789215,East China Normal University|Institute of Biomedical Sciences,East China Normal University,2,0.74808,0.79354,0.21148,0.22263,0.87405,0.87545,0.58431,0.58836,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-01-22,Larval,Larval,Blood,Hematopoietic System
30068,SRR27676307,SRX23343656,SRS20205509,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;CUT TAG,,,,,smart seq of setdb1b control 2,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 2|id</u><u>:7</u><u>|BioSampleModel:Model organism or animal,,,,,,,,,smart seq of setdb1b control 2,smart seq of setdb1b control 2,smart seq of setdb1b control 2,smart seq of setdb1b control of replicate 2,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485121,,,smart-seq of setdb1b control_2_R1.fastq.gz.gz smart-seq of setdb1b control_2_R2.fastq.gz.gz,fastq fastq,7963596600.0,26545322.0,smart seq of setdb1b control 2 R1.fastq.gz.gz,0:150 1:150,A:2522387513;C:1217203824;G:1776725064;T:2447251088;N:29111,150,150,,,2522387513,1217203824,1776725064,2447251088,29111,SRX23343656,SRS20205509,SRA1789215,East China Normal University|Institute of Biomedical Sciences,East China Normal University,2,0.77121,0.80578,0.22631,0.23757,0.85953,0.86298,0.58219,0.58387,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-01-22,Larval,Larval,Blood,Hematopoietic System
30069,SRR27676308,SRX23343655,SRS20205508,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;CUT TAG,,,,,smart seq of setdb1b control 1,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:96hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 1|id</u><u>:6</u><u>|BioSampleModel:Model organism or animal,,,,,,,,,smart seq of setdb1b control 1,smart seq of setdb1b control 1,smart seq of setdb1b control 1,smart seq of setdb1b control of replicate 1,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485121,,,smart-seq of setdb1b control_1_R2.fastq.gz.gz smart-seq of setdb1b control_1_R1.fastq.gz.gz,fastq fastq,11867370900.0,39557903.0,smart seq of setdb1b control 1 R1.fastq.gz.gz,0:150 1:150,A:3969636478;C:1678555005;G:2520767064;T:3698368678;N:43675,150,150,,,3969636478,1678555005,2520767064,3698368678,43675,SRX23343655,SRS20205508,SRA1789215,East China Normal University|Institute of Biomedical Sciences,East China Normal University,2,0.73517,0.73836,0.23036,0.23129,0.86407,0.86675,0.59652,0.59533,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-01-22,Larval,Larval,Blood,Hematopoietic System
30070,SRR27676309,SRX23343654,SRS20205505,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;CUT TAG,,,,,RNA seq of atf7ip mt 2,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 2|id</u><u>:5</u><u>|BioSampleModel:Model organism or animal,,,,,,,,,mRNAseq of atf7ip mt,RNA seq of atf7ip mt 2,RNA seq of atf7ip mt 2,mRNAseq of atf7ip mt of replicate 2,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485121,,,RNA-seq of atf7ip mt_2_R2.fastq.gz.gz RNA-seq of atf7ip mt_2_R1.fastq.gz.gz,fastq fastq,2881485000.0,9604950.0,RNA seq of atf7ip mt 2 R1.fastq.gz.gz,0:150 1:150,A:714870764;C:672086586;G:819085358;T:675370688;N:71604,150,150,,,714870764,672086586,819085358,675370688,71604,SRX23343654,SRS20205505,SRA1789215,East China Normal University|Institute of Biomedical Sciences,East China Normal University,2,0.95105,0.94782,0.0877,0.08683,0.67838,0.68085,0.4943,0.49308,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-01-22,Larval,Larval,Blood,Hematopoietic System
30071,SRR27676310,SRX23343653,SRS20205506,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;CUT TAG,,,,,RNA seq of atf7ip mt 1,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 1|id</u><u>:4</u><u>|BioSampleModel:Model organism or animal,,,,,,,,,mRNAseq of atf7ip mt,RNA seq of atf7ip mt 1,RNA seq of atf7ip mt 1,mRNAseq of atf7ip mt of replicate 1,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485121,,,RNA-seq of atf7ip mt_1_R2.fastq.gz.gz RNA-seq of atf7ip mt_1_R1.fastq.gz.gz,fastq fastq,5215476900.0,17384923.0,RNA seq of atf7ip mt 1 R1.fastq.gz.gz,0:150 1:150,A:1305694077;C:1250588317;G:1437727006;T:1221425310;N:42190,150,150,,,1305694077,1250588317,1437727006,1221425310,42190,SRX23343653,SRS20205506,SRA1789215,East China Normal University|Institute of Biomedical Sciences,East China Normal University,2,0.95459,0.9546,0.09418,0.0933,0.67353,0.67643,0.49356,0.49989,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-01-22,Larval,Larval,Blood,Hematopoietic System
30072,SRR27676311,SRX23343652,SRS20205507,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;CUT TAG,,,,,RNA seq of atf7ip control 3,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 3|id</u><u>:3</u><u>|BioSampleModel:Model organism or animal,,,,,,,,,mRNAseq of atf7ip control,RNA seq of atf7ip control 3,RNA seq of atf7ip control 3,mRNAseq of atf7ip control of replicate 3,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485121,,,RNA-seq of atf7ip control_3_R2.fastq.gz.gz RNA-seq of atf7ip control_3_R1.fastq.gz.gz,fastq fastq,6742549200.0,22475164.0,RNA seq of atf7ip control 3 R1.fastq.gz.gz,0:150 1:150,A:1698977237;C:1657996046;G:1800441072;T:1584967439;N:167406,150,150,,,1698977237,1657996046,1800441072,1584967439,167406,SRX23343652,SRS20205507,SRA1789215,East China Normal University|Institute of Biomedical Sciences,East China Normal University,2,0.96114,0.9601,0.05191,0.05152,0.69219,0.69398,0.48597,0.48633,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-01-22,Larval,Larval,Blood,Hematopoietic System
30073,SRR27676312,SRX23343651,SRS20205504,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;CUT TAG,,,,,RNA seq of atf7ip control 2,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 2|id</u><u>:2</u><u>|BioSampleModel:Model organism or animal,,,,,,,,,mRNAseq of atf7ip control,RNA seq of atf7ip control 2,RNA seq of atf7ip control 2,mRNAseq of atf7ip control of replicate 2,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485121,,,RNA-seq of atf7ip control_2_R2.fastq.gz.gz RNA-seq of atf7ip control_2_R1.fastq.gz.gz,fastq fastq,6962540400.0,23208468.0,RNA seq of atf7ip control 2 R1.fastq.gz.gz,0:150 1:150,A:1794934846;C:1640272261;G:1855642638;T:1671491013;N:199642,150,150,,,1794934846,1640272261,1855642638,1671491013,199642,SRX23343651,SRS20205504,SRA1789215,East China Normal University|Institute of Biomedical Sciences,East China Normal University,2,0.95531,0.95468,0.05949,0.05926,0.71019,0.71129,0.50401,0.50622,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-01-22,Larval,Larval,Blood,Hematopoietic System
30074,SRR27676313,SRX23343650,SRS20205503,SRP485121,PRJNA1067443,RNA seq&smart seq&CUT TAG,PRJNA1067443,Other,RNA seq&amp;smart seq&amp;CUT TAG,,,,,RNA seq of atf7ip control 1,,strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:missing|dev stage:72hpf|collection date:missing|geo loc name:missing|sex:pooled male and female|tissue:hematopoietic stem and progenitor cell|replicate:replicate = biological replicate 1|id</u><u>:1</u><u>|BioSampleModel:Model organism or animal,,,,,,,,,mRNAseq of atf7ip control,RNA seq of atf7ip control 1,RNA seq of atf7ip control 1,mRNAseq of atf7ip control of replicate 1,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485121,,,RNA-seq of atf7ip control_1_R1.fastq.gz.gz RNA-seq of atf7ip control_1_R2.fastq.gz.gz,fastq fastq,8543359800.0,28477866.0,RNA seq of atf7ip control 1 R1.fastq.gz.gz,0:150 1:150,A:2200058170;C:2049588985;G:2219737118;T:2073765388;N:210139,150,150,,,2200058170,2049588985,2219737118,2073765388,210139,SRX23343650,SRS20205503,SRA1789215,East China Normal University|Institute of Biomedical Sciences,East China Normal University,2,0.96026,0.95618,0.05646,0.05613,0.68424,0.6856,0.48963,0.49334,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-01-22,Larval,Larval,Blood,Hematopoietic System
31522,SRR28418937,SRX24023264,SRS20817617,SRP497230,PRJNA1090848,Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq],GSE262188,Transcriptome Analysis,Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however  the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision  its dynamic and role in HSPC development is poorly investigated. Here  we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably  PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions  which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then  conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors  such as PU.1 .,,pubmed:38886858,,HPSC rep3 RNA seq 3month,GSM8159257,,source name:hematopoietic stem cell|tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry|geo loc name:missing|collection date:missing,HPSC rep3 RNA seq 3month,The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering  high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample,hematopoietic stem cell,,Briefly  ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1×  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina,,tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry,GSM8159257,GSM8159257: HPSC rep3 RNA seq 3month; Danio rerio; RNA Seq,GSM8159257 r1,GSM8159257,1,Briefly  ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1×  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP497230,,loader:fastq load.py,RNA-seq_Adult_HPSC_rep3_R1.fq.gz RNA-seq_Adult_HPSC_rep3_R2.fq.gz,fastq fastq,11621758500.0,38739195.0,GSM8159257 r1,0:150 1:150,A:3144084931;C:2632272493;G:2693165513;T:3151802925;N:432638,150,150,,,3144084931,2632272493,2693165513,3151802925,432638,SRX24023264,SRS20817617,SRA1831889,South China University of Technology,South China University of Technology,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-03-21,Adult,Adult,Blood,Hematopoietic System
31523,SRR28418938,SRX24023263,SRS20817616,SRP497230,PRJNA1090848,Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq],GSE262188,Transcriptome Analysis,Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however  the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision  its dynamic and role in HSPC development is poorly investigated. Here  we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably  PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions  which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then  conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors  such as PU.1 .,,pubmed:38886858,,HPSC rep2 RNA seq 3month,GSM8159256,,source name:hematopoietic stem cell|tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry|geo loc name:missing|collection date:missing,HPSC rep2 RNA seq 3month,The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering  high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample,hematopoietic stem cell,,Briefly  ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1×  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina,,tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry,GSM8159256,GSM8159256: HPSC rep2 RNA seq 3month; Danio rerio; RNA Seq,GSM8159256 r1,GSM8159256,1,Briefly  ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1×  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP497230,,loader:fastq load.py,RNA-seq_Adult_HPSC_rep2_R1.fq.gz RNA-seq_Adult_HPSC_rep2_R2.fq.gz,fastq fastq,9951217200.0,33170724.0,GSM8159256 r1,0:150 1:150,A:2755384814;C:2209586340;G:2237522365;T:2748523249;N:200432,150,150,,,2755384814,2209586340,2237522365,2748523249,200432,SRX24023263,SRS20817616,SRA1831889,South China University of Technology,South China University of Technology,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-03-21,Adult,Adult,Blood,Hematopoietic System
