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 25302,SRR25793493,SRX21515745,SRS18742910,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,Single cell Pr1phros ADULT miR 144 mutant Danio rerio,miR 144,,isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:blood|BioSampleModel:Model organism or animal,,,,,,,,,Single cell Pr1phros ADULT miR 144 mutant Danio rerio,CD 144 1,CD 144 1,Single cell library cloning was done with 10X Genomics,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,unspecified,PAIRED,ILLUMINA,NextSeq 2000,,SRP457465,,,CD_144_1_S3_R1.fastq CD_144_1_S3_R2.fastq,fastq fastq,12899093774.0,108395746.0,CD 144 1 S3 R1.fastq,0:28 1:91,A:3225260764;C:3211986177;G:3151471558;T:3308055659;N:2319616,28,91,,,3225260764,3211986177,3151471558,3308055659,2319616,SRX21515745,SRS18742910,SRA1701829,University of East Anglia|Biological Sciences,University of East Anglia,2,0.00483,0.97382,0.00157,0.05913,0.99439,0.86815,0.46634,0.45907,28,91,T,B,sc-like readlen,illumina,nextseq_v2,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-30,Adult,Adult,Blood,Hematopoietic System 25303,SRR25793494,SRX21515744,SRS18742909,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,Single cell Pr1phros ADULT Wild type Danio rerio,WT,,isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:blood|BioSampleModel:Model organism or animal,,,,,,,,,Single cell Pr1phros ADULT Wild type Danio rerio,CD wt 1,CD wt 1,Single cell library cloning was done with 10X Genomics,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,unspecified,PAIRED,ILLUMINA,NextSeq 2000,,SRP457465,,,CD_wt_1_S2_R1.fastq CD_wt_1_S2_R2.fastq,fastq fastq,12715533299.0,106853221.0,CD wt 1 S2 R1.fastq,0:28 1:91,A:3324705878;C:3042843364;G:3105568183;T:3240105528;N:2310346,28,91,,,3324705878,3042843364,3105568183,3240105528,2310346,SRX21515744,SRS18742909,SRA1701829,University of East Anglia|Biological Sciences,University of East Anglia,2,0.00593,0.93177,0.00191,0.09596,0.99257,0.84394,0.42447,0.4869,28,91,T,B,sc-like readlen,illumina,nextseq_v2,unknown,unknown,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-30,Adult,Adult,Blood,Hematopoietic System 25304,SRR25793376,SRX21515638,SRS18742880,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes miR 144 adult,miR 144 adult,,isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 1,144 1 adult blood,144 1 adult blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-144AL1_S10.fastq,fastq,781435052.0,17368946.0,DC 144AL1 S10.fastq,0:44.99,A:207445570;C:148430622;G:177122903;T:245179579;N:3256378,44,,,,207445570,148430622,177122903,245179579,3256378,SRX21515638,SRS18742880,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.8759,,0.28126,,0.95051,,0.47905,,22,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Adult,Adult,Blood,Hematopoietic System 25305,SRR25793377,SRX21515637,SRS18742882,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes Wild type adult,WT adult,,isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 3,WT3 adult blood,WT3 adult blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-WTA3_S6.fastq,fastq,601997398.0,17290043.0,DC WTA3 S6.fastq,0:34.82,A:136034449;C:142779447;G:177204517;T:134955264;N:11023721,34,,,,136034449,142779447,177204517,134955264,11023721,SRX21515637,SRS18742882,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.32909,,0.08525,,0.95288,,0.60214,,22,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Adult,Adult,Blood,Hematopoietic System 25306,SRR25793378,SRX21515636,SRS18742882,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes Wild type adult,WT adult,,isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 2,WT2 adult blood,WT2 adult blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-WTA2_S5.fastq,fastq,669871903.0,17381581.0,DC WTA2 S5.fastq,0:38.54,A:169704437;C:140964096;G:160484620;T:189596855;N:9121895,38,,,,169704437,140964096,160484620,189596855,9121895,SRX21515636,SRS18742882,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.69865,,0.19099,,0.93432,,0.47502,,68,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Adult,Adult,Blood,Hematopoietic