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
28902,SRR26827532,SRX22524052,SRS19535497,SRP471831,PRJNA1040223,The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish,GSE247730,Transcriptome Analysis,Neutrophils and erythrocytes are vital to the immune system and oxygen transport  respectively. However  the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research  zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study  we showed that erythrocytes predominantly reside inside the blood vessels of the CHT  while neutrophils stay outside. Ectopic vascular endothelium  induced by Bone Morphogenetic Protein 2bBmp2b overexpression  attracts both cell types  with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter  which is specifically expressed in vein  lymphatic vessels and CHT vein endothelial cells  rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.,,,,vein endothelium cells  Day5 rep2,GSM7899809,,source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing,vein endothelium cells  Day5 rep2,Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built  and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region  a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations  using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r  project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,Caudal hematopoietic tissue,,Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.,,tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment,GSM7899809,GSM7899809: vein endothelium cells  Day5 rep2; Danio rerio; RNA Seq,GSM7899809 r1,GSM7899809,1,Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP471831,,loader:fastq load.py,vein_endothelium_cells-2_1.fq.gz vein_endothelium_cells-2_2.fq.gz,fastq fastq,9110989800.0,30369966.0,GSM7899809 r1,0:150 1:150,A:2454542720;C:2090617752;G:2126374129;T:2439172440;N:282759,150,150,,,2454542720,2090617752,2126374129,2439172440,282759,SRX22524052,SRS19535497,SRA1750986,South China University of Technology,South China University of Technology,2,0.89413,0.89048,0.1507,0.14922,0.78466,0.78496,0.5263,0.5335,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2023-11-14,Larval,Larval,Blood,Hematopoietic System
28903,SRR26827533,SRX22524051,SRS19535496,SRP471831,PRJNA1040223,The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish,GSE247730,Transcriptome Analysis,Neutrophils and erythrocytes are vital to the immune system and oxygen transport  respectively. However  the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research  zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study  we showed that erythrocytes predominantly reside inside the blood vessels of the CHT  while neutrophils stay outside. Ectopic vascular endothelium  induced by Bone Morphogenetic Protein 2bBmp2b overexpression  attracts both cell types  with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter  which is specifically expressed in vein  lymphatic vessels and CHT vein endothelial cells  rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.,,,,vein endothelium cells  Day5 rep1,GSM7899808,,source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing,vein endothelium cells  Day5 rep1,Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built  and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region  a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations  using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r  project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,Caudal hematopoietic tissue,,Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.,,tissue:Caudal hematopoietic tissue|cell type:vein endothelium cells|genotype:Wildtype|treatment:no treatment,GSM7899808,GSM7899808: vein endothelium cells  Day5 rep1; Danio rerio; RNA Seq,GSM7899808 r1,GSM7899808,1,Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP471831,,loader:fastq load.py,vein_endothelium_cells-1_2.fq.gz vein_endothelium_cells-1_1.fq.gz,fastq fastq,8585973300.0,28619911.0,GSM7899808 r1,0:150 1:150,A:2253650188;C:2015841518;G:2037568162;T:2278266858;N:646574,150,150,,,2253650188,2015841518,2037568162,2278266858,646574,SRX22524051,SRS19535496,SRA1750986,South China University of Technology,South China University of Technology,2,0.8876,0.88392,0.14777,0.14719,0.78969,0.79038,0.53142,0.53136,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2023-11-14,Larval,Larval,Blood,Hematopoietic System
28904,SRR26827534,SRX22524050,SRS19535495,SRP471831,PRJNA1040223,The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish,GSE247730,Transcriptome Analysis,Neutrophils and erythrocytes are vital to the immune system and oxygen transport  respectively. However  the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research  zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study  we showed that erythrocytes predominantly reside inside the blood vessels of the CHT  while neutrophils stay outside. Ectopic vascular endothelium  induced by Bone Morphogenetic Protein 2bBmp2b overexpression  attracts both cell types  with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter  which is specifically expressed in vein  lymphatic vessels and CHT vein endothelial cells  rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.,,,,non vein endothelium cells  Control  Day5 rep2,GSM7899807,,source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing,non vein endothelium cells  Control  Day5 rep2,Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built  and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region  a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations  using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r  project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,Caudal hematopoietic tissue,,Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.,,tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment,GSM7899807,GSM7899807: non vein endothelium cells  Control  Day5 rep2; Danio rerio; RNA Seq,GSM7899807 r1,GSM7899807,1,Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP471831,,loader:fastq load.py,non-vein_endothelium_cells-2_1.fq.gz non-vein_endothelium_cells-2_2.fq.gz,fastq fastq,9363942600.0,31213142.0,GSM7899807 r1,0:150 1:150,A:2523111369;C:2155598161;G:2171776473;T:2513164552;N:292045,150,150,,,2523111369,2155598161,2171776473,2513164552,292045,SRX22524050,SRS19535495,SRA1750986,South China University of Technology,South China University of Technology,2,0.93879,0.93706,0.10971,0.10945,0.76721,0.76737,0.51346,0.51513,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2023-11-14,Larval,Larval,Blood,Hematopoietic System