31524,SRR28418939,SRX24023262,SRS20817615,SRP497230,PRJNA1090848,Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA seq],GSE262188,Transcriptome Analysis,Development of hematopoietic stem and progenitor cells HSPC is a multi staged complex process that conserved between zebrafish and mammals; however  the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision  its dynamic and role in HSPC development is poorly investigated. Here  we performed chromatin structure and multi omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably  PU.1 was identified as a potential factor mediating formation of promoter involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions  which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision. Overall design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC we get RNA seq results from adult sample. Then  conjoint analysis of RNA seq with other datas can reveal the function of transcriptional factors  such as PU.1 .,,pubmed:38886858,,HPSC rep1 RNA seq 3month,GSM8159255,,source name:hematopoietic stem cell|tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry|geo loc name:missing|collection date:missing,HPSC rep1 RNA seq 3month,The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatspv.0.23.2 withpaired end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed. post filtering  high quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters. FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform. Assembly: GRCz10 Supplementary files format and content: tab delimited text file includes raw counts for each Sample,hematopoietic stem cell,,Briefly  ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1×  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina,,tissue:hematopoietic stem cell|cell line:TgCD41:GFP gata1:dsRed|cell type:hematopoietic stem cell|genotype:CD41+gata1 |time:3month|treatment:flow cytometry,GSM8159255,GSM8159255: HPSC rep1 RNA seq 3month; Danio rerio; RNA Seq,GSM8159255 r1,GSM8159255,1,Briefly  ∼10 ng of total RNA for each sample was utilized for first strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase 100 U  RNase inhibitor 10 U  dNTP mix 10 mM each  SS III first strand buffer 1×  DTT 5 mM  betaine 1 M  MgCl2 6 mM and TSO 1 μM. The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP497230,,loader:fastq load.py,RNA-seq_Adult_HPSC_rep1_R1.fq.gz RNA-seq_Adult_HPSC_rep1_R2.fq.gz,fastq fastq,11096617200.0,36988724.0,GSM8159255 r1,0:150 1:150,A:3071303610;C:2460399138;G:2510824334;T:3053621175;N:468943,150,150,,,3071303610,2460399138,2510824334,3053621175,468943,SRX24023262,SRS20817615,SRA1831889,South China University of Technology,South China University of Technology,,,,,,,,,,,,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2024-03-21,Adult,Adult,Blood,Hematopoietic System
37103,SRR891512,SRX298192,SRS673882,SRP024369,PRJNA207719,Tissue specific transcriptome profiling of zebrafish,PRJNA207719,Other,Tissue specific transcriptome profiling of zebrafish.,,,,,Danio rerio blood,,sex:missing|strain:wild type|tissue:blood|health state:normal|collection date:2013|geo loc name:India|biomaterial provider:CSIR Institute of Genomics and Integrative Biology|age:adult|BioSampleModel:Model organism or animal,,,,,,,,,Tissue specific transcriptome of zebrafish,Transcriptome of zebrafish Danio rerio blood,zebrafish blood,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,PAIRED,ILLUMINA,Illumina Genome Analyzer IIx,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>102</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>52</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP024369,,,lane6_NoIndex_L006_R2_cat.fastq lane6_NoIndex_L006_R1_cat.fastq,fastq fastq,2122070832.0,20804616.0,Transcriptome of zebrafish Danio rerio blood,0:51 1:51,A:508869849;C:550502747;G:580539251;T:481927903;N:231082,51,51,,,508869849,550502747,580539251,481927903,231082,SRX298192,SRS673882,SRA089174,CSIR-IGIB,CSIR-Institute of Genomics and Integrative Biology CSIR-Institute of Genomics and Integrative Biology,2,0.78255,0.77496,0.03257,0.03239,0.75672,0.75542,0.44135,0.44382,51,51,B,B,biological fallback assumption,illumina,early_illumina,unknown,random_priming,unknown,bulk,unknown,unknown,,India,2013-06-10,Adult,Adult,Blood,Hematopoietic System
38257,SRR1609758,SRX730411,SRS719632,SRP048807,PRJNA263496,Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish,GSE62221,Transcriptome Analysis,The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28°C to mild 18°C and severe 10°C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures,,pubmed:26227973,,spleen10,GSM1523053,,source name:spleen|tissue:spleen|temperature:10°C|strain:Tubingen|age:6 mpf,spleen10,Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,spleen,fish were maintained 12h to adapt low temperatures and then killed by pithing,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:spleen|temperature:10°C|strain:Tubingen|age:6 mpf,GSM1523053,GSM1523053: spleen10; Danio rerio; RNA Seq,GSM1523053,,1,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1523053,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP048807,,,spleen10_2.fq.gz spleen10_1.fq.gz,fastq fastq,5089614600.0,25448073.0,GSM1523053 r1,0:100 1:100,A:1315179584;C:1230198758;G:1227165313;T:1316987828;N:83117,100,100,,,1315179584,1230198758,1227165313,1316987828,83117,SRX730411,SRS719632,SRA189240,GEO,Shanghai Ocean University,2,0.9612,0.9561,0.04114,0.04116,0.77518,0.77926,0.42558,0.42199,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2014-10-09,Adult,Adult,Spleen,Hematopoietic System
38258,SRR1609757,SRX730410,SRS719631,SRP048807,PRJNA263496,Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish,GSE62221,Transcriptome Analysis,The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28°C to mild 18°C and severe 10°C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures,,pubmed:26227973,,spleen18,GSM1523052,,source name:spleen|tissue:spleen|temperature:18°C|strain:Tubingen|age:6 mpf,spleen18,Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,spleen,fish were maintained 12h to adapt low temperatures and then killed by pithing,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:spleen|temperature:18°C|strain:Tubingen|age:6 mpf,GSM1523052,GSM1523052: spleen18; Danio rerio; RNA Seq,GSM1523052,,1,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1523052,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP048807,,,spleen18_1.fq.gz spleen18_2.fq.gz,fastq fastq,4494055400.0,22470277.0,GSM1523052 r1,0:100 1:100,A:1167396911;C:1079923943;G:1078183614;T:1168479101;N:71831,100,100,,,1167396911,1079923943,1078183614,1168479101,71831,SRX730410,SRS719631,SRA189240,GEO,Shanghai Ocean University,2,0.96809,0.96224,0.02675,0.02626,0.80012,0.80369,0.28419,0.28966,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2014-10-09,Adult,Adult,Spleen,Hematopoietic System
38259,SRR1609756,SRX730409,SRS719630,SRP048807,PRJNA263496,Global identification of the gene networks and cis regulatory elements of the cold response in zebrafish,GSE62221,Transcriptome Analysis,The transcriptional programs of ectothermic teleosts are directly influenced by water temperature. Although various cold responsive transcriptional patterns have been determined in fishes  the systematic molecular networks governing the temperature responses are still unknown. We profiled the transcriptional responses in eight tissues of zebrafish exposed to graded cold temperatures  ranging from normal 28°C to mild 18°C and severe 10°C cold  using RNA seq. The tissues varied in the number of cold responsive genes  of which the kidney appeared to be most sensitive  whereas the brain was the least. Fuzzy k means clustering revealed 34 gene clusters of distinct expression patterns  demonstrating diverse tissue specific responses in conjunction with multiple aspects of ubiquitous cross tissue responses to cold. Thirty one GO terms were over represented upon cold treatment. These terms are involved in basic cellular processes  such as RNA splicing and proton transport  as well tissue specific processes  such as ‘negative regulation of endopeptidase activity’ in the kidney. To identify the cis regulatory elements governing the concerted cold responses  the promoters of the genes that demonstrated strong co regulation were analyzed using an enriched motif discovery program  DREME. Eleven motifs  6 known and 5 novel  were identified. These motifs belong to the genes corresponding to the 16 over represented GO terms identified above. Some motifs  such as the AP 1 and STAT1 binding sites  are known to be stress responsive. By integrating comprehensive cold induced transcriptional changes with a cis motif identification tool  we identified genome wide regulatory networks for the cold response in zebrafish. The identified networks provided new insights into molecular mechanisms of thermal responses in teleosts. Overall design: Examination of gene expression of 24 samples eight tissues at three temperatures,,pubmed:26227973,,spleen28,GSM1523051,,source name:spleen|tissue:spleen|temperature:28°C|strain:Tubingen|age:6 mpf,spleen28,Illumina Casava1.7 software used for basecalling. The raw reads were assessed for their quality using FASTX toolkit http://hannonlab.cshl.edu/fastx toolkit. Reads with a Phred quality score less than 5 over the 95% nt would be removed. TopHat was used to map the reads to the reference genome. Then HTSeq count http://www huber.embl.de/users/anders/HTSeq/doc/overview.html  which is a python based script  was then applied to count the number of reads mapped to the genes. Reads Per Kilobase of exon per Megabase of library size RPKM were calculated using a protocol from Chepelev et al.  Nucleic Acids Research  2009. In short  exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: zebrafish genome sequence and gtf files were downloaded from the Ensembl release 72 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...,spleen,fish were maintained 12h to adapt low temperatures and then killed by pithing,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,,tissue:spleen|temperature:28°C|strain:Tubingen|age:6 mpf,GSM1523051,GSM1523051: spleen28; Danio rerio; RNA Seq,GSM1523051,,1,Tissues were removed  flash frozen on dry ice  and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM1523051,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP048807,,,spleen28_2.fq.gz spleen28_1.fq.gz,fastq fastq,3499734800.0,17498674.0,GSM1523051 r1,0:100 1:100,A:912324481;C:841616616;G:837795621;T:907938558;N:59524,100,100,,,912324481,841616616,837795621,907938558,59524,SRX730409,SRS719630,SRA189240,GEO,Shanghai Ocean University,2,0.95732,0.95047,0.04767,0.04837,0.75507,0.7613,0.5152,0.51185,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,China,2014-10-09,Adult,Adult,Spleen,Hematopoietic System
