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
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
25308,SRR25793380,SRX21515634,SRS18742881,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    embryo,miR 144 embryo,,isolate:miR 144 mutant|age:Embryo|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 2 dpf replicate 3,144 3 embryo blood,144 3 embryo 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-144EL3_S18.fastq,fastq,687309797.0,17039739.0,DC 144EL3 S18.fastq,0:40.34,A:159186558;C:130452893;G:155820002;T:181676510;N:60173834,40,,,,159186558,130452893,155820002,181676510,60173834,SRX21515634,SRS18742881,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.52966,,0.16941,,0.97615,,0.58418,,61,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,Blood,Hematopoietic System
25309,SRR25793381,SRX21515633,SRS18742881,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    embryo,miR 144 embryo,,isolate:miR 144 mutant|age:Embryo|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 2 dpf replicate 2,144 2 embryo blood,144 2 embryo 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-144EL2_S17.fastq,fastq,495318731.0,14459195.0,DC 144EL2 S17.fastq,0:34.26,A:110392869;C:106378418;G:128881687;T:107956679;N:41709078,34,,,,110392869,106378418,128881687,107956679,41709078,SRX21515633,SRS18742881,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.32147,,0.04496,,0.97569,,0.58512,,31,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,Blood,Hematopoietic System
25310,SRR25793382,SRX21515632,SRS18742881,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    embryo,miR 144 embryo,,isolate:miR 144 mutant|age:Embryo|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 2 dpf replicate 1,144 1 embryo blood,144 1 embryo 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-144EL1_S16.fastq,fastq,974854100.0,20079553.0,DC 144EL1 S16.fastq,0:48.55,A:233861010;C:192987350;G:215192262;T:269960344;N:62853134,48,,,,233861010,192987350,215192262,269960344,62853134,SRX21515632,SRS18742881,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.77953,,0.18084,,0.90905,,0.74157,,75,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,Blood,Hematopoietic System
25311,SRR25793383,SRX21515631,SRS18742879,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   embryo,WT embryo,,isolate:Wildtype|age:Embryo|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 2 dpf replicate 3,WT3 embryo blood,WT3 embryo 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-WTE3_S15.fastq,fastq,657139116.0,15618072.0,DC WTE3 S15.fastq,0:42.08,A:154495614;C:122942896;G:147719345;T:179403193;N:52578068,42,,,,154495614,122942896,147719345,179403193,52578068,SRX21515631,SRS18742879,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.56358,,0.19381,,0.96757,,0.6115,,76,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,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
25314,SRR25793386,SRX21515628,SRS18742879,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   embryo,WT embryo,,isolate:Wildtype|age:Embryo|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 2 dpf replicate 2,WT2 embryo blood,WT2 embryo 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-WTE2_S14.fastq,fastq,250958009.0,9755304.0,DC WTE2 S14.fastq,0:25.73,A:43225839;C:41823862;G:54150092;T:43159724;N:68598492,25,,,,43225839,41823862,54150092,43159724,68598492,SRX21515628,SRS18742879,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.34114,,0.05466,,0.96664,,0.54625,,47,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,Blood,Hematopoietic System
25315,SRR25793387,SRX21515627,SRS18742879,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   embryo,WT embryo,,isolate:Wildtype|age:Embryo|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 2 dpf replicate 1,WT1 embryo blood,WT1 embryo 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-WTE1_S13.fastq,fastq,816518564.0,19556325.0,DC WTE1 S13.fastq,0:41.75,A:187091550;C:151287428;G:179967901;T:221475884;N:76695801,41,,,,187091550,151287428,179967901,221475884,76695801,SRX21515627,SRS18742879,SRA1701831,University of East Anglia|Biological Sciences,University of East Anglia,1,0.61681,,0.1874,,0.95101,,0.56879,,29,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,lexogen,bulk,unknown,unknown,,United Kingdom,2023-08-30,Hatching,Embryo,Blood,Hematopoietic System