28905,SRR26827535,SRX22524049,SRS19535494,SRP471831,PRJNA1040223,The Caudal Hematopoietic Tissue is Differentially Required for Erythrocytes and Neutrophils from Definitive Hematopoiesis in Zebrafish,GSE247730,Transcriptome Analysis,Neutrophils and erythrocytes are vital to the immune system and oxygen transport  respectively. However  the mechanisms by which hematopoietic niches support their development remain incompletely understood. In hematopoiesis research  zebrafish larvae are a common model for studying the development of definitive neutrophils and erythrocytes in the caudal hematopoietic tissue. In this study  we showed that erythrocytes predominantly reside inside the blood vessels of the CHT  while neutrophils stay outside. Ectopic vascular endothelium  induced by Bone Morphogenetic Protein 2bBmp2b overexpression  attracts both cell types  with erythrocytes inside and neutrophils outside. CHT removal has minimal impact on definitive neutrophils from the ventral wall of the dorsal aorta VDA but severely affects definitive erythrocytes from the same source. Bulk RNA sequencing identified epoa as a vital factor for erythrocyte generation within CHT endothelium. Overexpression of epoa through the lyve1b promoter  which is specifically expressed in vein  lymphatic vessels and CHT vein endothelial cells  rescued the erythrocyte reduction in epoa mutants. Our study reveals that the caudal hematopoietic tissue is differentially required for definitive erythrocytes and neutrophils. Overall design: We then performed gene expression profiling analysis using data obtained from BULK RNA seq of 5dpf vein endothelium cells and endothelium cells.,,,,non vein endothelium cells  Control  Day5 rep1,GSM7899806,,source name:Caudal hematopoietic tissue|tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment|geo loc name:missing|collection date:missing,non vein endothelium cells  Control  Day5 rep1,Filtering of Clean Reads by fastp version 0.18.0.The parameters were as follows:1 removing reads containing adapters; 2 removing reads containing more than 10% of unknown nucleotides N; 3 removing low quality reads containing more than 50% of low quality Q value≤20 bases. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database.The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation. An index of the reference genome was built  and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 with “ rna strandness RF” and other parameters set as a default.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region  a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations  using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments Principal component analysis PCA was performed with R package gmodels http://www.r  project.org/ in this experience;RNAs differential expression analysis was performed by DESeq2; Assembly: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample,Caudal hematopoietic tissue,,Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.,,tissue:Caudal hematopoietic tissue|cell type:non vein endothelium cells|genotype:Wildtype|treatment:no treatment,GSM7899806,GSM7899806: non vein endothelium cells  Control  Day5 rep1; Danio rerio; RNA Seq,GSM7899806 r1,GSM7899806,1,Non vein endothelium cells and vein endothelium cells were collected from 5dpf of  Tgkdrl:GFP;lyve1b:DsRed CHT collector CHT double positive cells and GFP+ single cells for cell sorting.Total RNA was extracted using Trizol reagent kit Invitrogen  Carlsbad  CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies  Palo Alto  CA  USA .the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs  Ipswich  MA  USA. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou  China.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP471831,,loader:fastq load.py,non-vein_endothelium_cells-1_1.fq.gz non-vein_endothelium_cells-1_2.fq.gz,fastq fastq,8396176800.0,27987256.0,GSM7899806 r1,0:150 1:150,A:2190594419;C:1990596503;G:2019391921;T:2194713332;N:880625,150,150,,,2190594419,1990596503,2019391921,2194713332,880625,SRX22524049,SRS19535494,SRA1750986,South China University of Technology,South China University of Technology,2,0.94508,0.94385,0.0967,0.09697,0.77642,0.77632,0.49896,0.49962,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,bulk,bulk,,China,2023-11-14,Larval,Larval,Blood,Hematopoietic System
30018,SRR27988043,SRX23641260,SRS20476222,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /   36 hpf blood,zebrafish hamp /  36 hpf blood replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq  hamp /   36 hpf blood  replicate 3,B 6,B 6,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,KO-3_R2_001.fastq.gz KO-3_R1_001.fastq.gz,fastq fastq,8752665900.0,29175553.0,KO 3 R1 001.fastq.gz,0:150 1:150,A:2204170575;C:2174083961;G:2224694970;T:2149603712;N:112682,150,150,,,2204170575,2174083961,2224694970,2149603712,112682,SRX23641260,SRS20476222,SRA1803422,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.91553,0.91645,0.01276,0.01288,0.85884,0.85839,0.35101,0.40996,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-02-16,Pharyngula,Embryo,Blood,Hematopoietic System
30019,SRR27988044,SRX23641259,SRS20476221,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /   36 hpf blood,zebrafish hamp /  36 hpf blood replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq  hamp /   36 hpf blood  replicate 2,B 5,B 5,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,KO-2_R1_001.fastq.gz KO-2_R2_001.fastq.gz,fastq fastq,8060498700.0,26868329.0,KO 2 R1 001.fastq.gz,0:150 1:150,A:2045797336;C:1985847523;G:2035528018;T:1993222840;N:102983,150,150,,,2045797336,1985847523,2035528018,1993222840,102983,SRX23641259,SRS20476221,SRA1803422,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.9213,0.92027,0.0167,0.01676,0.8242,0.82475,0.41081,0.41111,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-02-16,Pharyngula,Embryo,Blood,Hematopoietic System