40807,SRR3381847,SRX1704280,SRS1396343,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 3 blood,GSM2122871,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 3 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122871,GSM2122871: Treated 3 blood; Danio rerio; RNA Seq,GSM2122871,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s6_1_GSLv3-7_38_SL139795.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_38_SL139795.fastq.gz,fastq fastq,1349428600.0,13494286.0,GSM2122871 r1,0:50 1:50,A:391483366;C:283353944;G:288253777;T:386190051;N:147462,50,50,,,391483366,283353944,288253777,386190051,147462,SRX1704280,SRS1396343,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.88853,0.89204,0.22815,0.23941,0.73917,0.73979,0.53637,0.53893,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40808,SRR3381848,SRX1704280,SRS1396343,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 3 blood,GSM2122871,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 3 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122871,GSM2122871: Treated 3 blood; Danio rerio; RNA Seq,GSM2122871,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s5_1_GSLv3-7_38_SL139795.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_38_SL139795.fastq.gz,fastq fastq,1020366100.0,10203661.0,GSM2122871 r2,0:50 1:50,A:296023946;C:213173706;G:215342808;T:295806226;N:19414,50,50,,,296023946,213173706,215342808,295806226,19414,SRX1704280,SRS1396343,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.88792,0.89203,0.21382,0.24279,0.7652,0.7444,0.53618,0.54254,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40809,SRR3381849,SRX1704280,SRS1396343,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 3 blood,GSM2122871,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 3 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122871,GSM2122871: Treated 3 blood; Danio rerio; RNA Seq,GSM2122871,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s6_1_GSLv3-7_38_SL139795.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_38_SL139795.fastq.gz,fastq fastq,1008129000.0,10081290.0,GSM2122871 r3,0:50 1:50,A:292536545;C:210308039;G:212529262;T:292736486;N:18668,50,50,,,292536545,210308039,212529262,292736486,18668,SRX1704280,SRS1396343,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.88682,0.89249,0.21573,0.24321,0.7657,0.74456,0.53948,0.54456,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40810,SRR3381850,SRX1704280,SRS1396343,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 3 blood,GSM2122871,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 3 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122871,GSM2122871: Treated 3 blood; Danio rerio; RNA Seq,GSM2122871,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s5_1_GSLv3-7_38_SL139795.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_38_SL139795.fastq.gz,fastq fastq,1348814000.0,13488140.0,GSM2122871 r4,0:50 1:50,A:391186639;C:283404571;G:288274584;T:385756613;N:191593,50,50,,,391186639,283404571,288274584,385756613,191593,SRX1704280,SRS1396343,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.88673,0.89303,0.22875,0.24107,0.74276,0.74134,0.53585,0.54514,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40811,SRR3381843,SRX1704279,SRS1396344,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 2 blood,GSM2122870,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 2 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122870,GSM2122870: Treated 2 blood; Danio rerio; RNA Seq,GSM2122870,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s6_1_GSLv3-7_37_SL139794.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_37_SL139794.fastq.gz,fastq fastq,1251398700.0,12513987.0,GSM2122870 r1,0:50 1:50,A:383059535;C:243111832;G:248681985;T:376401618;N:143730,50,50,,,383059535,243111832,248681985,376401618,143730,SRX1704279,SRS1396344,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.86725,0.86597,0.35725,0.37228,0.74312,0.73961,0.53136,0.53663,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40812,SRR3381844,SRX1704279,SRS1396344,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 2 blood,GSM2122870,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 2 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122870,GSM2122870: Treated 2 blood; Danio rerio; RNA Seq,GSM2122870,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s5_1_GSLv3-7_37_SL139794.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_37_SL139794.fastq.gz,fastq fastq,959597100.0,9595971.0,GSM2122870 r2,0:50 1:50,A:294644349;C:184893976;G:188222172;T:291818696;N:17907,50,50,,,294644349,184893976,188222172,291818696,17907,SRX1704279,SRS1396344,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.86953,0.86626,0.33903,0.3765,0.77264,0.74432,0.53426,0.53782,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40813,SRR3381845,SRX1704279,SRS1396344,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 2 blood,GSM2122870,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 2 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122870,GSM2122870: Treated 2 blood; Danio rerio; RNA Seq,GSM2122870,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s5_1_GSLv3-7_37_SL139794.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_37_SL139794.fastq.gz,fastq fastq,1245250000.0,12452500.0,GSM2122870 r3,0:50 1:50,A:381219052;C:241987476;G:247543915;T:374295403;N:204154,50,50,,,381219052,241987476,247543915,374295403,204154,SRX1704279,SRS1396344,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.86789,0.86686,0.35484,0.37206,0.74119,0.73679,0.50299,0.53759,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40814,SRR3381846,SRX1704279,SRS1396344,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 2 blood,GSM2122870,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 2 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122870,GSM2122870: Treated 2 blood; Danio rerio; RNA Seq,GSM2122870,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s6_1_GSLv3-7_37_SL139794.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_37_SL139794.fastq.gz,fastq fastq,950337100.0,9503371.0,GSM2122870 r4,0:50 1:50,A:291821125;C:182753545;G:186179426;T:289565320;N:17684,50,50,,,291821125,182753545,186179426,289565320,17684,SRX1704279,SRS1396344,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.86635,0.86476,0.34245,0.3786,0.77309,0.74474,0.50694,0.53099,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40815,SRR3381839,SRX1704278,SRS1396345,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 1 blood,GSM2122869,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122869,GSM2122869: Treated 1 blood; Danio rerio; RNA Seq,GSM2122869,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s5_1_GSLv3-7_36_SL139793.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_36_SL139793.fastq.gz,fastq fastq,1067516000.0,10675160.0,GSM2122869 r1,0:50 1:50,A:289362409;C:244764167;G:247658920;T:285596522;N:133982,50,50,,,289362409,244764167,247658920,285596522,133982,SRX1704278,SRS1396345,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90704,0.92219,0.1113,0.11316,0.73645,0.73746,0.52358,0.53128,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40816,SRR3381840,SRX1704278,SRS1396345,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 1 blood,GSM2122869,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122869,GSM2122869: Treated 1 blood; Danio rerio; RNA Seq,GSM2122869,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s5_1_GSLv3-7_36_SL139793.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_36_SL139793.fastq.gz,fastq fastq,802301400.0,8023014.0,GSM2122869 r2,0:50 1:50,A:216222361;C:183743858;G:183958773;T:218361744;N:14664,50,50,,,216222361,183743858,183958773,218361744,14664,SRX1704278,SRS1396345,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90734,0.92073,0.10828,0.11414,0.75816,0.74156,0.52518,0.53162,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40817,SRR3381841,SRX1704278,SRS1396345,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 1 blood,GSM2122869,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122869,GSM2122869: Treated 1 blood; Danio rerio; RNA Seq,GSM2122869,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s6_1_GSLv3-7_36_SL139793.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_36_SL139793.fastq.gz,fastq fastq,1068410400.0,10684104.0,GSM2122869 r3,0:50 1:50,A:289709397;C:244889156;G:247758297;T:285941886;N:111664,50,50,,,289709397,244889156,247758297,285941886,111664,SRX1704278,SRS1396345,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90673,0.9217,0.11124,0.11262,0.73779,0.73819,0.52628,0.53419,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40818,SRR3381842,SRX1704278,SRS1396345,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Treated 1 blood,GSM2122869,,source name:whole blood  cortisol|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,Treated 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  cortisol,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:cortisol,GSM2122869,GSM2122869: Treated 1 blood; Danio rerio; RNA Seq,GSM2122869,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s6_1_GSLv3-7_36_SL139793.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_36_SL139793.fastq.gz,fastq fastq,792180400.0,7921804.0,GSM2122869 r4,0:50 1:50,A:213515752;C:181199374;G:181507201;T:215943851;N:14222,50,50,,,213515752,181199374,181507201,215943851,14222,SRX1704278,SRS1396345,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90574,0.92099,0.11022,0.11558,0.75773,0.74158,0.52565,0.52697,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40819,SRR3381835,SRX1704277,SRS1396346,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 3 blood,GSM2122868,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 3 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122868,GSM2122868: Control 3 blood; Danio rerio; RNA Seq,GSM2122868,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s6_1_GSLv3-7_35_SL139792.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_35_SL139792.fastq.gz,fastq fastq,1006437300.0,10064373.0,GSM2122868 r1,0:50 1:50,A:270736589;C:231073543;G:230348781;T:274259695;N:18692,50,50,,,270736589,231073543,230348781,274259695,18692,SRX1704277,SRS1396346,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.89576,0.91552,0.11015,0.11108,0.77108,0.75708,0.52238,0.55295,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40820,SRR3381836,SRX1704277,SRS1396346,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 3 blood,GSM2122868,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 3 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122868,GSM2122868: Control 3 blood; Danio rerio; RNA Seq,GSM2122868,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s5_1_GSLv3-7_35_SL139792.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_35_SL139792.fastq.gz,fastq fastq,1019872300.0,10198723.0,GSM2122868 r2,0:50 1:50,A:274310405;C:234397316;G:233653220;T:277492635;N:18724,50,50,,,274310405,234397316,233653220,277492635,18724,SRX1704277,SRS1396346,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.89872,0.91671,0.10908,0.10998,0.76848,0.7559,0.55678,0.52913,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40821,SRR3381837,SRX1704277,SRS1396346,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 3 blood,GSM2122868,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 3 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122868,GSM2122868: Control 3 blood; Danio rerio; RNA Seq,GSM2122868,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s6_1_GSLv3-7_35_SL139792.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_35_SL139792.fastq.gz,fastq fastq,1350419100.0,13504191.0,GSM2122868 r3,0:50 1:50,A:365416324;C:310498635;G:312632921;T:361739733;N:131487,50,50,,,365416324,310498635,312632921,361739733,131487,SRX1704277,SRS1396346,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.89828,0.91602,0.11147,0.11073,0.74941,0.75053,0.54012,0.53979,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40822,SRR3381838,SRX1704277,SRS1396346,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 3 blood,GSM2122868,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 3 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122868,GSM2122868: Control 3 blood; Danio rerio; RNA Seq,GSM2122868,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s5_1_GSLv3-7_35_SL139792.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_35_SL139792.fastq.gz,fastq fastq,1352817900.0,13528179.0,GSM2122868 r4,0:50 1:50,A:366001448;C:311109301;G:313269573;T:362247619;N:189959,50,50,,,366001448,311109301,313269573,362247619,189959,SRX1704277,SRS1396346,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.89762,0.91702,0.11094,0.1109,0.74864,0.7498,0.53153,0.55731,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40823,SRR3381831,SRX1704276,SRS1396347,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 2 blood,GSM2122867,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 2 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122867,GSM2122867: Control 2 blood; Danio rerio; RNA Seq,GSM2122867,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s5_1_GSLv3-7_34_SL139791.