System 25307,SRR25793379,SRX21515635,SRS18742882,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes Wild type adult,WT adult,,isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes Wild type Danio rerio ADULT replicate 1,WT1 adult blood,WT1 adult blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-WTA1_S4.fastq,fastq,824193699.0,17465379.0,DC WTA1 S4.fastq,0:47.19,A:209553199;C:169966117;G:194322860;T:244145525;N:6205998,47,,,,209553199,169966117,194322860,244145525,6205998,SRX21515635,SRS18742882,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.76241,,0.25975,,0.94619,,0.50211,,66,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Adult,Adult,Blood,Hematopoietic System 25312,SRR25793384,SRX21515630,SRS18742880,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes miR 144 adult,miR 144 adult,,isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 3,144 3 adult blood,144 3 adult blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-144AL3_S12.fastq,fastq,498938612.0,14861511.0,DC 144AL3 S12.fastq,0:33.57,A:137243823;C:96735877;G:109220779;T:152042235;N:3695898,33,,,,137243823,96735877,109220779,152042235,3695898,SRX21515630,SRS18742880,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.82213,,0.16617,,0.95053,,0.46386,,22,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Adult,Adult,Blood,Hematopoietic System 25313,SRR25793385,SRX21515629,SRS18742880,SRP457465,PRJNA1010662,The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis.,PRJNA1010662,Other,Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation.,,,,RNA seq Erythrocytes miR 144 adult,miR 144 adult,,isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:Blood|BioSampleModel:Model organism or animal,,,,,,,,,Quant seq Erythrocytes miR 144 mutant Danio rerio ADULT replicate 2,144 2 adult blood,144 2 adult blood,Libraries were made using QuantSeq three prime mRNA Seq Library Prep Kit for IlluminaLexogen,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP457465,,,DC-144AL2_S11.fastq,fastq,497890134.0,10636306.0,DC 144AL2 S11.fastq,0:46.81,A:134598214;C:94036725;G:109501897;T:158719603;N:1033695,46,,,,134598214,94036725,109501897,158719603,1033695,SRX21515629,SRS18742880,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.88496,,0.29132,,0.96002,,0.53343,,22,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Adult,Adult,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,1020Application ReadForward11Application ReadReverse52,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 41038,SRR3581671,SRX1797269,SRS1465191,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,Fluorescence activated cell sorted macrophages1,iRed1,,breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Fluorescence activated cell sorted macrophages|BioSampleModel:Model organism or animal,,,,,,,,,iRed1,iRed1,iRed1,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,iRed1.fastq.gz,fastq,2227229772.0,43671172.0,iRed1.fastq.gz,0:51,A:643185725;C:477251583;G:480258902;T:626515881;N:17681,51,,,,643185725,477251583,480258902,626515881,17681,SRX1797269,SRS1465191,SRA429036,Duke University|Molecular Genetics & Microbiology,Duke University,1,0.88005,,0.11318,,0.76197,,0.49474,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Adult,Adult,Blood,Hematopoietic System 41039,SRR3581670,SRX1797268,SRS1465190,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,D rerio dissected M marinum granuloma5,disGran5,,breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal,,,,,,,,,disGran5,disGran5,disGran5,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,disGran5.fastq.gz,fastq,2097698850.0,41131350.0,disGran5.fastq.gz,0:51,A:606466942;C:449212134;G:448063993;T:593938942;N:16839,51,,,,606466942,449212134,448063993,593938942,16839,SRX1797268,SRS1465190,SRA429035,Duke University|Molecular Genetics & Microbiology,Duke