30020,SRR27988045,SRX23641258,SRS20476220,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,hamp /   36 hpf blood,zebrafish hamp /  36 hpf blood replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:hamp knockdown|sample type:tissue sample|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq  hamp /   36 hpf blood  replicate 1,B 4,B 4,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,KO-1_R1_001.fastq.gz KO-1_R2_001.fastq.gz,fastq fastq,8707637700.0,29025459.0,KO 1 R1 001.fastq.gz,0:150 1:150,A:2222026435;C:2133480283;G:2182087972;T:2169932447;N:110563,150,150,,,2222026435,2133480283,2182087972,2169932447,110563,SRX23641258,SRS20476220,SRA1803422,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.91531,0.91359,0.02185,0.0221,0.81213,0.8128,0.37868,0.42351,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-02-16,Pharyngula,Embryo,Blood,Hematopoietic System
30021,SRR27988046,SRX23641257,SRS20476219,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 36 hpf blood,zebrafish wild type 36 hpf blood replicate 3,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq  wild type  36 hpf blood  replicate 3,B 3,B 3,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT-3_R1_001.fastq.gz WT-3_R2_001.fastq.gz,fastq fastq,8829371400.0,29431238.0,WT 3 R1 001.fastq.gz,0:150 1:150,A:2278837675;C:2141723937;G:2193442375;T:2215253519;N:113894,150,150,,,2278837675,2141723937,2193442375,2215253519,113894,SRX23641257,SRS20476219,SRA1803422,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.90531,0.9043,0.03015,0.03017,0.8101,0.8112,0.43085,0.43002,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-02-16,Pharyngula,Embryo,Blood,Hematopoietic System
30022,SRR27988047,SRX23641256,SRS20476218,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 36 hpf blood,zebrafish wild type 36 hpf blood replicate 2,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq  wild type  36 hpf blood  replicate 2,B 2,B 2,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT-2_R1_001.fastq.gz WT-2_R2_001.fastq.gz,fastq fastq,7365643800.0,24552146.0,WT 2 R1 001.fastq.gz,0:150 1:150,A:1867985067;C:1819016430;G:1870006707;T:1808540769;N:94827,150,150,,,1867985067,1819016430,1870006707,1808540769,94827,SRX23641256,SRS20476218,SRA1803422,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.90612,0.90536,0.01714,0.01746,0.88109,0.88156,0.32469,0.39232,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-02-16,Pharyngula,Embryo,Blood,Hematopoietic System
30023,SRR27988048,SRX23641255,SRS20476217,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,,wild type 36 hpf blood,zebrafish wild type 36 hpf blood replicate 1,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf|dev stage:36 hpf|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:blood|genotype:wild type|sample type:tissue sample|treatment:replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq  wild type  36 hpf blood  replicate 1,B 1,B 1,bulk RNA seq,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,WT-1_R1_001.fastq.gz WT-1_R2_001.fastq.gz,fastq fastq,8631863400.0,28772878.0,WT 1 R1 001.fastq.gz,0:150 1:150,A:2186212554;C:2135990723;G:2179142081;T:2130408485;N:109557,150,150,,,2186212554,2135990723,2179142081,2130408485,109557,SRX23641255,SRS20476217,SRA1803422,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.90461,0.90281,0.01388,0.01365,0.83871,0.83895,0.36511,0.41074,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc_generic,bulk,bulk,,China,2024-02-16,Pharyngula,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
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
42501,SRR5683317,SRX2918465,SRS2284474,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round2 cryo3,GSM2668116,,source name:Mpeg 14 xxx post injury Round2 cryo3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,Mpeg 14 xxx post injury Round2 cryo3,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round2 cryo3,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,GSM2668116,GSM2668116: Mpeg 14 xxx post injury Round2 cryo3; Danio rerio; RNA Seq,GSM2668116,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668116,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,cryo3_14dpi_B_R1.fastq.gz cryo3_14dpi_B_R2.fastq.gz,fastq fastq,7861934638.0,49554149.0,GSM2668116 r1,0:79.32 1:79.33,A:2180198909;C:1707559679;G:1786562980;T:2185442888;N:2170182,79,79,,,2180198909,1707559679,1786562980,2185442888,2170182,SRX2918465,SRS2284474,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.92041,0.92378,0.14221,0.14168,0.79799,0.8016,0.45038,0.35896,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42502,SRR5683316,SRX2918464,SRS2284472,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round2 cryo2,GSM2668115,,source name:Mpeg 14 xxx post injury Round2 cryo2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,Mpeg 14 xxx post injury Round2 cryo2,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round2 cryo2,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,GSM2668115,GSM2668115: Mpeg 14 xxx post injury Round2 cryo2; Danio rerio; RNA Seq,GSM2668115,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668115,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,cryo2_14dpi_B_R1.fastq.gz cryo2_14dpi_B_R2.fastq.gz,fastq fastq,8095516200.0,51058824.0,GSM2668115 r1,0:79.28 1:79.28,A:2251179258;C:1721305507;G:1814673340;T:2305885309;N:2472786,79,79,,,2251179258,1721305507,1814673340,2305885309,2472786,SRX2918464,SRS2284472,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.89889,0.89756,0.18338,0.17899,0.81219,0.81525,0.43098,0.4397,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42503,SRR5683314,SRX2918463,SRS2284471,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round2 cryo1 merged,GSM2668114,,source name:Mpeg 14 xxx post injury Round2 cryo1 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,Mpeg 14 xxx post injury Round2 cryo1 merged,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round2 cryo1 