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_34_SL139791.fastq.gz,fastq fastq,1320276500.0,13202765.0,GSM2122867 r1,0:50 1:50,A:347340148;C:314346533;G:315984111;T:342435896;N:169812,50,50,,,347340148,314346533,315984111,342435896,169812,SRX1704276,SRS1396347,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.92673,0.93522,0.1474,0.1486,0.77695,0.77822,0.5491,0.55404,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40824,SRR3381832,SRX1704276,SRS1396347,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 2 blood,GSM2122867,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 2 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122867,GSM2122867: Control 2 blood; Danio rerio; RNA Seq,GSM2122867,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s6_1_GSLv3-7_34_SL139791.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_34_SL139791.fastq.gz,fastq fastq,980312400.0,9803124.0,GSM2122867 r2,0:50 1:50,A:256051139;C:233456025;G:232307447;T:258480444;N:17345,50,50,,,256051139,233456025,232307447,258480444,17345,SRX1704276,SRS1396347,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.92686,0.9359,0.1445,0.14733,0.79537,0.78244,0.55823,0.5607,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40825,SRR3381833,SRX1704276,SRS1396347,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 2 blood,GSM2122867,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 2 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122867,GSM2122867: Control 2 blood; Danio rerio; RNA Seq,GSM2122867,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s5_1_GSLv3-7_34_SL139791.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_34_SL139791.fastq.gz,fastq fastq,996477700.0,9964777.0,GSM2122867 r3,0:50 1:50,A:260257795;C:237526121;G:236299803;T:262375630;N:18351,50,50,,,260257795,237526121,236299803,262375630,18351,SRX1704276,SRS1396347,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.9292,0.93713,0.143,0.14889,0.79531,0.7834,0.55615,0.55279,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40826,SRR3381834,SRX1704276,SRS1396347,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 2 blood,GSM2122867,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 2 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122867,GSM2122867: Control 2 blood; Danio rerio; RNA Seq,GSM2122867,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s6_1_GSLv3-7_34_SL139791.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_34_SL139791.fastq.gz,fastq fastq,1319184300.0,13191843.0,GSM2122867 r4,0:50 1:50,A:347098468;C:314043165;G:315610117;T:342302442;N:130108,50,50,,,347098468,314043165,315610117,342302442,130108,SRX1704276,SRS1396347,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.92671,0.93595,0.14826,0.14877,0.77792,0.77873,0.55524,0.5557,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40827,SRR3381825,SRX1704275,SRS1396348,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 1 blood,GSM2122866,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122866,GSM2122866: Control 1 blood; Danio rerio; RNA Seq,GSM2122866,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s6_1_GSLv3-7_33_SL139790.fastq.gz C8BH2ANXX_s6_2_GSLv3-7_33_SL139790.fastq.gz,fastq fastq,692276000.0,6922760.0,GSM2122866 r1,0:50 1:50,A:191405813;C:153586292;G:152965257;T:194306049;N:12589,50,50,,,191405813,153586292,152965257,194306049,12589,SRX1704275,SRS1396348,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.9083,0.91142,0.16578,0.17743,0.75789,0.74221,0.55181,0.54476,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40828,SRR3381826,SRX1704275,SRS1396348,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 1 blood,GSM2122866,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122866,GSM2122866: Control 1 blood; Danio rerio; RNA Seq,GSM2122866,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s5_1_GSLv3-7_33_SL139790.fastq.gz C8DY1ANXX_s5_2_GSLv3-7_33_SL139790.fastq.gz,fastq fastq,911479300.0,9114793.0,GSM2122866 r2,0:50 1:50,A:253240601;C:202627238;G:203390297;T:252105631;N:115533,50,50,,,253240601,202627238,203390297,252105631,115533,SRX1704275,SRS1396348,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90729,0.91334,0.17307,0.1777,0.73316,0.73419,0.55981,0.56826,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40829,SRR3381827,SRX1704275,SRS1396348,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 1 blood,GSM2122866,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122866,GSM2122866: Control 1 blood; Danio rerio; RNA Seq,GSM2122866,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DY1ANXX_s6_1_GSLv3-7_33_SL139790.fastq.gz C8DY1ANXX_s6_2_GSLv3-7_33_SL139790.fastq.gz,fastq fastq,910041600.0,9100416.0,GSM2122866 r3,0:50 1:50,A:252924440;C:202200821;G:202972517;T:251856107;N:87715,50,50,,,252924440,202200821,202972517,251856107,87715,SRX1704275,SRS1396348,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90819,0.91345,0.17288,0.17678,0.73582,0.73448,0.55482,0.56579,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40830,SRR3381828,SRX1704275,SRS1396348,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 1 blood,GSM2122866,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122866,GSM2122866: Control 1 blood; Danio rerio; RNA Seq,GSM2122866,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8BH2ANXX_s5_1_GSLv3-7_33_SL139790.fastq.gz C8BH2ANXX_s5_2_GSLv3-7_33_SL139790.fastq.gz,fastq fastq,701940200.0,7019402.0,GSM2122866 r4,0:50 1:50,A:194036996;C:155992188;G:155284640;T:196613376;N:13000,50,50,,,194036996,155992188,155284640,196613376,13000,SRX1704275,SRS1396348,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90959,0.91386,0.16429,0.17705,0.75544,0.7391,0.548,0.57224,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40831,SRR3381829,SRX1704275,SRS1396348,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 1 blood,GSM2122866,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122866,GSM2122866: Control 1 blood; Danio rerio; RNA Seq,GSM2122866,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DKGANXX_s8_1_GSLv3-7_33_SL139790.fastq.gz C8DKGANXX_s8_2_GSLv3-7_33_SL139790.fastq.gz,fastq fastq,1596331500.0,15963315.0,GSM2122866 r5,0:50 1:50,A:444854958;C:353331559;G:354367449;T:442888766;N:888768,50,50,,,444854958,353331559,354367449,442888766,888768,SRX1704275,SRS1396348,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90554,0.91175,0.17327,0.17968,0.73669,0.73728,0.55044,0.5651,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
40832,SRR3381830,SRX1704275,SRS1396348,SRP073272,PRJNA318414,Cortisol treated zebrafish embryos develop into pro inflammatory adults with aberrant immune gene regulation [adults],GSE80260,Transcriptome Analysis,Chronic early life stress increases adult susceptibility to numerous health problems linked to chronic inflammation. One way that this may occur is via glucocorticoid induced developmental programming. To gain insight into such programming  we treated zebrafish embryos with cortisol and examined the effects on adults. In maturity  the treated fish maintained elevated basal cortisol levels in the absence of exogenous cortisol  and constitutively mis expressed genes involved in defense response and its regulation. Adults derived from cortisol treated embryos displayed defective tailfin regeneration  heightened basal expression of pro inflammatory genes  and failure to appropriately regulate those genes following injury or immunological challenge. These results support the hypothesis that chronically elevated glucocorticoid signaling early in life directs development of a pro inflammatory adult phenotype  at the expense of immunoregulation and somatic regenerative capacity. Overall design: 30 samples total were analyzed. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to DMSO control as embryos. 9 caudal fins samples 0  2 and 4dpa  3 blood samples and 3 muscle samples from adults exposed to cortisol 1 micromolar as embryos.,parent bioproject:PRJNA318502,pubmed:27444789,,Control 1 blood,GSM2122866,,source name:whole blood  DMSO control|strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,Control 1 blood,Sequence quality was assessed using Fastqc QC v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Reads were trimmed using Trimmomatic v 0.3; Bolger et al.  2014. Trimmed reads were aligned to the zebrafish Danio rerio transcriptome annotated by Ensembl version 83 of the GRCz10 genome assembly using RSEM version 1.2.25 Li and Dewey  2011 and Bowtie 1.1.2 Langmead et al.  2009. Differentially expressed transcripts were determined using R/edgeR version 3.10.2 Robinson et al.  2010. Genome build: Danio rerio GRCz10 Supplementary files format and content: Tab delimited text files with read counts counts per million per sample.,whole blood  DMSO control,DMSO or 1 micromolar cortisol was added to larval medium for first 5 days of development  and then maintained to 4.5 month under normal conditions.,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,AB zebrafish were maintained at 28 degrees Celsius at the MDI Biological Laboratory Animal Core.,strain/background:AB|tissue:whole blood|age:adult|embryonic treatment:DMSO,GSM2122866,GSM2122866: Control 1 blood; Danio rerio; RNA Seq,GSM2122866,,1,RNA EZplus kit from Qiagen. Illumina TruSeq PolyA+ mRNA libraries.,GEO Accession:GSM2122866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP073272,,,C8DKGANXX_s7_1_GSLv3-7_33_SL139790.fastq.gz C8DKGANXX_s7_2_GSLv3-7_33_SL139790.fastq.gz,fastq fastq,1600754600.0,16007546.0,GSM2122866 r6,0:50 1:50,A:446178544;C:354456079;G:355435947;T:443937350;N:746680,50,50,,,446178544,354456079,355435947,443937350,746680,SRX1704275,SRS1396348,SRA411416,GEO,"Molecular and Biomedical Sciences, University of Maine",2,0.90709,0.91238,0.17011,0.17723,0.74054,0.73994,0.55938,0.55607,50,50,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,trueseq,bulk,unknown,unknown,,United States,2016-04-13,Adult,Adult,Blood,Hematopoietic System
44935,SRR6308293,SRX3408679,SRS2701475,SRP125291,PRJNA419036,Danio rerio strain:ASWT Transcriptome or Gene expression,PRJNA419036,Other,A genome wide map of circular RNA in adult zebrafish.,,,,Zf blood,Zf blood,,strain:ASWT|age:1year|sex:male|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,A genome wide map of circular RNA in adult zebrafish,Zf blood,Zf blood,Tissue were isolated from adult zebrafish anaesthetized using 0.004% Tricaine Sigma  USA. Extreme care was taken to avoid contamination to obtain pure homogenous tissue samples. The tissues were repeatedly washed in PBS to remove contaminating debris. The tissue samples were homogenized in Trizol for cell lysis Invitrogen  USA. RNA was isolated from the homogenized tissue samples using RNeasy kit Qiagen  USA. Sample preparation for sequencing was carried out using Truseq stranded RNA sample preparation kit Illumina  USA as per supplier's instructions. In order to remove the ribosomal RNA rRNA  one microgram of total RNA was hybridised with Ribo zero gold rRNA removal probe. Upon removing rRNA  the samples were processed for fragmentation in the presence of ionic cations at 37 degree Celcius. First stranded complementary DNA cDNA was prepared by random hexamers and superscript II reverse transcriptase Invitrogen  USA in presence of Actinomycin D to facilitate RNA dependent synthesis for improving strand specificity. The second strand was synthesised with second strand cDNA mix containing dUTP instead of dTTP and subjected to A base addition followed by adapter ligation. Final libraries were prepared by amplifying adapter ligated double strand cDNA. Clusters were generated on Hiseq flow cell v3 Illumina in cBot according to standard protocol Illumina USA.,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP125291,,,Zf_blood_R1.fastq Zf_blood_R2.fastq,fastq fastq,3815054252.0,20461146.0,Zf blood R1.fastq,0:97.58 1:88.87,A:1003195592;C:903122443;G:887002461;T:1021496839;N:236917,97,88,,,1003195592,903122443,887002461,1021496839,236917,SRX3408679,SRS2701475,SRA631861,CSIR-Institute of Genomics and Integrative Biology|Genomic Medicine,CSIR-Institute of Genomics and Integrative Biology,2,0.88344,0.89187,0.31874,0.32265,0.75398,0.75706,0.6181,0.61725,100,54,B,B,biological fallback assumption,illumina,hiseq_era,unknown,random_priming,ribozero,bulk,unknown,unknown,,India,2017-11-20,Adult,Adult,Blood,Hematopoietic System