University,1,0.89212,,0.09154,,0.76788,,0.51096,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Adult,Adult,Blood,Hematopoietic System 41040,SRR3581669,SRX1797267,SRS1465187,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,D rerio dissected M marinum granuloma4,disGran4,,breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal,,,,,,,,,disGran4,disGran4,disGran4,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,disGran4.fastq.gz,fastq,2969920485.0,58233735.0,disGran4.fastq.gz,0:51,A:861895830;C:635643178;G:635675729;T:836681349;N:24399,51,,,,861895830,635643178,635675729,836681349,24399,SRX1797267,SRS1465187,SRA429034,Duke University|Molecular Genetics & Microbiology,Duke University,1,0.87215,,0.09876,,0.7498,,0.55116,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Adult,Adult,Blood,Hematopoietic System 41041,SRR3581668,SRX1797266,SRS1465186,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,D rerio dissected M marinum granuloma3,disGran3,,breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal,,,,,,,,,disGran3,disGran3,disGran3,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,disGran3.fastq.gz,fastq,2398905207.0,47037357.0,disGran3.fastq.gz,0:51,A:693817641;C:513302774;G:516121702;T:675643798;N:19292,51,,,,693817641,513302774,516121702,675643798,19292,SRX1797266,SRS1465186,SRA429033,Duke University|Molecular Genetics & Microbiology,Duke University,1,0.88631,,0.10719,,0.75465,,0.51255,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Adult,Adult,Blood,Hematopoietic System 41042,SRR3581667,SRX1797265,SRS1465185,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,D rerio dissected M marinum granuloma2,disGran2,,breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal,,,,,,,,,disGran2,disGran2,disGran2,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,disGran2.fastq.gz,fastq,2108649213.0,41346063.0,disGran2.fastq.gz,0:51,A:606624392;C:457029369;G:459017347;T:585961261;N:16844,51,,,,606624392,457029369,459017347,585961261,16844,SRX1797265,SRS1465185,SRA429032,Duke University|Molecular Genetics & Microbiology,Duke University,1,0.88259,,0.10405,,0.74282,,0.536,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Adult,Adult,Blood,Hematopoietic System 41043,SRR3581315,SRX1797076,SRS1465045,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,D rerio dissected M marinum granuloma1,disGran1,,breed:*AB|dev stage:Adult|sex:pooled male and female|tissue:Dissected granuloma|BioSampleModel:Model organism or animal,,,,,,,,,disGran1,disGran1,disGran1,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,disGran1.fastq.gz,fastq,2529627234.0,49600534.0,disGran1.fastq.gz,0:51,A:738849065;C:530442613;G:521673896;T:738641232;N:20428,51,,,,738849065,530442613,521673896,738641232,20428,SRX1797076,SRS1465045,SRA428910,Duke University|Molecular Genetics & Microbiology,Duke University,1,0.81713,,0.09754,,0.75213,,0.51283,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-07-24,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 49188,SRR7785379,SRX4640375,SRS3738589,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H67,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:wild type|replicate:replicate2|BioSampleModel:Model organism or animal,,,,,,,,,H67,H67,H67,Wild type zebrafish control 2,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H67_S2_L001_R2_001.fastq.gz H67_S2_L001_R1_001.fastq.gz,fastq fastq,18477819300.0,61592731.0,H67 S2 L001 R2 001.fastq.gz,0:150 1:150,A:4887782016;C:4375793599;G:4438933003;T:4775205744;N:104938,150,150,,,4887782016,4375793599,4438933003,4775205744,104938,SRX4640375,SRS3738589,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.93322,0.93319,0.06946,0.06963,0.6747,0.68083,0.47183,0.47148,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-20,Adult,Adult,Blood,Hematopoietic System 49189,SRR7785380,SRX4640374,SRS3738594,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H66,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:wild