merged,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,GSM2668114,GSM2668114: Mpeg 14 xxx post injury Round2 cryo1 merged; Danio rerio; RNA Seq,GSM2668114,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668114,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,14dpicryo1_mpeg_B_R1_May.fastq.gz 14dpicryo1_mpeg_B_R2_May.fastq.gz,fastq fastq,3423280266.0,21561025.0,GSM2668114 r1,0:79.38 1:79.39,A:1107875201;C:594804208;G:621478979;T:1098524417;N:597461,79,79,,,1107875201,594804208,621478979,1098524417,597461,SRX2918463,SRS2284471,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.82792,0.82592,0.70435,0.70409,0.7963,0.81209,0.49674,0.50012,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42504,SRR5683315,SRX2918463,SRS2284471,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round2 cryo1 merged,GSM2668114,,source name:Mpeg 14 xxx post injury Round2 cryo1 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,Mpeg 14 xxx post injury Round2 cryo1 merged,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round2 cryo1 merged,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,GSM2668114,GSM2668114: Mpeg 14 xxx post injury Round2 cryo1 merged; Danio rerio; RNA Seq,GSM2668114,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668114,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,14dpicryo1_mpeg_B_R1_June.fastq.gz 14dpicryo1_mpeg_B_R2_June.fastq.gz,fastq fastq,610753180.0,3844389.0,GSM2668114 r2,0:79.43 1:79.44,A:194990113;C:106753101;G:111444912;T:197419441;N:145613,79,79,,,194990113,106753101,111444912,197419441,145613,SRX2918463,SRS2284471,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.83295,0.83136,0.71203,0.71039,0.79902,0.80957,0.50147,0.50457,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42505,SRR5683313,SRX2918462,SRS2284470,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round2 sham3,GSM2668113,,source name:Mpeg 14 xxx post injury Round2 sham3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 14 xxx post injury Round2 sham3,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round2 sham3,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668113,GSM2668113: Mpeg 14 xxx post injury Round2 sham3; Danio rerio; RNA Seq,GSM2668113,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668113,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,sham3_14dpi_B_R1.fastq.gz sham3_14dpi_B_R2.fastq.gz,fastq fastq,6045529728.0,38096625.0,GSM2668113 r1,0:79.34 1:79.35,A:1692396398;C:1295917589;G:1361588402;T:1694052830;N:1574509,79,79,,,1692396398,1295917589,1361588402,1694052830,1574509,SRX2918462,SRS2284470,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.91926,0.91739,0.11828,0.11628,0.82223,0.82534,0.47847,0.49838,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42506,SRR5683309,SRX2918461,SRS2284469,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round1 sham3 merged,GSM2668112,,source name:Mpeg 14 xxx post injury Round1 sham3 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 14 xxx post injury Round1 sham3 merged,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round1 sham3 merged,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668112,GSM2668112: Mpeg 14 xxx post injury Round1 sham3 merged; Danio rerio; RNA Seq,GSM2668112,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668112,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,14dpisham3_mpeg_B_R1_May.fastq.gz 14dpisham3_mpeg_B_R2_May.fastq.gz,fastq fastq,3088232153.0,19713193.0,GSM2668112 r1,0:78.31 1:78.34,A:921823592;C:606907388;G:646058581;T:910627373;N:2815219,78,78,,,921823592,606907388,646058581,910627373,2815219,SRX2918461,SRS2284469,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.87257,0.87547,0.20876,0.20608,0.81253,0.81773,0.44997,0.46461,80,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42507,SRR5683311,SRX2918461,SRS2284469,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round1 sham3 merged,GSM2668112,,source name:Mpeg 14 xxx post injury Round1 sham3 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 14 xxx post injury Round1 sham3 merged,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round1 sham3 merged,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668112,GSM2668112: Mpeg 14 xxx post injury Round1 sham3 merged; Danio rerio; RNA Seq,GSM2668112,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668112,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,14dpisham3_mpeg_B_R1_June.fastq.gz 14dpisham3_mpeg_B_R2_June.fastq.gz,fastq fastq,846302505.0,5389309.0,GSM2668112 r2,0:78.51 1:78.53,A:245478169;C:167755451;G:179179261;T:253210722;N:678902,78,78,,,245478169,167755451,179179261,253210722,678902,SRX2918461,SRS2284469,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.87646,0.87747,0.20632,0.20462,0.81272,0.81897,0.46568,0.46082,78,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42508,SRR5683308,SRX2918460,SRS2284468,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round1 sham2,GSM2668111,,source name:Mpeg 14 xxx post injury Round1 sham2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 14 xxx post injury Round1 sham2,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round1 sham2,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668111,GSM2668111: Mpeg 14 xxx post injury Round1 sham2; Danio rerio; RNA Seq,GSM2668111,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668111,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,14dpisham2_mpeg_B_R1.fastq.gz 14dpisham2_mpeg_B_R2.fastq.gz,fastq fastq,6035307225.0,38834475.0,GSM2668111 r1,0:77.69 1:77.73,A:1766010265;C:1217065541;G:1295674905;T:1748007248;N:8549266,77,77,,,1766010265,1217065541,1295674905,1748007248,8549266,SRX2918460,SRS2284468,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.87025,0.87255,0.16504,0.16092,0.82075,0.8252,0.48031,0.38246,80,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42509,SRR5683307,SRX2918459,SRS2284467,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 14 xxx post injury Round1 sham1,GSM2668110,,source name:Mpeg 14 xxx post injury Round1 sham1|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 14 xxx post injury Round1 sham1,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 14 xxx post injury