49188,SRR7785379,SRX4640375,SRS3738589,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H67,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:wild type|replicate:replicate2|BioSampleModel:Model organism or animal,,,,,,,,,H67,H67,H67,Wild type zebrafish control 2,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H67_S2_L001_R2_001.fastq.gz H67_S2_L001_R1_001.fastq.gz,fastq fastq,18477819300.0,61592731.0,H67 S2 L001 R2 001.fastq.gz,0:150 1:150,A:4887782016;C:4375793599;G:4438933003;T:4775205744;N:104938,150,150,,,4887782016,4375793599,4438933003,4775205744,104938,SRX4640375,SRS3738589,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.93322,0.93319,0.06946,0.06963,0.6747,0.68083,0.47183,0.47148,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-20,Adult,Adult,Blood,Hematopoietic System
49189,SRR7785380,SRX4640374,SRS3738594,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H66,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:wild type|replicate:replicate1|BioSampleModel:Model organism or animal,,,,,,,,,H66,H66,H66,Wild type zebrafish control 1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H66_S1_L001_R2_001.fastq.gz H66_S1_L001_R1_001.fastq.gz,fastq fastq,20487126300.0,68290421.0,H66 S1 L001 R2 001.fastq.gz,0:150 1:150,A:5445452582;C:4824876569;G:4904146081;T:5312533433;N:117635,150,150,,,5445452582,4824876569,4904146081,5312533433,117635,SRX4640374,SRS3738594,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.93306,0.9336,0.08694,0.08764,0.66687,0.6734,0.46489,0.47008,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-20,Adult,Adult,Blood,Hematopoietic System
49190,SRR7785381,SRX4640373,SRS3738593,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H124,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:Tol2 EVI 1 EGFP transgenic|replicate:replicate1|BioSampleModel:Model organism or animal,,,,,,,,,H124,H124,H124,Tol2 EVI 1 EGFP transgenic zebrafish sample 1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H124_S1_L001_R1_001.fastq.gz H124_S1_L001_R2_001.fastq.gz,fastq fastq,13178593800.0,43928646.0,H124 S1 L001 R1 001.fastq.gz,0:150 1:150,A:3507220604;C:3103991247;G:3164157369;T:3403051995;N:172585,150,150,,,3507220604,3103991247,3164157369,3403051995,172585,SRX4640373,SRS3738593,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.94147,0.94277,0.08109,0.08136,0.69483,0.70011,0.47542,0.47593,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-20,Adult,Adult,Blood,Hematopoietic System
49191,SRR7785382,SRX4640372,SRS3738592,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H93,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:wild type|replicate:replicate3|BioSampleModel:Model organism or animal,,,,,,,,,H93,H93,H93,Wild type zebrafish control 3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H93_S3_L001_R1_001.fastq.gz H93_S3_L001_R2_001.fastq.gz,fastq fastq,18197379600.0,60657932.0,H93 S3 L001 R1 001.fastq.gz,0:150 1:150,A:4814246240;C:4308418881;G:4375398316;T:4699211054;N:105109,150,150,,,4814246240,4308418881,4375398316,4699211054,105109,SRX4640372,SRS3738592,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.9312,0.93173,0.07454,0.07498,0.67065,0.6773,0.46807,0.47334,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-20,Adult,Adult,Blood,Hematopoietic System
49192,SRR7785383,SRX4640371,SRS3738590,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H126,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:Tol2 EVI 1 EGFP transgenic|replicate:replicate3|BioSampleModel:Model organism or animal,,,,,,,,,H126,H126,H126,Tol2 EVI 1 EGFP transgenic zebrafish sample 3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H126_S3_L001_R1_001.fastq.gz H126_S3_L001_R2_001.fastq.gz,fastq fastq,14979601800.0,49932006.0,H126 S3 L001 R2 001.fastq.gz,0:150 1:150,A:3961375940;C:3551410264;G:3640700651;T:3825918931;N:196014,150,150,,,3961375940,3551410264,3640700651,3825918931,196014,SRX4640371,SRS3738590,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.93717,0.93908,0.05823,0.05891,0.70552,0.71256,0.46146,0.45779,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-20,Adult,Adult,Blood,Hematopoietic System
49193,SRR7785384,SRX4640370,SRS3738588,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover  overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H125,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:Tol2 EVI 1 EGFP transgenic|replicate:replicate2|BioSampleModel:Model organism or animal,,,,,,,,,H125,H125,H125,Tol2 EVI 1 EGFP transgenic zebrafish sample 2,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H125_S2_L001_R1_001.fastq.gz H125_S2_L001_R2_001.fastq.gz,fastq fastq,16012998000.0,53376660.0,H125 S2 L001 R1 001.fastq.gz,0:150 1:150,A:4365269809;C:3662731840;G:3768367416;T:4216409682;N:219253,150,150,,,4365269809,3662731840,3768367416,4216409682,219253,SRX4640370,SRS3738588,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.9402,0.94198,0.09449,0.09528,0.71999,0.72512,0.46106,0.47624,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2018-09-04,Adult,Adult,Blood,Hematopoietic System
51876,SRR8922974,SRX5704273,SRS4643334,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: WT6,GSM3728533,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type,erythroid cells: WT6,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type,GSM3728533,GSM3728533: erythroid cells: WT6; Danio rerio; RNA Seq,GSM3728533,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728533,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_TAGCTT_LWT6.1_val_1.fq.gz J633_AHFHNLBGX2_TAGCTT_LWT6.2_val_2.fq.gz,fastq fastq,8611605345.0,32335443.0,GSM3728533 r1,0:133.59 1:132.74,A:1724489451;C:2542199793;G:2626828499;T:1716562999;N:1524603,133,132,,,1724489451,2542199793,2626828499,1716562999,1524603,SRX5704273,SRS4643334,SRA875634,GEO,Albert Einstein College of Medicine,2,0.91241,0.96131,0.10384,0.10826,0.77761,0.7767,0.69985,0.69519,128,128,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51877,SRR8922973,SRX5704272,SRS4643333,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: WT5,GSM3728532,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type,erythroid cells: WT5,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type,GSM3728532,GSM3728532: erythroid cells: WT5; Danio rerio; RNA Seq,GSM3728532,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728532,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_TGACCA_LWT5.1_val_1.fq.gz J633_AHFHNLBGX2_TGACCA_LWT5.2_val_2.fq.gz,fastq fastq,8110446942.0,28906836.0,GSM3728532 r1,0:140.70 1:139.87,A:1479901358;C:2533764326;G:2613647627;T:1481710129;N:1423502,140,139,,,1479901358,2533764326,2613647627,1481710129,1423502,SRX5704272,SRS4643333,SRA875634,GEO,Albert Einstein College of Medicine,2,0.92578,0.97511,0.09182,0.09201,0.80503,0.80324,0.76985,0.7675,150,150,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51878,SRR8922972,SRX5704271,SRS4643332,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: WT4,GSM3728531,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type,erythroid cells: WT4,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type,GSM3728531,GSM3728531: erythroid cells: WT4; Danio rerio; RNA Seq,GSM3728531,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728531,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_TTAGGC_LWT4.2_val_2.fq.gz J633_AHFHNLBGX2_TTAGGC_LWT4.1_val_1.fq.gz,fastq fastq,8627466135.0,32957109.0,GSM3728531 r1,0:131.12 1:130.66,A:1686521982;C:2592728511;G:2670950174;T:1675745501;N:1519967,131,130,,,1686521982,2592728511,2670950174,1675745501,1519967,SRX5704271,SRS4643332,SRA875634,GEO,Albert Einstein College of Medicine,2,0.91773,0.96731,0.11151,0.1134,0.78792,0.78597,0.73657,0.73692,104,104,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51879,SRR8922971,SRX5704270,SRS4643331,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: WT3,GSM3728530,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type,erythroid cells: WT3,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:wild type,GSM3728530,GSM3728530: erythroid cells: WT3; Danio rerio; RNA Seq,GSM3728530,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728530,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_CGATGT_LWT3.2_val_2.fq.gz J633_AHFHNLBGX2_CGATGT_LWT3.1_val_1.fq.gz,fastq fastq,7675701402.0,28099783.0,GSM3728530 r1,0:136.90 1:136.26,A:1496106079;C:2307580110;G:2386093773;T:1484556287;N:1365153,136,136,,,1496106079,2307580110,2386093773,1484556287,1365153,SRX5704270,SRS4643331,SRA875634,GEO,Albert Einstein College of Medicine,2,0.91833,0.96754,0.10771,0.10822,0.80135,0.80158,0.76757,0.7524,150,150,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51880,SRR8922970,SRX5704269,SRS4643330,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: WT2,GSM3728529,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,erythroid cells: WT2,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,GSM3728529,GSM3728529: erythroid cells: WT2; Danio rerio; RNA Seq,GSM3728529,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728529,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_ATCACG_LWT2.2_val_2.fq.gz J633_AHFHNLBGX2_ATCACG_LWT2.1_val_1.fq.gz,fastq fastq,8749226933.0,32236600.0,GSM3728529 r1,0:135.97 1:135.43,A:1818348438;C:2523018672;G:2595068272;T:1811215171;N:1576380,135,135,,,1818348438,2523018672,2595068272,1811215171,1576380,SRX5704269,SRS4643330,SRA875634,GEO,Albert Einstein College of Medicine,2,0.91533,0.96543,0.12825,0.13005,0.77394,0.77344,0.70772,0.67993,143,143,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51881,SRR8922969,SRX5704268,SRS4643329,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: Mut6,GSM3728528,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,erythroid cells: Mut6,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,GSM3728528,GSM3728528: erythroid cells: Mut6; Danio rerio; RNA Seq,GSM3728528,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728528,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_GGCTAC_LMut6.2_val_2.fq.gz J633_AHFHNLBGX2_GGCTAC_LMut6.1_val_1.fq.gz,fastq fastq,7989745578.0,29813232.0,GSM3728528 r1,0:134.59 1:133.41,A:1487912329;C:2465671654;G:2552013900;T:1482837472;N:1310223,134,133,,,1487912329,2465671654,2552013900,1482837472,1310223,SRX5704268,SRS4643329,SRA875634,GEO,Albert Einstein College of Medicine,2,0.91636,0.96506,0.12513,0.13214,0.80255,0.80277,0.77309,0.77779,106,106,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51882,SRR8922968,SRX5704267,SRS4643327,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: Mut5,GSM3728527,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,erythroid cells: Mut5,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,GSM3728527,GSM3728527: erythroid cells: Mut5; Danio rerio; RNA Seq,GSM3728527,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728527,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_GATCAG_LMut5.2_val_2.fq.gz J633_AHFHNLBGX2_GATCAG_LMut5.1_val_1.fq.gz,fastq fastq,8500296799.0,30812271.0,GSM3728527 r1,0:138.28 1:137.59,A:1566669253;C:2640866820;G:2726747970;T:1564531299;N:1481457,138,137,,,1566669253,2640866820,2726747970,1564531299,1481457,SRX5704267,SRS4643327,SRA875634,GEO,Albert Einstein College of Medicine,2,0.91987,0.9688,0.10388,0.10646,0.80338,0.80176,0.75914,0.71799,52,52,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51883,SRR8922967,SRX5704266,SRS4643328,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: Mut4,GSM3728526,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,erythroid cells: Mut4,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,GSM3728526,GSM3728526: erythroid cells: Mut4; Danio rerio; RNA Seq,GSM3728526,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728526,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_ACTTGA_LMut4.2_val_2.fq.gz J633_AHFHNLBGX2_ACTTGA_LMut4.1_val_1.fq.gz,fastq fastq,8415322795.0,32199684.0,GSM3728526 r1,0:130.80 1:130.55,A:1593557159;C:2583771193;G:2657553064;T:1578891748;N:1549631,130,130,,,1593557159,2583771193,2657553064,1578891748,1549631,SRX5704266,SRS4643328,SRA875634,GEO,Albert Einstein College of Medicine,2,0.92078,0.97122,0.12063,0.12061,0.81994,0.81822,0.76635,0.7826,149,148,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51884,SRR8922966,SRX5704265,SRS4643326,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: Mut3,GSM3728525,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,erythroid cells: Mut3,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,GSM3728525,GSM3728525: erythroid cells: Mut3; Danio rerio; RNA Seq,GSM3728525,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728525,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_CAGATC_LMut3.2_val_2.fq.gz J633_AHFHNLBGX2_CAGATC_LMut3.1_val_1.fq.gz,fastq fastq,5373096143.0,19350806.0,GSM3728525 r1,0:139.04 1:138.63,A:990313321;C:1667762750;G:1723819167;T:990236765;N:964140,139,138,,,990313321,1667762750,1723819167,990236765,964140,SRX5704265,SRS4643326,SRA875634,GEO,Albert Einstein College of Medicine,2,0.92305,0.97223,0.10386,0.10158,0.8062,0.80415,0.79641,0.78792,150,149,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