type|replicate:replicate1|BioSampleModel:Model organism or animal,,,,,,,,,H66,H66,H66,Wild type zebrafish control 1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H66_S1_L001_R2_001.fastq.gz H66_S1_L001_R1_001.fastq.gz,fastq fastq,20487126300.0,68290421.0,H66 S1 L001 R2 001.fastq.gz,0:150 1:150,A:5445452582;C:4824876569;G:4904146081;T:5312533433;N:117635,150,150,,,5445452582,4824876569,4904146081,5312533433,117635,SRX4640374,SRS3738594,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.93306,0.9336,0.08694,0.08764,0.66687,0.6734,0.46489,0.47008,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-20,Adult,Adult,Blood,Hematopoietic System 49190,SRR7785381,SRX4640373,SRS3738593,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H124,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:Tol2 EVI 1 EGFP transgenic|replicate:replicate1|BioSampleModel:Model organism or animal,,,,,,,,,H124,H124,H124,Tol2 EVI 1 EGFP transgenic zebrafish sample 1,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H124_S1_L001_R1_001.fastq.gz H124_S1_L001_R2_001.fastq.gz,fastq fastq,13178593800.0,43928646.0,H124 S1 L001 R1 001.fastq.gz,0:150 1:150,A:3507220604;C:3103991247;G:3164157369;T:3403051995;N:172585,150,150,,,3507220604,3103991247,3164157369,3403051995,172585,SRX4640373,SRS3738593,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.94147,0.94277,0.08109,0.08136,0.69483,0.70011,0.47542,0.47593,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-20,Adult,Adult,Blood,Hematopoietic System 49191,SRR7785382,SRX4640372,SRS3738592,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H93,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:wild type|replicate:replicate3|BioSampleModel:Model organism or animal,,,,,,,,,H93,H93,H93,Wild type zebrafish control 3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H93_S3_L001_R1_001.fastq.gz H93_S3_L001_R2_001.fastq.gz,fastq fastq,18197379600.0,60657932.0,H93 S3 L001 R1 001.fastq.gz,0:150 1:150,A:4814246240;C:4308418881;G:4375398316;T:4699211054;N:105109,150,150,,,4814246240,4308418881,4375398316,4699211054,105109,SRX4640372,SRS3738592,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.9312,0.93173,0.07454,0.07498,0.67065,0.6773,0.46807,0.47334,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-20,Adult,Adult,Blood,Hematopoietic System 49192,SRR7785383,SRX4640371,SRS3738590,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H126,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:Tol2 EVI 1 EGFP transgenic|replicate:replicate3|BioSampleModel:Model organism or animal,,,,,,,,,H126,H126,H126,Tol2 EVI 1 EGFP transgenic zebrafish sample 3,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H126_S3_L001_R1_001.fastq.gz H126_S3_L001_R2_001.fastq.gz,fastq fastq,14979601800.0,49932006.0,H126 S3 L001 R2 001.fastq.gz,0:150 1:150,A:3961375940;C:3551410264;G:3640700651;T:3825918931;N:196014,150,150,,,3961375940,3551410264,3640700651,3825918931,196014,SRX4640371,SRS3738590,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.93717,0.93908,0.05823,0.05891,0.70552,0.71256,0.46146,0.45779,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2019-09-20,Adult,Adult,Blood,Hematopoietic System 49193,SRR7785384,SRX4640370,SRS3738588,SRP159583,PRJNA489308,Over expression of EVI 1 oncogene regulate multi pathway to affect zebrafish embryogenesis and hemopoiesis,PRJNA489308,Other,Our group established Tg Tol GFP EVI 1 zebrafish line and detected survival rate and developmental abnormality in injected embryos. And we found Tg Tol GFP EVI 1 zebrafish embryos underwent abnormal hematopoiesis and aberrant expression of human EVI 1 perturbs hematopoiesis to promote myeloid myeloid and suppress erythroid lineage fates. Moreover overexpression of human EVI 1 induced immature hematopoietic cells emerged in blood circulation. We used whole genome transcriptome analysis RNA Seq to determine differential gene expression in peripheral blood between wildtype larvae and EVI 1 transgenic zebrafish