Round1 sham1,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668110,GSM2668110: Mpeg 14 xxx post injury Round1 sham1; Danio rerio; RNA Seq,GSM2668110,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668110,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,14dpisham1_mpeg_B_R1.fastq.gz 14dpisham1_mpeg_B_R2.fastq.gz,fastq fastq,12977926933.0,85345256.0,GSM2668110 r1,0:76.00 1:76.06,A:3815859192;C:2608097642;G:2746153398;T:3772773322;N:35043379,76,76,,,3815859192,2608097642,2746153398,3772773322,35043379,SRX2918459,SRS2284467,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.84194,0.84592,0.19588,0.19184,0.82022,0.82373,0.49431,0.48674,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42510,SRR5683306,SRX2918458,SRS2284466,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 5 xxx post injury resec2,GSM2668109,,source name:Mpeg 5 xxx post injury resec2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,Mpeg 5 xxx post injury resec2,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 5 xxx post injury resec2,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,GSM2668109,GSM2668109: Mpeg 5 xxx post injury resec2; Danio rerio; RNA Seq,GSM2668109,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668109,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_5dpi_resec2_R1.fastq.gz mpeg_5dpi_resec2_R2.fastq.gz,fastq fastq,3383380650.0,21264204.0,GSM2668109 r1,0:79.56 1:79.56,A:1033165656;C:667727603;G:708080342;T:973980006;N:427043,79,79,,,1033165656,667727603,708080342,973980006,427043,SRX2918458,SRS2284466,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.86066,0.85477,0.25065,0.25874,0.8072,0.81586,0.45299,0.45757,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42511,SRR5683305,SRX2918457,SRS2284465,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 5 xxx post injury resec1,GSM2668108,,source name:Mpeg 5 xxx post injury resec1|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,Mpeg 5 xxx post injury resec1,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 5 xxx post injury resec1,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,GSM2668108,GSM2668108: Mpeg 5 xxx post injury resec1; Danio rerio; RNA Seq,GSM2668108,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668108,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_5dpi_resec1_R1.fastq.gz mpeg_5dpi_resec1_R2.fastq.gz,fastq fastq,6869873301.0,43173364.0,GSM2668108 r1,0:79.56 1:79.56,A:2031090336;C:1426974358;G:1499082453;T:1911947654;N:778500,79,79,,,2031090336,1426974358,1499082453,1911947654,778500,SRX2918457,SRS2284465,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.89183,0.88662,0.13918,0.13872,0.81284,0.81736,0.39007,0.49219,78,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42512,SRR5683304,SRX2918456,SRS2284463,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 5 xxx post injury cryo4,GSM2668107,,source name:Mpeg 5 xxx post injury cryo4|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,Mpeg 5 xxx post injury cryo4,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 5 xxx post injury cryo4,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,GSM2668107,GSM2668107: Mpeg 5 xxx post injury cryo4; Danio rerio; RNA Seq,GSM2668107,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668107,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_5dpi_cryo4_R1.fastq.gz mpeg_5dpi_cryo4_R2.fastq.gz,fastq fastq,6277247450.0,39463081.0,GSM2668107 r1,0:79.53 1:79.54,A:1929673813;C:1267115857;G:1307899881;T:1772085832;N:472067,79,79,,,1929673813,1267115857,1307899881,1772085832,472067,SRX2918456,SRS2284463,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.85203,0.8343,0.24868,0.25,0.81308,0.82647,0.48925,0.50311,80,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42513,SRR5683303,SRX2918455,SRS2284464,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 5 xxx post injury cryo1,GSM2668106,,source name:Mpeg 5 xxx post injury cryo1|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,Mpeg 5 xxx post injury cryo1,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 5 xxx post injury cryo1,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,GSM2668106,GSM2668106: Mpeg 5 xxx post injury cryo1; Danio rerio; RNA Seq,GSM2668106,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668106,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_5dpi_cryo1_R1.fastq.gz mpeg_5dpi_cryo1_R2.fastq.gz,fastq fastq,4027290734.0,25319007.0,GSM2668106 r1,0:79.53 1:79.53,A:1233222560;C:810894366;G:838434971;T:1144395366;N:343471,79,79,,,1233222560,810894366,838434971,1144395366,343471,SRX2918455,SRS2284464,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.85923,0.84321,0.1985,0.20039,0.83625,0.84236,0.49381,0.48397,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42514,SRR5683302,SRX2918454,SRS2284462,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 5 xxx post injury sham3,GSM2668105,,source name:Mpeg 5 xxx post injury sham3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 5 xxx post injury sham3,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 5 xxx post injury sham3,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668105,GSM2668105: Mpeg 5 xxx post injury sham3; Danio rerio; RNA Seq,GSM2668105,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668105,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_5dpi_sham3_R2.fastq.gz mpeg_5dpi_sham3_R1.fastq.gz,fastq fastq,8115490925.0,51002382.0,GSM2668105 r1,0:79.56 1:79.56,A:2440332785;C:1628963788;G:1720872185;T:2324279946;N:1042221,79,79,,,2440332785,1628963788,1720872185,2324279946,1042221,SRX2918454,SRS2284462,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.85247,0.84621,0.27035,0.27069,0.85084,0.85451,0.45753,0.45612,80,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42515,SRR5683300,SRX2918453,SRS2284461,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 5 xxx post injury sham2 merged,GSM2668104,,source name:Mpeg 5 xxx post injury sham2 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 5 xxx post injury sham2 merged,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 5 xxx post injury sham2 merged,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668104,GSM2668104: Mpeg 5 xxx post injury sham2 merged; Danio rerio; RNA Seq,GSM2668104,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668104,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,5dpisham2_mpeg_A_R2_April.fastq.gz 5dpisham2_mpeg_A_R1_April.fastq.gz,fastq fastq,3860992328.0,24366329.0,GSM2668104 r1,0:79.22 1:79.23,A:1130628484;C:798981479;G:837808724;T:1092372622;N:1201019,79,79,,,1130628484,798981479,837808724,1092372622,1201019,SRX2918453,SRS2284461,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.89802,0.89614,0.23222,0.22961,0.79894,0.8056,0.40655,0.416,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42516,SRR5683301,SRX2918453,SRS2284461,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 5 xxx post injury sham2 merged,GSM2668104,,source name:Mpeg 5 xxx post injury sham2 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 5 xxx post injury sham2 merged,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 5 xxx post injury sham2 merged,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668104,GSM2668104: Mpeg 5 xxx post injury sham2 merged; Danio rerio; RNA Seq,GSM2668104,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668104,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,5dpisham2_mpeg_A_R2_June.fastq.gz 5dpisham2_mpeg_A_R1_June.fastq.gz,fastq fastq,1457479078.0,9196316.0,GSM2668104 r2,0:79.24 1:79.24,A:416316844;C:300713902;G:316902348;T:423075764;N:470220,79,79,,,416316844,300713902,316902348,423075764,470220,SRX2918453,SRS2284461,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.89427,0.89319,0.2414,0.23951,0.80259,0.80842,0.40686,0.41528,80,78,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42517,SRR5683299,SRX2918452,SRS2284460,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 1 xxx post injury resec4,GSM2668103,,source name:Mpeg 1 xxx post injury resec4|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,Mpeg 1 xxx post injury resec4,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 1 xxx post injury resec4,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,GSM2668103,GSM2668103: Mpeg 1 xxx post injury resec4; Danio rerio; RNA Seq,GSM2668103,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668103,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_1dpi_resec4_R1.fastq.gz mpeg_1dpi_resec4_R2.fastq.gz,fastq fastq,5609751993.0,35249823.0,GSM2668103 r1,0:79.57 1:79.57,A:1726370842;C:1096706423;G:1151202056;T:1634668514;N:804158,79,79,,,1726370842,1096706423,1151202056,1634668514,804158,SRX2918452,SRS2284460,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.85046,0.84548,0.24214,0.24515,0.77538,0.78123,0.4936,0.48972,80,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42518,SRR5683298,SRX2918451,SRS2284459,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg xxx post injury resec3,GSM2668102,,source name:Mpeg xxx post injury resec3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,Mpeg xxx post injury resec3,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg xxx post injury resec3,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,GSM2668102,GSM2668102: Mpeg xxx post injury resec3; Danio rerio; RNA Seq,GSM2668102,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668102,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_1dpi_resec3_R2.fastq.gz mpeg_1dpi_resec3_R1.fastq.gz,fastq fastq,5982719209.0,37588800.0,GSM2668102 r1,0:79.58 1:79.58,A:1830395391;C:1164413802;G:1227508893;T:1759666888;N:734235,79,79,,,1830395391,1164413802,1227508893,1759666888,734235,SRX2918451,SRS2284459,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.84899,0.84538,0.24802,0.24928,0.77352,0.77958,0.48455,0.48731,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42519,SRR5683297,SRX2918450,SRS2284458,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg xxx post injury resec2,GSM2668101,,source name:Mpeg xxx post injury resec2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,Mpeg xxx post injury resec2,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg xxx post injury resec2,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse,GSM2668101,GSM2668101: Mpeg xxx post injury resec2; Danio rerio; RNA Seq,GSM2668101,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668101,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_1dpi_resec2_R2.fastq.gz mpeg_1dpi_resec2_R1.fastq.gz,fastq fastq,5076782892.0,31911484.0,GSM2668101 r1,0:79.54 1:79.55,A:1549105925;C:1013432083;G:1063735890;T:1449731944;N:777050,79,79,,,1549105925,1013432083,1063735890,1449731944,777050,SRX2918450,SRS2284458,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.8623,0.85895,0.22428,0.22646,0.77378,0.78246,0.4794,0.47986,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42520,SRR5683296,SRX2918449,SRS2284457,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 1 xxx post injury cryo3,GSM2668100,,source name:Mpeg 1 xxx post injury cryo3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,Mpeg 1 xxx post injury cryo3,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 1 xxx post injury cryo3,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,GSM2668100,GSM2668100: Mpeg 1 xxx post injury cryo3; Danio rerio; RNA Seq,GSM2668100,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668100,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_1dpi_cryo3_R1.fastq.gz mpeg_1dpi_cryo3_R2.fastq.gz,fastq fastq,11880750994.0,75033249.0,GSM2668100 r1,0:79.16 1:79.18,A:3655884756;C:2399881665;G:2467642327;T:3355036709;N:2305537,79,79,,,3655884756,2399881665,2467642327,3355036709,2305537,SRX2918449,SRS2284457,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.88646,0.87912,0.09292,0.08786,0.84867,0.85184,0.60254,0.60389,80,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42521,SRR5683295,SRX2918448,SRS2284456,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 1 xxx post injury cryo2,GSM2668099,,source name:Mpeg 1 xxx post injury cryo2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,Mpeg 1 xxx post injury cryo2,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 1 xxx post injury cryo2,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse,GSM2668099,GSM2668099: Mpeg 1 xxx post injury