39665,SRR2027911,SRX1029315,SRS937775,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPosMmarinumGFPPos rep3,GSM1686459,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPosMmarinumGFPPos rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686459,GSM1686459: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep3; Danio rerio; RNA Seq,GSM1686459,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686459,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_06_ATTCCT_L003_R1_001.fastq.gz,fastq,988427889.0,19380939.0,GSM1686459 r1,0:51,A:322268594;C:166925867;G:171531103;T:327506982;N:195343,51,,,,322268594,166925867,171531103,327506982,195343,SRX1029315,SRS937775,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.6999,,0.24019,,0.85358,,0.56832,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39666,SRR2027910,SRX1029314,SRS937773,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPosMmarinumGFPPos rep2,GSM1686458,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPosMmarinumGFPPos rep2,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686458,GSM1686458: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep2; Danio rerio; RNA Seq,GSM1686458,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686458,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_05_ACTGAT_L003_R1_001.fastq.gz,fastq,846771207.0,16603357.0,GSM1686458 r1,0:51,A:268435928;C:150903620;G:153931870;T:273331733;N:168056,51,,,,268435928,150903620,153931870,273331733,168056,SRX1029314,SRS937773,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.72025,,0.17943,,0.87937,,0.5683,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39667,SRR2027909,SRX1029313,SRS937774,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPosMmarinumGFPPos rep1,GSM1686457,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPosMmarinumGFPPos rep1,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP positive|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686457,GSM1686457: 6dpf mpeg1:mCherryPosMmarinumGFPPos rep1; Danio rerio; RNA Seq,GSM1686457,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686457,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_04_GAGTGG_L003_R1_001.fastq.gz,fastq,807459642.0,15832542.0,GSM1686457 r1,0:51,A:260516660;C:140425216;G:145411663;T:260942267;N:163836,51,,,,260516660,140425216,145411663,260942267,163836,SRX1029313,SRS937774,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.7097,,0.17187,,0.93304,,0.64092,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39668,SRR2027908,SRX1029312,SRS937776,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3,GSM1686456,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686456,GSM1686456: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep3; Danio rerio; RNA Seq,GSM1686456,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686456,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_03_CGTACG_L003_R1_001.fastq.gz,fastq,1523483526.0,29872226.0,GSM1686456 r1,0:51,A:499019794;C:267493952;G:277264815;T:479405699;N:299266,51,,,,499019794,267493952,277264815,479405699,299266,SRX1029312,SRS937776,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.67328,,0.15117,,0.91179,,0.54858,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39669,SRR2027907,SRX1029311,SRS937777,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2,GSM1686455,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686455,GSM1686455: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep2; Danio rerio; RNA Seq,GSM1686455,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686455,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_02_GTTTCG_L003_R1_001.fastq.gz,fastq,938675094.0,18405394.0,GSM1686455 r1,0:51,A:284384359;C:173449465;G:178039777;T:302612825;N:188668,51,,,,284384359,173449465,178039777,302612825,188668,SRX1029311,SRS937777,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.72884,,0.14723,,0.90767,,0.57414,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
39670,SRR2027906,SRX1029310,SRS937778,SRP058376,PRJNA284108,RNAseq profiling of zebrafish larval macrophages reveals similarities with human M1 and M2 transcriptome signatures,GSE68920,Transcriptome Analysis,We used different zebrafish transgenic lines to sort macrophages  neutrophils and immature lymphoid cells from 5 dpf 6 dpf zebrafish larvae and analyzed their transcriptomes. Comparison between the different transcriptomes and gene ontology analysis revealed specificities for each cell population. Comparison with previously published data showed that zebrafish larval macrophages expressed several known human M1 and M2 macrophages. Transcriptome analysis of uninfected and infected macrophages from embryos infected by of Mycobacterium marinum revealed infection induced transcriptional changes and a shift towards M1 transcriptomic signature. Overall design: For infection experiments  zebrafish embryos were manually dechorionated at 24 hpf and were infected by injection in the caudal vein of 125 colony forming unit of Mycobacterium marinum M strain expressing GFP. Embryos were grown into egg water refresh every day and incubated for 5 days at 28°C. 0.003% 1 phenyl 2 thiourea Sigma Aldrich was added post 1 