51885,SRR8922965,SRX5704264,SRS4643325,SRP192854,PRJNA533283,RNA seq of erythroid cells from 24 hpf sf3b1 mutant and sibling zebrafish,GSE129952,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of the splicing factor Sf3b1 are lowered in embryonic zebrafish. Results provide insight the role of Sf3b1 in erythropoietic development. Overall design: mRNA profiling of gata1 positive erythroid cells isolated from 24 hpf sf3b1 mutant and sibling zebrafish using Illumina NextSeq500. Five samples were sequenced for each.,,,,erythroid cells: Mut1,GSM3728524,,tissue:erythroid cells|age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,erythroid cells: Mut1,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq220 and EdgeR21 Bioconductor packages. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file includeS FPKM values for each Sample,erythroid cells,,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,,age:24 hpf type:gata1 positive erythroid cells|genotype/variation:sf3b1 mutant,GSM3728524,GSM3728524: erythroid cells: Mut1; Danio rerio; RNA Seq,GSM3728524,,1,Gata1 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Ribosomal RNA was depleted with Ribogone Clontech. Libraries were made following the protocol and using the reagents from the SMARTer Stranded RNA Seq Kit Clontech.,GEO Accession:GSM3728524,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP192854,,,J633_AHFHNLBGX2_GCCAAT_LMut1.1_val_1.fq.gz J633_AHFHNLBGX2_GCCAAT_LMut1.2_val_2.fq.gz,fastq fastq,7256147960.0,27513744.0,GSM3728524 r1,0:132.21 1:131.52,A:1506751800;C:2097058291;G:2163719918;T:1487337753;N:1280198,132,131,,,1506751800,2097058291,2163719918,1487337753,1280198,SRX5704264,SRS4643325,SRA875634,GEO,Albert Einstein College of Medicine,2,0.90512,0.95369,0.12564,0.13165,0.77153,0.77098,0.74915,0.74717,122,122,B,B,biological fallback assumption,illumina,nextseq,full_length,rrna_depletion,smarter,bulk,unknown,unknown,,United States,2019-04-17,Pharyngula,Embryo,Blood,Hematopoietic System
53009,SRR9662030,SRX6422906,SRS5079696,SRP213938,PRJNA553572,A map of cis regulatory elements and 3D genome structures in zebrafish,GSE134055,Other,The zebrafish has been widely used for the study of human disease and development  as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome  however  has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects  we performed RNA seq  ATAC seq  ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall  we have identified 235 596 cis regulatory elements  which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish  human  and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore  through the analysis of Hi C data in zebrafish brain and muscle  we observed different levels of 3D genome organization  including compartment  topological associating domains TADs  and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and  embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3  RNA Seq  11 of them were examined using ATAC seq  WGBS and ChIP seq H3K9me3 and H3K9me2  and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that  for the samples GSM4661977 GSM4662088  [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.,,pubmed:33239788;pubmed:35649578,,YueLab RNA Seq Spleen rep2,GSM3934898,,source name:Tissue|strain:Tuebingen|tissue:Spleen,YueLab RNA Seq Spleen rep2,RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following  setting: ChIP seq q value <10e 2  p value<10e 5  Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged,Tissue,,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions,strain:Tuebingen|tissue:Spleen,GSM3934898,GSM3934898: YueLab RNA Seq Spleen rep2; Danio rerio; RNA Seq,GSM3934898,,1,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,GEO Accession:GSM3934898,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer,,SRP213938,,,YueLab-RNA-Seq-Spleen-rep2_1.fastq.gz YueLab-RNA-Seq-Spleen-rep2_2.fastq.gz,fastq fastq,8309777463.0,41837414.0,GSM3934898 r1,0:98.87 1:99.75,A:2235106866;C:1723612712;G:1748992271;T:2601473305;N:592309,98,99,,,2235106866,1723612712,1748992271,2601473305,592309,SRX6422906,SRS5079696,SRA919194,GEO,"Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine",2,0.9718,0.97965,0.15676,0.11996,0.7347,0.73831,0.49813,0.50156,99,100,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-07-09,Pharyngula,Embryo,Spleen,Hematopoietic System
53010,SRR9662029,SRX6422905,SRS5079695,SRP213938,PRJNA553572,A map of cis regulatory elements and 3D genome structures in zebrafish,GSE134055,Other,The zebrafish has been widely used for the study of human disease and development  as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome  however  has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects  we performed RNA seq  ATAC seq  ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall  we have identified 235 596 cis regulatory elements  which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish  human  and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore  through the analysis of Hi C data in zebrafish brain and muscle  we observed different levels of 3D genome organization  including compartment  topological associating domains TADs  and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and  embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3  RNA Seq  11 of them were examined using ATAC seq  WGBS and ChIP seq H3K9me3 and H3K9me2  and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that  for the samples GSM4661977 GSM4662088  [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records.,,pubmed:33239788;pubmed:35649578,,YueLab RNA Seq Spleen rep1,GSM3934897,,source name:Tissue|strain:Tuebingen|tissue:Spleen,YueLab RNA Seq Spleen rep1,RNA seq reads were aligned to zv10 genome assembly using STAR; ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using BWA HiC reads were aligned to zv10 genome assembly using Bowtie2 The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq peaks were called using MACS2 with the following  setting: ChIP seq q value <10e 2  p value<10e 5  Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5 HiC matrix was generated using HiC Pro Genome build: zv10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged,Tissue,,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions,strain:Tuebingen|tissue:Spleen,GSM3934897,GSM3934897: YueLab RNA Seq Spleen rep1; Danio rerio; RNA Seq,GSM3934897,,1,For each RNA seq experiment  the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk  ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron  green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly  polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented  then followed by reverse transcription  end repair  adenylation  adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina.,GEO Accession:GSM3934897,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina Genome Analyzer,,SRP213938,,,YueLab-RNA-Seq-Spleen-rep1_1.fastq.gz YueLab-RNA-Seq-Spleen-rep1_2.fastq.gz,fastq fastq,1940987484.0,9748717.0,GSM3934897 r1,0:99.62 1:99.48,A:522271746;C:424963046;G:430836475;T:562779653;N:136564,99,99,,,522271746,424963046,430836475,562779653,136564,SRX6422905,SRS5079695,SRA919194,GEO,"Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine",2,0.97325,0.97976,0.13741,0.12217,0.72129,0.73261,0.50119,0.4956,100,99,B,B,biological fallback assumption,illumina,early_illumina,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2019-07-09,Pharyngula,Embryo,Spleen,Hematopoietic System
55483,SRR10510897,SRX7199568,SRS5705123,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Injury 6,GSM4186881,,tissue:Macrophage lineage cells|age:4 dpf,Injury 6,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186881,GSM4186881: Injury 6; Danio rerio; RNA Seq,GSM4186881,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186881,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0012L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0012L01_2.fastq.gz,fastq fastq,2370267700.0,23702677.0,GSM4186881 r1,0:50 1:50,A:606210613;C:401855240;G:580678813;T:781359784;N:163250,50,50,,,606210613,401855240,580678813,781359784,163250,SRX7199568,SRS5705123,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.71766,0.68121,0.304,0.29349,0.9694,0.97047,0.60698,0.47166,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55484,SRR10510896,SRX7199567,SRS5705122,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Injury 5,GSM4186880,,tissue:Macrophage lineage cells|age:4 dpf,Injury 5,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186880,GSM4186880: Injury 5; Danio rerio; RNA Seq,GSM4186880,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186880,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0011L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0011L01_2.fastq.gz,fastq fastq,3104558400.0,31045584.0,GSM4186880 r1,0:50 1:50,A:787529128;C:520514424;G:755538210;T:1040764721;N:211917,50,50,,,787529128,520514424,755538210,1040764721,211917,SRX7199567,SRS5705122,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.71708,0.6862,0.33746,0.32646,0.97104,0.97195,0.57901,0.57237,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55485,SRR10510895,SRX7199566,SRS5705121,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Injury 4,GSM4186879,,tissue:Macrophage lineage cells|age:4 dpf,Injury 4,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186879,GSM4186879: Injury 4; Danio rerio; RNA Seq,GSM4186879,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186879,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0010L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0010L01_2.fastq.gz,fastq fastq,3141608300.0,31416083.0,GSM4186879 r1,0:50 1:50,A:835441484;C:680585583;G:723722079;T:901640444;N:218710,50,50,,,835441484,680585583,723722079,901640444,218710,SRX7199566,SRS5705121,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.84591,0.82203,0.24837,0.24573,0.76729,0.77287,0.55164,0.55075,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55486,SRR10510894,SRX7199565,SRS5705120,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Injury 3,GSM4186878,,tissue:Macrophage lineage cells|age:4 dpf,Injury 3,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186878,GSM4186878: Injury 3; Danio rerio; RNA Seq,GSM4186878,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186878,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0009L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0009L01_2.fastq.gz,fastq