cryo2; Danio rerio; RNA Seq,GSM2668099,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668099,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_1dpi_cryo2_R1.fastq.gz mpeg_1dpi_cryo2_R2.fastq.gz,fastq fastq,8232458249.0,51981300.0,GSM2668099 r1,0:79.19 1:79.19,A:2515938515;C:1635124065;G:1691955854;T:2387623909;N:1815906,79,79,,,2515938515,1635124065,1691955854,2387623909,1815906,SRX2918448,SRS2284456,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.84555,0.8442,0.15288,0.14711,0.85123,0.85222,0.49769,0.49241,80,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42522,SRR5683294,SRX2918447,SRS2284455,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 1 xxx post injury sham3,GSM2668098,,source name:Mpeg 1 xxx post injury sham3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 1 xxx post injury sham3,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 1 xxx post injury sham3,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668098,GSM2668098: Mpeg 1 xxx post injury sham3; Danio rerio; RNA Seq,GSM2668098,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668098,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_1dpi_sham3_R1.fastq.gz mpeg_1dpi_sham3_R2.fastq.gz,fastq fastq,8496331498.0,53397150.0,GSM2668098 r1,0:79.56 1:79.56,A:2502482113;C:1814852881;G:1898533497;T:2279486892;N:976115,79,79,,,2502482113,1814852881,1898533497,2279486892,976115,SRX2918447,SRS2284455,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.91041,0.90731,0.06459,0.06347,0.87945,0.88032,0.49844,0.49408,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42523,SRR5683293,SRX2918446,SRS2284453,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 1 xxx post injury sham2,GSM2668097,,source name:Mpeg 1 xxx post injury sham2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 1 xxx post injury sham2,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 1 xxx post injury sham2,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668097,GSM2668097: Mpeg 1 xxx post injury sham2; Danio rerio; RNA Seq,GSM2668097,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668097,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_1dpi_sham2_R1.fastq.gz mpeg_1dpi_sham2_R2.fastq.gz,fastq fastq,14052650652.0,88376646.0,GSM2668097 r1,0:79.50 1:79.50,A:4126576983;C:3017594179;G:3122815728;T:3783988637;N:1675125,79,79,,,4126576983,3017594179,3122815728,3783988637,1675125,SRX2918446,SRS2284453,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.90317,0.90144,0.09764,0.10054,0.82714,0.83088,0.45243,0.46936,80,80,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,Adult,Adult,Blood,Hematopoietic System
42524,SRR5683292,SRX2918445,SRS2284454,SRP109201,PRJNA390533,Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair,GSE100029,Transcriptome Analysis,Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.,,pubmed:32001677,,Mpeg 1 xxx post injury sham1,GSM2668096,,source name:Mpeg 1 xxx post injury sham1|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,Mpeg 1 xxx post injury sham1  ,Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10,Mpeg 1 xxx post injury sham1  ,,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,,strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse,GSM2668096,GSM2668096: Mpeg 1 xxx post injury sham1  ; Danio rerio; RNA Seq,GSM2668096,,1,For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl­2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B  every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g  4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9  40 mM NaCl  90 mM KCl  0.5 mM EDTA  0.5 mM spermidine  0.15 mM spermine  1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification  nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR  cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip  cat # RT L1000S  both pre treated with NPB/BSA for 30 minutes  and added to a MiniMACS separator magnet OctoMACS Separator  Miltenyl Biotec  cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific  cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet  Invitrogen  cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies  cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies  cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #’s 634888  634889  634890  634891  634892  634893  and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.,GEO Accession:GSM2668096,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP109201,,,mpeg_1dpi_sham1_R1.fastq.gz mpeg_1dpi_sham1_R2.fastq.gz,fastq fastq,7915875034.0,49807715.0,GSM2668096 r1,0:79.47 1:79.46,A:2336098216;C:1599111229;G:1685489518;T:2293887279;N:1288792,79,79,,,2336098216,1599111229,1685489518,2293887279,1288792,SRX2918445,SRS2284454,SRA574274,GEO,"Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine",2,0.86023,0.86553,0.15948,0.1498,0.84258,0.8434,0.46511,0.46972,80,79,B,B,biological fallback assumption,illumina,nextseq,full_length,random_priming,nextera,sc,single_cell_plate,smartseq,,United Kingdom,2017-06-14,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
47869,SRR6908743,SRX3856808,SRS3100400,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM9 eosinophils,GSM3070146,,tissue:WKM9 eosinophils|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM9 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM9 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070146,GSM3070146: WKM9 eosinophils; Danio rerio; RNA Seq,GSM3070146,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070146,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_eosinophils_L001_R1_001.fastq.gz WKM9_eosinophils_L001_R2_001.fastq.gz,fastq fastq,1378279915.0,9133302.0,GSM3070146 r1,0:75.43 1:75.48,A:398409215;C:214050926;G:243007260;T:522806293;N:6221,75,75,,,398409215,214050926,243007260,522806293,6221,SRX3856808,SRS3100400,SRA675960,GEO,Hubrecht Institute,2,0.32967,0.72245,0.27664,0.49284,0.96217,0.88688,0.44743,0.5676,76,73,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47870,SRR6908744,SRX3856808,SRS3100400,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM9 eosinophils,GSM3070146,,tissue:WKM9 eosinophils|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM9 