larvae.,,,,,H125,,breed:AB strain|age:3 month|sex:male|tissue:Peripheral blood|genotype:Tol2 EVI 1 EGFP transgenic|replicate:replicate2|BioSampleModel:Model organism or animal,,,,,,,,,H125,H125,H125,Tol2 EVI 1 EGFP transgenic zebrafish sample 2,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP159583,,,H125_S2_L001_R1_001.fastq.gz H125_S2_L001_R2_001.fastq.gz,fastq fastq,16012998000.0,53376660.0,H125 S2 L001 R1 001.fastq.gz,0:150 1:150,A:4365269809;C:3662731840;G:3768367416;T:4216409682;N:219253,150,150,,,4365269809,3662731840,3768367416,4216409682,219253,SRX4640370,SRS3738588,SRA766519,"Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University|Department: Department of Haematology","Department of Haematology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University",2,0.9402,0.94198,0.09449,0.09528,0.71999,0.72512,0.46106,0.47624,150,150,B,B,biological fallback assumption,illumina,hiseq_era,full_length,random_priming,unknown,bulk,unknown,unknown,,China,2018-09-04,Adult,Adult,Blood,Hematopoietic System 61983,SRR13080692,SRX9527457,SRS7734428,SRP293088,PRJNA679243,A Non Canonical Type 2 Immune Response Coordinates Tuberculous Granuloma Formation and Epithelialization,GSE161712,Other,Using the zebrafish M. marinum model we identify the basis of granuloma macrophage transformation. Single cell RNA seq analysis of zebrafish granulomas as well as analysis of M. tuberculosis infected macaques reveal that even in the presence of robust type 1 immune responses countervailing type 2 signals associate with macrophage epithelialization. We find that type 2 immune signaling mediated via stat6 is absolutely required for epithelialization and granuloma formation. Overall design: Wildtype zebrafish M. marinum granuloma single cell RNAseq profile.,,pubmed:33761328,,*AB wildtype zebrafish M.marinum granuloma cells,GSM4913139,,source name:WT Zebrafish granuloma cels|tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB,*AB wildtype zebrafish M.marinum granuloma cells,10X Cell Ranger was used to demultiplex raw base call BCL files generated by an Illumina sequencer into FASTQ before aligning them to the Ensembl zebrafish genome assembly GRCz11.96 performed filtering barcode and UMI counting. Genome build: GRCz11.96 Supplementary files format and content: WTGran.matrix.mtx: Gene barcode matrix in Market Exchange Format MEX for Mus musculus Uninjured Control & Injured1d tibialis anterior muscle cells. Columns correspond to individual cellsbarcodes while rows correspond to genes. Supplementary files format and content: WTGran.features.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column. Supplementary files format and content: WTGran.barcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx.,WT Zebrafish granuloma cels,,Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell 3’ GEM Library and Gel Bead Kit v3.,Adult wildtype *AB zebrafish were infected with 350 fluorescent bacteria of M. marinum.,tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB,GSM4913139,GSM4913139: *AB wildtype zebrafish M.marinum granuloma cells; Danio rerio; RNA Seq,GSM4913139,,1,Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell three prime GEM Library and Gel Bead Kit v3.,GEO Accession:GSM4913139,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP293088,,loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=5761 S1 L001 I1 001.fastq.gz read2PairFiles=5761 S1 L001 R1 001.fastq.gz read3PairFiles=5761 S1 L001 R2 001.fastq.gz,5761_S1_L001_I1_001.fastq.gz 5761_S1_L001_R1_001.fastq.gz 5761_S1_L001_R2_001.fastq.gz,fastq fastq fastq,13295345266.0,104687758.0,GSM4913139 r1,0:8 1:28 2:91,A:3755348831;C:2900888340;G:2979576059;T:3656820253;N:2711783,8,28,91,,3755348831,2900888340,2979576059,3656820253,2711783,SRX9527457,SRS7734428,SRA1160946,GEO,"Tobin, Molecular Genetics and Microbiology, Duke University",1,0.92709,,0.13791,,0.81929,,0.57724,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-18,Adult,Adult,Blood,Hematopoietic