fastq,3113500800.0,31135008.0,GSM4186878 r1,0:50 1:50,A:766956694;C:669677107;G:744420894;T:932232213;N:213892,50,50,,,766956694,669677107,744420894,932232213,213892,SRX7199565,SRS5705120,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.71164,0.6754,0.17946,0.17464,0.81734,0.82373,0.53588,0.60496,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55487,SRR10510893,SRX7199564,SRS5705119,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Injury 2,GSM4186877,,tissue:Macrophage lineage cells|age:4 dpf,Injury 2,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186877,GSM4186877: Injury 2; Danio rerio; RNA Seq,GSM4186877,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186877,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0002L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0002L01_2.fastq.gz,fastq fastq,2894623100.0,28946231.0,GSM4186877 r1,0:50 1:50,A:761759953;C:626039697;G:669398895;T:837222282;N:202273,50,50,,,761759953,626039697,669398895,837222282,202273,SRX7199564,SRS5705119,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.83047,0.80183,0.22927,0.22366,0.76715,0.77419,0.54395,0.53733,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55488,SRR10510892,SRX7199563,SRS5705118,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Injury 1,GSM4186876,,tissue:Macrophage lineage cells|age:4 dpf,Injury 1,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186876,GSM4186876: Injury 1; Danio rerio; RNA Seq,GSM4186876,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186876,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0007L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0007L01_2.fastq.gz,fastq fastq,2953684900.0,29536849.0,GSM4186876 r1,0:50 1:50,A:779744552;C:654064489;G:682109837;T:837563725;N:202297,50,50,,,779744552,654064489,682109837,837563725,202297,SRX7199563,SRS5705118,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.85999,0.8342,0.23302,0.22629,0.76788,0.77664,0.53288,0.54359,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55489,SRR10510891,SRX7199562,SRS5705117,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Sham 6,GSM4186875,,tissue:Macrophage lineage cells|age:4 dpf,Sham 6,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186875,GSM4186875: Sham 6; Danio rerio; RNA Seq,GSM4186875,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186875,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0006L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0006L01_2.fastq.gz,fastq fastq,3041448600.0,30414486.0,GSM4186875 r1,0:50 1:50,A:814525300;C:665527185;G:697073297;T:864112866;N:209952,50,50,,,814525300,665527185,697073297,864112866,209952,SRX7199562,SRS5705117,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.8565,0.83045,0.26068,0.25484,0.75998,0.76828,0.53257,0.51687,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55490,SRR10510890,SRX7199561,SRS5705116,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Sham 5,GSM4186874,,tissue:Macrophage lineage cells|age:4 dpf,Sham 5,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186874,GSM4186874: Sham 5; Danio rerio; RNA Seq,GSM4186874,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186874,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0005L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0005L01_2.fastq.gz,fastq fastq,2978747900.0,29787479.0,GSM4186874 r1,0:50 1:50,A:790529419;C:644687609;G:687572262;T:855752767;N:205843,50,50,,,790529419,644687609,687572262,855752767,205843,SRX7199561,SRS5705116,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.84039,0.81667,0.25482,0.25083,0.75763,0.76461,0.53837,0.52682,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55491,SRR10510889,SRX7199560,SRS5705115,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Sham 4,GSM4186873,,tissue:Macrophage lineage cells|age:4 dpf,Sham 4,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186873,GSM4186873: Sham 4; Danio rerio; RNA Seq,GSM4186873,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186873,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0004L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0004L01_2.fastq.gz,fastq fastq,3157421300.0,31574213.0,GSM4186873 r1,0:50 1:50,A:848052952;C:676336291;G:722614661;T:910199331;N:218065,50,50,,,848052952,676336291,722614661,910199331,218065,SRX7199560,SRS5705115,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.83939,0.81586,0.27396,0.2703,0.75416,0.76096,0.52309,0.53651,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55492,SRR10510888,SRX7199559,SRS5705114,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Sham 3,GSM4186872,,tissue:Macrophage lineage cells|age:4 dpf,Sham 3,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186872,GSM4186872: Sham 3; Danio rerio; RNA Seq,GSM4186872,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186872,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0003L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0003L01_2.fastq.gz,fastq fastq,3393847300.0,33938473.0,GSM4186872 r1,0:50 1:50,A:891770304;C:744780247;G:797806720;T:959255404;N:234625,50,50,,,891770304,744780247,797806720,959255404,234625,SRX7199559,SRS5705114,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.84784,0.82366,0.23636,0.23442,0.7651,0.77344,0.52664,0.52603,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55493,SRR10510887,SRX7199558,SRS5705113,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Sham 2,GSM4186871,,tissue:Macrophage lineage cells|age:4 dpf,Sham 2,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186871,GSM4186871: Sham 2; Danio rerio; RNA Seq,GSM4186871,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186871,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0008L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0008L01_2.fastq.gz,fastq fastq,3597238000.0,35972380.0,GSM4186871 r1,0:50 1:50,A:971087314;C:774572159;G:820049074;T:1031281870;N:247583,50,50,,,971087314,774572159,820049074,1031281870,247583,SRX7199558,SRS5705113,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.85164,0.83175,0.26819,0.26552,0.75621,0.76378,0.52787,0.53623,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
55494,SRR10510886,SRX7199557,SRS5705112,SRP231168,PRJNA591000,RNA seq analysis of transcriptomic changes in macrophage lineage cells post acute neural injury in larval zebrafish,GSE140810,Transcriptome Analysis,Both brain resident microglia and peripheral macrophages are important cellular effectors of the inflammatory response to neural injury. They respond to neural injury by secreting a wide range of effector molecules including cytokines  chemokines and neurotrophic factors. To identify additional secreted signalling molecules  we used RNA seq gene expression profiling to detect changes in the transcriptome of macrophage lineage cells post acute neural injury in larval zebrafish. GO term analysis was then used to analyse the list of differentially expressed genes and identify secreted signalling molecules among them. Overall design: The transcriptomes of FACS purified macrophage lineage cells from mpeg1:GFP transgenic zebrafish larvae with or without xxx injury were compared.,,pubmed:32366533,,Sham 1,GSM4186870,,tissue:Macrophage lineage cells|age:4 dpf,Sham 1,Reads were trimmed using Cutadapt version cutadapt 1.9.dev2. Reads were trimmed for quality at the 3’ end using a quality threshold of 30 and for adapter sequences of the TruSeq DNA Nano kit AGATCGGAAGAGC. Reads post trimming were required to have a minimum length of 35. The reference used for mapping was the Danio rerio GRCz10 genome from Ensembl. The annotation used for counting was the standard GTF format annotation for that reference annotation version 84. Reads were aligned to the reference genome using STAR version 2.5.2b specifying paired end reads and the option   outSAMtype BAM Unsorted. All other parameters were left at default. Reads were assigned to features of type ‘exon’ in the input annotation grouped by gene id in the reference genome using featureCounts version 1.5.1. Strandness was set to ‘reverse’ and a minimum alignment quality of 10 was specified. Gene names and other fields were derived from input annotation and added to the count/expression matrices. The raw counts table was filtered to remove genes consisting predominantly of near zero counts  filtering on counts per million CPM to avoid artefacts due to library depth. Specifically  a row of the expression matrix was required to have values greater than 0.1 in at least 3 samples  corresponding to the smallest sample group as defined by Group  once any samples were removed where applicable. Reads were normalised using the weighted trimmed mean of M values method  passing ‘TMM’ as the method to the calcNormFactors method of edgeR. A principal components analysis was undertaken on normalised and filtered expression data to explore observed patterns with respect to experimental factors. The cumulative proportion of variance associated with each factor was used to study the level of structure in the data  while associations between continuous value ranges in principal components and categorical experimental factors was assessed with an ANOVA test. Three samples Injury 3  Injury 5 and Injury 6 were identified as having high duplication rate and low mapping rate during bioinformatics QC. The high levels of variation in these three samples caused signal from the remaining samples to be overwhelmed  and it was clear that inclusion of the poor quality samples would negatively affect the results of the analysis. In summary samples Injury 3  Injury 5 and Injury 6 were removed  and filtering and normalisation re performed  prior to generation of subsequent plots and downstream analysis. Differential analysis was carried out with edgeR version 3.20.1. Fold changes were estimated as per the default behaviour of edgeR  to avoid artefacts which occur with empirical calculation. Statistical assessment of differential expression was carried out with the quasi likelihood QL F test. Genome build: GRCz10 Supplementary files format and content: A comma separated value file of normalised gene wise counts  gene wise differential expression log fold changes and false discovery rates for every sample passed to downstream analysis.,Macrophage lineage cells,Neural injury was induced in mpeg1:GFP transgenic zebrafish larvae at 4 dpf by piercing the optic tectum with a fine metal pin. At 2 xxx post injury hpi  sham and injured larvae were anaesthesised  larval heads were transected  the tissue was homogenised  and GFP+ cells were isolated from the resulting cell suspension using FACS. Sorted cells from about 180 larvae were used per sample. Six samples each were generated for 'Sham' and 'Injury' experimental conditions.,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,,age:4 dpf,GSM4186870,GSM4186870: Sham 1; Danio rerio; RNA Seq,GSM4186870,,1,RNA was extracted from sorted cells using a RNeasy Plus Micro kit Qiagen. RNA was reverse transcribed and amplified using an Ovation RNA Seq System V2 NuGEN with an input of at least 500 ng RNA per sample. Libraries were prepared using a manual TruSeq DNA Nano gel free library kit Illumina.,GEO Accession:GSM4186870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP231168,,,180809_A00291_0059_BH3FLKDRXX_2_11398HL0001L01_1.fastq.gz 180809_A00291_0059_BH3FLKDRXX_2_11398HL0001L01_2.fastq.gz,fastq fastq,3476774400.0,34767744.0,GSM4186870 r1,0:50 1:50,A:916708367;C:758990814;G:811017343;T:989817555;N:240321,50,50,,,916708367,758990814,811017343,989817555,240321,SRX7199557,SRS5705112,SRA1000323,GEO,"Centre for Discovery Brain Sciences, University of Edinburgh",2,0.84104,0.81935,0.24072,0.23754,0.75515,0.76347,0.52881,0.53924,50,50,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-21,Larval,Larval,Blood,Hematopoietic System