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM9 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070146,GSM3070146: WKM9 eosinophils; Danio rerio; RNA Seq,GSM3070146,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070146,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_eosinophils_L002_R1_001.fastq.gz WKM9_eosinophils_L002_R2_001.fastq.gz,fastq fastq,1347027331.0,8926023.0,GSM3070146 r2,0:75.43 1:75.48,A:386373331;C:208319487;G:242442973;T:509887930;N:3610,75,75,,,386373331,208319487,242442973,509887930,3610,SRX3856808,SRS3100400,SRA675960,GEO,Hubrecht Institute,2,0.32008,0.72405,0.26859,0.48848,0.96512,0.88791,0.46692,0.55937,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47871,SRR6908745,SRX3856808,SRS3100400,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM9 eosinophils,GSM3070146,,tissue:WKM9 eosinophils|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM9 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM9 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070146,GSM3070146: WKM9 eosinophils; Danio rerio; RNA Seq,GSM3070146,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070146,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_eosinophils_L003_R1_001.fastq.gz WKM9_eosinophils_L003_R2_001.fastq.gz,fastq fastq,1241011911.0,8223327.0,GSM3070146 r3,0:75.44 1:75.48,A:356514159;C:192418351;G:221034567;T:471023588;N:21246,75,75,,,356514159,192418351,221034567,471023588,21246,SRX3856808,SRS3100400,SRA675960,GEO,Hubrecht Institute,2,0.31504,0.71934,0.26517,0.48722,0.96932,0.89499,0.47715,0.56814,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47872,SRR6908746,SRX3856808,SRS3100400,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM9 eosinophils,GSM3070146,,tissue:WKM9 eosinophils|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM9 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM9 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070146,GSM3070146: WKM9 eosinophils; Danio rerio; RNA Seq,GSM3070146,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070146,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_eosinophils_L004_R1_001.fastq.gz WKM9_eosinophils_L004_R2_001.fastq.gz,fastq fastq,1199788386.0,7950347.0,GSM3070146 r4,0:75.44 1:75.47,A:343966384;C:184985849;G:216629920;T:454187010;N:19223,75,75,,,343966384,184985849,216629920,454187010,19223,SRX3856808,SRS3100400,SRA675960,GEO,Hubrecht Institute,2,0.32136,0.71802,0.27107,0.48741,0.97098,0.90057,0.4616,0.56009,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47917,SRR6908693,SRX3856796,SRS3100388,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM4 eosinophils,GSM3070134,,tissue:WKM4 eosinophils|FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM4 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM4 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070134,GSM3070134: WKM4 eosinophils; Danio rerio; RNA Seq,GSM3070134,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070134,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM4_eosinophils_L001_R1_001.fastq.gz WKM4_eosinophils_L001_R2_001.fastq.gz,fastq fastq,1044383799.0,6918578.0,GSM3070134 r1,0:75.49 1:75.46,A:293266328;C:159927306;G:179144897;T:412003143;N:42125,75,75,,,293266328,159927306,179144897,412003143,42125,SRX3856796,SRS3100388,SRA675960,GEO,Hubrecht Institute,2,0.38953,0.76677,0.33438,0.55076,0.94775,0.83664,0.47684,0.51667,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47918,SRR6908694,SRX3856796,SRS3100388,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM4 eosinophils,GSM3070134,,tissue:WKM4 eosinophils|FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM4 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM4 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070134,GSM3070134: WKM4 eosinophils; Danio rerio; RNA Seq,GSM3070134,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070134,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM4_eosinophils_L002_R1_001.fastq.gz WKM4_eosinophils_L002_R2_001.fastq.gz,fastq fastq,1065518294.0,7059081.0,GSM3070134 r2,0:75.49 1:75.45,A:299578147;C:162208243;G:185866185;T:417812882;N:52837,75,75,,,299578147,162208243,185866185,417812882,52837,SRX3856796,SRS3100388,SRA675960,GEO,Hubrecht Institute,2,0.36825,0.75817,0.3148,0.55624,0.95061,0.84794,0.47713,0.52081,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47919,SRR6908695,SRX3856796,SRS3100388,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM4 eosinophils,GSM3070134,,tissue:WKM4 eosinophils|FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM4 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM4 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070134,GSM3070134: WKM4 eosinophils; Danio rerio; RNA Seq,GSM3070134,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070134,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM4_eosinophils_L003_R1_001.fastq.gz WKM4_eosinophils_L003_R2_001.fastq.gz,fastq fastq,1020526841.0,6760661.0,GSM3070134 r3,0:75.50 1:75.45,A:287644655;C:155831653;G:174910820;T:402133481;N:6232,75,75,,,287644655,155831653,174910820,402133481,6232,SRX3856796,SRS3100388,SRA675960,GEO,Hubrecht Institute,2,0.38266,0.76495,0.32861,0.55487,0.94909,0.84502,0.47881,0.50844,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47920,SRR6908696,SRX3856796,SRS3100388,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM4 eosinophils,GSM3070134,,tissue:WKM4 eosinophils|FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM4 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM4 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070134,GSM3070134: WKM4 eosinophils; Danio rerio; RNA Seq,GSM3070134,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070134,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM4_eosinophils_L004_R2_001.fastq.gz WKM4_eosinophils_L004_R1_001.fastq.gz,fastq fastq,1036249497.0,6864317.0,GSM3070134 r4,0:75.50 1:75.46,A:290241796;C:157806083;G:180760457;T:407436042;N:5119,75,75,,,290241796,157806083,180760457,407436042,5119,SRX3856796,SRS3100388,SRA675960,GEO,Hubrecht Institute,2,0.38456,0.76284,0.32829,0.54843,0.9497,0.84668,0.48302,0.51789,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System