System 61984,SRR13080693,SRX9527457,SRS7734428,SRP293088,PRJNA679243,A Non Canonical Type 2 Immune Response Coordinates Tuberculous Granuloma Formation and Epithelialization,GSE161712,Other,Using the zebrafish M. marinum model we identify the basis of granuloma macrophage transformation. Single cell RNA seq analysis of zebrafish granulomas as well as analysis of M. tuberculosis infected macaques reveal that even in the presence of robust type 1 immune responses countervailing type 2 signals associate with macrophage epithelialization. We find that type 2 immune signaling mediated via stat6 is absolutely required for epithelialization and granuloma formation. Overall design: Wildtype zebrafish M. marinum granuloma single cell RNAseq profile.,,pubmed:33761328,,*AB wildtype zebrafish M.marinum granuloma cells,GSM4913139,,source name:WT Zebrafish granuloma cels|tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB,*AB wildtype zebrafish M.marinum granuloma cells,10X Cell Ranger was used to demultiplex raw base call BCL files generated by an Illumina sequencer into FASTQ before aligning them to the Ensembl zebrafish genome assembly GRCz11.96 performed filtering barcode and UMI counting. Genome build: GRCz11.96 Supplementary files format and content: WTGran.matrix.mtx: Gene barcode matrix in Market Exchange Format MEX for Mus musculus Uninjured Control & Injured1d tibialis anterior muscle cells. Columns correspond to individual cellsbarcodes while rows correspond to genes. Supplementary files format and content: WTGran.features.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column. Supplementary files format and content: WTGran.barcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx.,WT Zebrafish granuloma cels,,Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell 3’ GEM Library and Gel Bead Kit v3.,Adult wildtype *AB zebrafish were infected with 350 fluorescent bacteria of M. marinum.,tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB,GSM4913139,GSM4913139: *AB wildtype zebrafish M.marinum granuloma cells; Danio rerio; RNA Seq,GSM4913139,,1,Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell three prime GEM Library and Gel Bead Kit v3.,GEO Accession:GSM4913139,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP293088,,loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=5895 S1 L001 I1 001.fastq.gz read2PairFiles=5895 S1 L001 R1 001.fastq.gz read3PairFiles=5895 S1 L001 R2 001.fastq.gz,5895_S1_L001_I1_001.fastq.gz 5895_S1_L001_R1_001.fastq.gz 5895_S1_L001_R2_001.fastq.gz,fastq fastq fastq,17723636384.0,139556192.0,GSM4913139 r2,0:8 1:28 2:91,A:4955483447;C:3902218538;G:4036183306;T:4807856940;N:21894153,8,28,91,,4955483447,3902218538,4036183306,4807856940,21894153,SRX9527457,SRS7734428,SRA1160946,GEO,"Tobin, Molecular Genetics and Microbiology, Duke University",1,0.9176,,0.13304,,0.81462,,0.57616,,91,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-18,Adult,Adult,Blood,Hematopoietic System 63869,SRR14144778,SRX10514122,SRS8637874,SRP313536,PRJNA719817,RORa is required for neutrophil migration,GSE171501,Transcriptome Analysis,We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control,,,,RORaDN 3,GSM5226363,,tissue:neutrophils|cell type:neutrophils|genotype:RORa dominant negative,RORaDN 3,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “ outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: “ s 1 –Q 10” for Samples 6 11 "" p Q 10"". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis",neutrophils,Transgenic lines expressing RORa dominant negative or mcherry were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..,zebrafish were grow in circulating system,cell type:neutrophils|genotype:RORa dominant negative,GSM5226363,GSM5226363: RORaDN 3; Danio rerio; RNA Seq,GSM5226363,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..,GEO Accession:GSM5226363,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP313536,,loader:fastq load.py,roraDN-3_S24_R1_001.fastq.gz roraDN-3_S24_R2_001.fastq.gz,fastq fastq,9541970758.0,47237479.0,GSM5226363 r1,0:101 1:101,A:2556115286;C:2215951997;G:2229754627;T:2539986639;N:162209,101,101,,,2556115286,2215951997,2229754627,2539986639,162209,SRX10514122,SRS8637874,SRA1215296,GEO,"Department of Biological Sciences, Purdue University",2,0.94352,0.93947,0.09023,0.08984,0.79224,0.79523,0.45486,0.45588,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2021-04-05,Adult,Adult,Blood,Hematopoietic System 63870,SRR14144777,SRX10514121,SRS8637873,SRP313536,PRJNA719817,RORa is required for neutrophil migration,GSE171501,Transcriptome Analysis,We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control,,,,RORaDN 2,GSM5226362,,tissue:neutrophils|cell type:neutrophils|genotype:RORa dominant negative,RORaDN 2,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “ outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: “ s 1 –Q 10” for Samples 6 11 "" p Q 10"". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis",neutrophils,Transgenic lines expressing RORa dominant negative or mcherry were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..,zebrafish were grow in circulating system,cell type:neutrophils|genotype:RORa dominant negative,GSM5226362,GSM5226362: RORaDN 2; Danio rerio; RNA Seq,GSM5226362,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..,GEO Accession:GSM5226362,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP313536,,loader:fastq load.py,roraDN-2_S23_R1_001.fastq.gz roraDN-2_S23_R2_001.fastq.gz,fastq fastq,7807589466.0,38651433.0,GSM5226362 r1,0:101 1:101,A:2096919144;C:1807670571;G:1821028016;T:2081836449;N:135286,101,101,,,2096919144,1807670571,1821028016,2081836449,135286,SRX10514121,SRS8637873,SRA1215296,GEO,"Department of Biological Sciences, Purdue University",2,0.94042,0.93784,0.09122,0.09133,0.80192,0.80405,0.44224,0.446,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2021-04-05,Adult,Adult,Blood,Hematopoietic System 63871,SRR14144776,SRX10514120,SRS8637872,SRP313536,PRJNA719817,RORa is required for neutrophil migration,GSE171501,Transcriptome Analysis,We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control,,,,RORaDN 1,GSM5226361,,tissue:neutrophils|cell type:neutrophils|genotype:RORa dominant negative,RORaDN 1,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “ outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: “ s 1 –Q 10” for Samples 6 11 "" p Q 10"". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis",neutrophils,Transgenic lines expressing RORa dominant negative or mcherry were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..,zebrafish were grow in circulating system,cell type:neutrophils|genotype:RORa dominant negative,GSM5226361,GSM5226361: RORaDN 1; Danio rerio; RNA Seq,GSM5226361,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..,GEO Accession:GSM5226361,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP313536,,loader:fastq load.py,roraDN-1_S22_R1_001.fastq.gz roraDN-1_S22_R2_001.fastq.gz,fastq fastq,10197330670.0,50481835.0,GSM5226361 r1,0:101 1:101,A:2788946417;C:2302836921;G:2316790438;T:2788574338;N:182556,101,101,,,2788946417,2302836921,2316790438,2788574338,182556,SRX10514120,SRS8637872,SRA1215296,GEO,"Department of Biological Sciences, Purdue University",2,0.92564,0.92366,0.09078,0.09026,0.81381,0.81542,0.50301,0.49369,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2021-04-05,Adult,Adult,Blood,Hematopoietic System 63872,SRR14144775,SRX10514119,SRS8637871,SRP313536,PRJNA719817,RORa is required for neutrophil migration,GSE171501,Transcriptome Analysis,We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control,,,,mCherry 3,GSM5226360,,tissue:neutrophils|cell type:neutrophils|genotype:control,mCherry 3,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “ outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: “ s 1 –Q 10” for Samples 6 11 "" p Q 10"". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis",neutrophils,Transgenic lines expressing RORa dominant negative or mcherry were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..,zebrafish were grow in circulating system,cell type:neutrophils|genotype:control,GSM5226360,GSM5226360: mCherry 3; Danio rerio; RNA Seq,GSM5226360,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..,GEO Accession:GSM5226360,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP313536,,loader:fastq load.py,ctrl_mcherry-3_S21_R1_001.fastq.gz ctrl_mcherry-3_S21_R2_001.fastq.gz,fastq fastq,8880772036.0,43964218.0,GSM5226360 r1,0:101 1:101,A:2381825109;C:2057122621;G:2068743076;T:2372921245;N:159985,101,101,,,2381825109,2057122621,2068743076,2372921245,159985,SRX10514119,SRS8637871,SRA1215296,GEO,"Department of Biological Sciences, Purdue University",2,0.93299,0.93061,0.09615,0.09601,0.80004,0.8017,0.43695,0.43475,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2021-04-05,Adult,Adult,Blood,Hematopoietic System 63873,SRR14144774,SRX10514118,SRS8637870,SRP313536,PRJNA719817,RORa is required for neutrophil migration,GSE171501,Transcriptome Analysis,We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control,,,,mCherry 2,GSM5226359,,tissue:neutrophils|cell type:neutrophils|genotype:control,mCherry 2,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “ outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: “ s 1 –Q 10” for Samples 6 11 "" p Q 10"". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis",neutrophils,Transgenic lines expressing RORa dominant negative or mcherry were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..,zebrafish were grow in circulating system,cell type:neutrophils|genotype:control,GSM5226359,GSM5226359: mCherry 2; Danio rerio; RNA Seq,GSM5226359,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..,GEO Accession:GSM5226359,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP313536,,loader:fastq load.py,ctrl_mcherry-2_S20_R1_001.fastq.gz ctrl_mcherry-2_S20_R2_001.fastq.gz,fastq fastq,9245210942.0,45768371.0,GSM5226359 r1,0:101 1:101,A:2490401320;C:2130041068;G:2145686856;T:2478916438;N:165260,101,101,,,2490401320,2130041068,2145686856,2478916438,165260,SRX10514118,SRS8637870,SRA1215296,GEO,"Department of Biological Sciences, Purdue University",2,0.93171,0.92876,0.08782,0.08787,0.79699,0.79886,0.44448,0.44757,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2021-04-05,Adult,Adult,Blood,Hematopoietic System 63874,SRR14144773,SRX10514117,SRS8637869,SRP313536,PRJNA719817,RORa is required for neutrophil migration,GSE171501,Transcriptome Analysis,We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control,,,,mCherry 1,GSM5226358,,tissue:neutrophils|cell type:neutrophils|genotype:control,mCherry 1,"Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter “ outSAMmapqUnique 60”. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5: “ s 1 –Q 10” for Samples 6 11 "" p Q 10"". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis",neutrophils,Transgenic lines expressing RORa dominant negative or mcherry were used.,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..,zebrafish were grow in circulating system,cell type:neutrophils|genotype:control,GSM5226358,GSM5226358: mCherry 1; Danio rerio; RNA Seq,GSM5226358,,1,tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories Inc..,GEO Accession:GSM5226358,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP313536,,loader:fastq load.py,ctrl_mcherry-1_S19_R1_001.fastq.gz ctrl_mcherry-1_S19_R2_001.fastq.gz,fastq fastq,8133040958.0,40262579.0,GSM5226358 r1,0:101 1:101,A:2181019795;C:1885103754;G:1889273889;T:2177502095;N:141425,101,101,,,2181019795,1885103754,1889273889,2177502095,141425,SRX10514117,SRS8637869,SRA1215296,GEO,"Department of Biological Sciences, Purdue University",2,0.9318,0.93011,0.09874,0.09885,0.79239,0.79488,0.42603,0.44023,101,101,B,B,biological fallback assumption,illumina,novaseq_era,unknown,small_rna,trueseq,sc,single_cell_plate,smartseq,,United States,2021-04-05,Adult,Adult,Blood,Hematopoietic System