58407,SRR11309042,SRX7913591,SRS6320433,SRP252869,PRJNA612697,RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish,GSE146995,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.,,pubmed:33651979,,cd41gfp WT3,GSM4411870,,tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf,cd41gfp WT3,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample,hematopoietic stem and progenitor cells,,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,,develpmental stage:40 hpf,GSM4411870,GSM4411870: cd41gfp WT3; Danio rerio; RNA Seq,GSM4411870,,1,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,GEO Accession:GSM4411870,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP252869,,,cd41gfp_WT3_2.fq.gz cd41gfp_WT3_1.fq.gz,fastq fastq,11085766500.0,36952555.0,GSM4411870 r1,0:150 1:150,A:2992020230;C:2573519486;G:2581891304;T:2938153427;N:182053,150,150,,,2992020230,2573519486,2581891304,2938153427,182053,SRX7913591,SRS6320433,SRA1055135,GEO,Albert Einstein College of Medicine,2,0.77434,0.77183,0.20553,0.20573,0.77171,0.77922,0.5109,0.495,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-15,Pharyngula,Embryo,Blood,Hematopoietic System
58408,SRR11309041,SRX7913590,SRS6320432,SRP252869,PRJNA612697,RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish,GSE146995,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.,,pubmed:33651979,,cd41gfp WT2,GSM4411869,,tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf,cd41gfp WT2,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample,hematopoietic stem and progenitor cells,,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,,develpmental stage:40 hpf,GSM4411869,GSM4411869: cd41gfp WT2; Danio rerio; RNA Seq,GSM4411869,,1,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,GEO Accession:GSM4411869,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP252869,,,cd41gfp_WT2_1.fq.gz cd41gfp_WT2_2.fq.gz,fastq fastq,11221423200.0,37404744.0,GSM4411869 r1,0:150 1:150,A:2921284710;C:2714470786;G:2708278380;T:2877145192;N:244132,150,150,,,2921284710,2714470786,2708278380,2877145192,244132,SRX7913590,SRS6320432,SRA1055135,GEO,Albert Einstein College of Medicine,2,0.75116,0.75065,0.18086,0.18146,0.79586,0.80016,0.52492,0.52828,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-15,Pharyngula,Embryo,Blood,Hematopoietic System
58409,SRR11309040,SRX7913589,SRS6320431,SRP252869,PRJNA612697,RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish,GSE146995,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.,,pubmed:33651979,,cd41gfp WT1,GSM4411868,,tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf,cd41gfp WT1,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample,hematopoietic stem and progenitor cells,,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,,develpmental stage:40 hpf,GSM4411868,GSM4411868: cd41gfp WT1; Danio rerio; RNA Seq,GSM4411868,,1,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,GEO Accession:GSM4411868,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP252869,,,cd41gfp_WT1_1.fq.gz cd41gfp_WT1_2.fq.gz,fastq fastq,11115852900.0,37052843.0,GSM4411868 r1,0:150 1:150,A:3004371197;C:2577587578;G:2575472481;T:2958199318;N:222326,150,150,,,3004371197,2577587578,2575472481,2958199318,222326,SRX7913589,SRS6320431,SRA1055135,GEO,Albert Einstein College of Medicine,2,0.76528,0.76415,0.19581,0.19637,0.77039,0.77579,0.65251,0.64941,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-15,Pharyngula,Embryo,Blood,Hematopoietic System
58410,SRR11309039,SRX7913588,SRS6320430,SRP252869,PRJNA612697,RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish,GSE146995,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.,,pubmed:33651979,,cd41gfp mut3,GSM4411867,,tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf mutant,cd41gfp mut3,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample,hematopoietic stem and progenitor cells,,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,,develpmental stage:40 hpf mutant,GSM4411867,GSM4411867: cd41gfp mut3; Danio rerio; RNA Seq,GSM4411867,,1,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,GEO Accession:GSM4411867,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP252869,,,cd41gfp_mut3_2.fq.gz cd41gfp_mut3_1.fq.gz,fastq fastq,11157315900.0,37191053.0,GSM4411867 r1,0:150 1:150,A:2980738665;C:2622591667;G:2625477229;T:2928292016;N:216323,150,150,,,2980738665,2622591667,2625477229,2928292016,216323,SRX7913588,SRS6320430,SRA1055135,GEO,Albert Einstein College of Medicine,2,0.77032,0.76857,0.22483,0.22518,0.78685,0.79226,0.64484,0.52439,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-15,Pharyngula,Embryo,Blood,Hematopoietic System
58411,SRR11309038,SRX7913587,SRS6320429,SRP252869,PRJNA612697,RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish,GSE146995,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.,,pubmed:33651979,,cd41gfp mut2,GSM4411866,,tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf mutant,cd41gfp mut2,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample,hematopoietic stem and progenitor cells,,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,,develpmental stage:40 hpf mutant,GSM4411866,GSM4411866: cd41gfp mut2; Danio rerio; RNA Seq,GSM4411866,,1,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,GEO Accession:GSM4411866,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP252869,,,cd41gfp_mut2_1.fq.gz cd41gfp_mut2_2.fq.gz,fastq fastq,10547871900.0,35159573.0,GSM4411866 r1,0:150 1:150,A:2823130170;C:2469329724;G:2474038085;T:2781202013;N:171908,150,150,,,2823130170,2469329724,2474038085,2781202013,171908,SRX7913587,SRS6320429,SRA1055135,GEO,Albert Einstein College of Medicine,2,0.77081,0.76762,0.19951,0.20063,0.78518,0.7905,0.62792,0.62645,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-15,Pharyngula,Embryo,Blood,Hematopoietic System
58412,SRR11309037,SRX7913586,SRS6320428,SRP252869,PRJNA612697,RNA seq of hematopoietic stem and progenitor cells from 40 hpf ddx41 mutant and sibling zebrafish,GSE146995,Transcriptome Analysis,The purpose of the experiment was to define the gene expression and splicing alterations occurring when the levels of dead box helicase 41 are lowered in embryonic zebrafish. Results provide insight the role of Ddx41 in hematopoietic development. Overall design: mRNA profiling of cd41 positive hematopoietic stem and progenitor cells isolated from 40 hpf ddx41 mutant and sibling zebrafish using Illumina NovaSeq. Three samples were sequenced for each genotype.,,pubmed:33651979,,cd41gfp mut1,GSM4411865,,tissue:hematopoietic stem and progenitor cells|develpmental stage:40 hpf mutant,cd41gfp mut1,basecalling was done with the Picard module IlluminaBasecallsToFastq Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired end reads were mapped using STAR aligner version 2.4.2a to the reference genome. Differential expression analysis was done using DESeq2 via DEApp. To calculate FPKM  Cufflinks version 2.2.1 was used. Genome build: GRcz10 Supplementary files format and content: tab delimited text file include gene counts for each sample,hematopoietic stem and progenitor cells,,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,,develpmental stage:40 hpf mutant,GSM4411865,GSM4411865: cd41gfp mut1; Danio rerio; RNA Seq,GSM4411865,,1,cd41 positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep Zymo. Libraries were made at BGI following their low input RNA protocol.,GEO Accession:GSM4411865,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP252869,,,cd41gfp_mut1_2.fq.gz cd41gfp_mut1_1.fq.gz,fastq fastq,11189402700.0,37298009.0,GSM4411865 r1,0:150 1:150,A:2871209944;C:2750231891;G:2743649245;T:2824098453;N:213167,150,150,,,2871209944,2750231891,2743649245,2824098453,213167,SRX7913586,SRS6320428,SRA1055135,GEO,Albert Einstein College of Medicine,2,0.74106,0.73935,0.17858,0.18025,0.80574,0.81231,0.60677,0.65263,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-15,Pharyngula,Embryo,Blood,Hematopoietic System
59515,SRR11926689,SRX8472335,SRS6772936,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,WT5,GSM4591370,,tissue:Healthy sorted thymus|cell type:thymocytes|genotype:Tglck:GFP|tumor stg:healthy|lab of sample collection and sequencing:Frazer lab,WT5,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,Healthy sorted  thymus,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:thymocytes|genotype:Tglck:GFP|tumor stg:healthy|lab of sample collection and sequencing:Frazer lab,GSM4591370,GSM4591370: WT5; Danio rerio; RNA Seq,GSM4591370,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591370,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP265974,,,FWTsample_5.fastq.gz FWTsample_5_R2.fastq.gz,fastq fastq,4633582858.0,22938529.0,GSM4591370 r1,0:101 1:101,A:1263929939;C:1047240206;G:1052800791;T:1263574247;N:6037675,101,101,,,1263929939,1047240206,1052800791,1263574247,6037675,SRX8472335,SRS6772936,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",2,0.91347,0.91728,0.27187,0.27409,0.76585,0.76859,0.45662,0.48071,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Thymus,Hematopoietic System
59516,SRR11926688,SRX8472334,SRS6772935,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,WT4,GSM4591369,,tissue:Healthy sorted thymus|cell type:thymocytes|genotype:Tglck:GFP|tumor stg:healthy|lab of sample collection and sequencing:Frazer lab,WT4,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,Healthy sorted  thymus,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:thymocytes|genotype:Tglck:GFP|tumor stg:healthy|lab of sample collection and sequencing:Frazer lab,GSM4591369,GSM4591369: WT4; Danio rerio; RNA Seq,GSM4591369,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591369,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP265974,,,FWTsample_4.fastq.gz FWTsample_4_R2.fastq.gz,fastq fastq,4113149600.0,20565748.0,GSM4591369 r1,0:100 1:100,A:1084628064;C:963840734;G:985823964;T:1078691018;N:165820,100,100,,,1084628064,963840734,985823964,1078691018,165820,SRX8472334,SRS6772935,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",2,0.9336,0.93539,0.11919,0.11989,0.76368,0.76757,0.4904,0.47498,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Thymus,Hematopoietic System
59517,SRR11926687,SRX8472333,SRS6772934,SRP265974,PRJNA637328,A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models,GSE151816,Transcriptome Analysis,We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition  RNA sequencing was performed on various additional zebrafish T ALL models shrek  hulk  otg  hMYC  sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1  shrek  hulk  otg T ALL samples  wild type thymocytes sequenced in the Speleman lab  wild type thymocytes sequenced in the Frazer lab. Shrek  otg  hulk  hMYC preleukemic thymocytes,,pubmed:32591643,,WT3,GSM4591368,,tissue:Healthy sorted thymus|cell type:thymocytes|genotype:Tglck:GFP|tumor stg:healthy|lab of sample collection and sequencing:Frazer lab,WT3,First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts,Healthy sorted  thymus,,Truseq stranded mRNA library prep illumina  #20020594,,cell type:thymocytes|genotype:Tglck:GFP|tumor stg:healthy|lab of sample collection and sequencing:Frazer lab,GSM4591368,GSM4591368: WT3; Danio rerio; RNA Seq,GSM4591368,,1,Truseq stranded mRNA library prep illumina  #20020594,GEO Accession:GSM4591368,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 3000,,SRP265974,,,FWTsample_3_R2.fastq.gz FWTsample_3.fastq.gz,fastq fastq,3966667200.0,19833336.0,GSM4591368 r1,0:100 1:100,A:1125938234;C:857622800;G:856236104;T:1122434590;N:4435472,100,100,,,1125938234,857622800,856236104,1122434590,4435472,SRX8472333,SRS6772934,SRA1083220,GEO,"Center for Medical Genetics, Ghent University",2,0.93918,0.92495,0.16292,0.15907,0.75866,0.76883,0.51794,0.51278,100,100,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Belgium,2020-06-04,Undetermined,Undetermined,Thymus,Hematopoietic System