day to prevent melanisation. post the incubation period  embryos were dissociated into single cell suspension by Trypsin treatment and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer. cDNA synthesis  amplification and library preparation were performed as previously described. Rougeot et al.  2014  Methods Mol Biol 1197:41 66.,,pubmed:31832066,,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1,GSM1686454,,source name:zebra fish larvae|tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome Zv9 using Bowtie and reads were mapped to zebrafish transcripts using TopHat and a modified version of the Ensembl Zv9 79 annotation containing few additional genes. Genome build: Zv9 Supplementary files format and content: tab separated value files include gene counts for each sample,zebra fish larvae,Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP.,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols http://ZFIN.org. Embryos were grown at 28 5°C in egg water 60µg/ml Instant Ocean sea salts containing 0.003% 1 phenyl 2 thiourea SigmaFor infected samples. Zebrafish embryos were manually dechorionated at 24 hpf and at 28 hpf they were micro injected into the caudal vein with 125 CFU of M. marinum M strain bacteria suspended in PBS/2%PVP. Aldrich,tissue:20 mpeg1 positive macrophages|cell population:GFP negative|developmental stage:6dpf|caudal vain infection:M marinum M strain 125cfu,GSM1686454,GSM1686454: 6dpf mpeg1:mCherryPos MmarinumGFPNeg rep1; Danio rerio; RNA Seq,GSM1686454,,1,Between 200 and 300 larvae per condition were collected at 6 dpf. Larvae were dissociated into single cell suspension by Trypsin treatment and fluorescent and 20 fluorescent cells per condition were sorted by FACS directly into cDNA synthesis buffer  without xxx extraction. cDNA were synthetized and amplified with the SMARTer cDNA synthesis kit for Illumina Sequencing Clonetech according to the manufacturer’s instructions. The integrity of the cDNA was confirmed by Lab on chip analysis using the 2100 Bioanalyzer Agilent Technologies. The sheared amplified cDNA  were used to make RNAseq libraries using the Illumina TruSeq RNA Sample Preparation Kit v2 Illumina Inc.  San Diego  USA. In the manufacturer’s instructions two modifications were made. In the adapter ligation step 1 µl instead of 2.5 µl adapter was used. In the library size selection step the library fragments were isolated with a double Ampure XP purification with a 0.7x beads to library ratio. The resulting mRNA Seq library was sequenced using an Illumina HiSeq2000 instrument according to the manufacturer’s description with a read length of 1 x 50 nucleotides.,GEO Accession:GSM1686454,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP058376,,,ZFG-14-09_01_GTGGCC_L003_R1_001.fastq.gz,fastq,1248324348.0,24476948.0,GSM1686454 r1,0:51,A:391067882;C:223380294;G:229132022;T:404526410;N:217740,51,,,,391067882,223380294,229132022,404526410,217740,SRX1029310,SRS937778,SRA268539,GEO,"Institute of Biology, Leiden University",1,0.70232,,0.14257,,0.92894,,0.59305,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,poly_a,smarter,bulk,unknown,unknown,,Netherlands,2015-05-15,Larval,Larval,Blood,Hematopoietic System
41032,SRR3581739,SRX1797279,SRS1465200,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,Larval non fluorescent cells post macrophage sorting3,C NF3,,breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal,,,,,,,,,C NF3,C NF3,C NF3,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,C_NF3.fastq.gz,fastq,1745512893.0,34225743.0,C NF3.fastq.gz,0:51,A:470456301;C:396221813;G:401458508;T:477287506;N:88765,51,,,,470456301,396221813,401458508,477287506,88765,SRX1797279,SRS1465200,SRA429046,Duke University|Molecular Genetics & Microbiology,Duke University,1,0.92839,,0.06821,,0.73099,,0.44395,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2016-05-25,Larval,Larval,Blood,Hematopoietic System
41033,SRR3581729,SRX1797278,SRS1465199,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,Larval non fluorescent cells post macrophage sorting2,C NF2,,breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal,,,,,,,,,C NF2,C NF2,C NF2,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,C_NF2.fastq.gz,fastq,2116510506.0,41500206.0,C NF2.fastq.gz,0:51,A:580244434;C:475940957;G:474848964;T:585459729;N:16422,51,,,,580244434,475940957,474848964,585459729,16422,SRX1797278,SRS1465199,SRA429045,Duke University|Molecular Genetics & Microbiology,Duke University,1,0.90388,,0.06926,,0.78963,,0.49501,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Larval,Larval,Blood,Hematopoietic System
41034,SRR3581718,SRX1797274,SRS1465196,SRP075626,PRJNA322629,Mycobacterial infection of adult zebrafish,PRJNA322629,Other,RNA seq based profiling of Mycobacterium marinum granulomas from adult zebrafish and matched macrophage samples.,,,,Larval non fluorescent cells post macrophage sorting1,C NF1,,breed:*AB|age:4dpf|dev stage:Larval|sex:not determined|tissue:Whole animal following macrophage depletion via FACS|BioSampleModel:Model organism or animal,,,,,,,,,C NF1,C NF1,C NF1,1,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP075626,,,C_NF1.fastq.gz,fastq,1492422690.0,29263190.0,C NF1.fastq.gz,0:51,A:421145406;C:327412398;G:328273236;T:415327504;N:264146,51,,,,421145406,327412398,328273236,415327504,264146,SRX1797274,SRS1465196,SRA429041,Duke University|Molecular Genetics & Microbiology,Duke University,1,0.82347,,0.08561,,0.75207,,0.45637,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,United States,2017-06-24,Larval,Larval,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
54715,SRR10136115,SRX6864204,SRS5401831,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,24: PBS injected fish3,GSM4083497,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,24: PBS injected fish3,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083497,GSM4083497: 24: PBS injected fish3; Danio rerio; RNA Seq,GSM4083497,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083497,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_24_18845_TGACCA_L001_R1_001.fastq.gz,fastq,175231359.0,3435909.0,GSM4083497 r1,0:51,A:43536404;C:41827219;G:40775397;T:49039258;N:53081,51,,,,43536404,41827219,40775397,49039258,53081,SRX6864204,SRS5401831,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.92557,,0.08034,,0.71354,,0.48221,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54716,SRR10136116,SRX6864204,SRS5401831,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,24: PBS injected fish3,GSM4083497,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,24: PBS injected fish3,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083497,GSM4083497: 24: PBS injected fish3; Danio rerio; RNA Seq,GSM4083497,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083497,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_24_18845_TGACCA_L002_R1_001.fastq.gz,fastq,183497490.0,3597990.0,GSM4083497 r2,0:51,A:45576151;C:43814900;G:42692291;T:51382292;N:31856,51,,,,45576151,43814900,42692291,51382292,31856,SRX6864204,SRS5401831,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.92775,,0.08176,,0.71305,,0.47131,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54717,SRR10136113,SRX6864203,SRS5401830,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,23: PBS injected fish2,GSM4083496,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,23: PBS injected fish2,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083496,GSM4083496: 23: PBS injected fish2; Danio rerio; RNA Seq,GSM4083496,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083496,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_23_18844_CGATGT_L001_R1_001.fastq.gz,fastq,178603683.0,3502033.0,GSM4083496 r1,0:51,A:43615081;C:43303795;G:41835813;T:49795688;N:53306,51,,,,43615081,43303795,41835813,49795688,53306,SRX6864203,SRS5401830,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.9227,,0.06923,,0.72547,,0.45761,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54718,SRR10136114,SRX6864203,SRS5401830,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,23: PBS injected fish2,GSM4083496,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,23: PBS injected fish2,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083496,GSM4083496: 23: PBS injected fish2; Danio rerio; RNA Seq,GSM4083496,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083496,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_23_18844_CGATGT_L002_R1_001.fastq.gz,fastq,186816264.0,3663064.0,GSM4083496 r2,0:51,A:45642596;C:45311565;G:43750888;T:52078681;N:32534,51,,,,45642596,45311565,43750888,52078681,32534,SRX6864203,SRS5401830,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.92517,,0.07013,,0.72561,,0.4586,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54719,SRR10136111,SRX6864202,SRS5401829,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,22: PBS injected fish1,GSM4083495,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,22: PBS injected fish1,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083495,GSM4083495: 22: PBS injected fish1; Danio rerio; RNA Seq,GSM4083495,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083495,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_22_18843_ATTCCT_L001_R1_001.fastq.gz,fastq,338607105.0,6639355.0,GSM4083495 r1,0:51,A:83848769;C:81493095;G:77979951;T:95181006;N:104284,51,,,,83848769,81493095,77979951,95181006,104284,SRX6864202,SRS5401829,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.93231,,0.07583,,0.70784,,0.47906,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54720,SRR10136112,SRX6864202,SRS5401829,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,22: PBS injected fish1,GSM4083495,,source name:PBS injected fish|tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,22: PBS injected fish1,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PBS injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Hematopoietic tissue without xxx cells|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083495,GSM4083495: 22: PBS injected fish1; Danio rerio; RNA Seq,GSM4083495,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083495,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_22_18843_ATTCCT_L002_R1_001.fastq.gz,fastq,351800346.0,6898046.0,GSM4083495 r2,0:51,A:87109106;C:84668841;G:81026500;T:98935234;N:60665,51,,,,87109106,84668841,81026500,98935234,60665,SRX6864202,SRS5401829,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.93354,,0.07513,,0.7049,,0.47898,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54721,SRR10136109,SRX6864201,SRS5401828,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,27: Metastases3,GSM4083494,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,27: Metastases3,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083494,GSM4083494: 27: Metastases3; Danio rerio; Homo sapiens; RNA Seq,GSM4083494,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083494,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_27_19265_CAGATC_L001_R1_001.fastq.gz,fastq,331816863.0,6506213.0,GSM4083494 r1,0:51,A:82933253;C:78905859;G:76570035;T:93218124;N:189592,51,,,,82933253,78905859,76570035,93218124,189592,SRX6864201,SRS5401828,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.81726,,0.07727,,0.71928,,0.47447,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54722,SRR10136110,SRX6864201,SRS5401828,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,27: Metastases3,GSM4083494,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,27: Metastases3,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083494,GSM4083494: 27: Metastases3; Danio rerio; Homo sapiens; RNA Seq,GSM4083494,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083494,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_27_19265_CAGATC_L002_R1_001.fastq.gz,fastq,345788568.0,6780168.0,GSM4083494 r2,0:51,A:86481669;C:82220901;G:79836085;T:97146784;N:103129,51,,,,86481669,82220901,79836085,97146784,103129,SRX6864201,SRS5401828,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.81844,,0.07678,,0.7189,,0.4755,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54723,SRR10136107,SRX6864200,SRS5401827,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,26: Metastases2,GSM4083493,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,26: Metastases2,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083493,GSM4083493: 26: Metastases2; Danio rerio; Homo sapiens; RNA Seq,GSM4083493,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083493,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_26_19264_GCCAAT_L001_R1_001.fastq.gz,fastq,381088575.0,7472325.0,GSM4083493 r1,0:51,A:93834091;C:91635540;G:89019328;T:106380009;N:219607,51,,,,93834091,91635540,89019328,106380009,219607,SRX6864200,SRS5401827,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.79302,,0.0612,,0.72803,,0.47524,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54724,SRR10136108,SRX6864200,SRS5401827,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,26: Metastases2,GSM4083493,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,26: Metastases2,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083493,GSM4083493: 26: Metastases2; Danio rerio; Homo sapiens; RNA Seq,GSM4083493,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083493,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_26_19264_GCCAAT_L002_R1_001.fastq.gz,fastq,396777450.0,7779950.0,GSM4083493 r2,0:51,A:97747141;C:95409433;G:92718325;T:110778709;N:123842,51,,,,97747141,95409433,92718325,110778709,123842,SRX6864200,SRS5401827,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.79294,,0.06073,,0.72636,,0.47389,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54725,SRR10136105,SRX6864199,SRS5401826,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,25: Metastases1,GSM4083492,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,25: Metastases1,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083492,GSM4083492: 25: Metastases1; Danio rerio; Homo sapiens; RNA Seq,GSM4083492,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083492,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_25_19263_ACAGTG_L001_R1_001.fastq.gz,fastq,335771148.0,6583748.0,GSM4083492 r1,0:51,A:82544663;C:80955820;G:79009084;T:93066010;N:195571,51,,,,82544663,80955820,79009084,93066010,195571,SRX6864199,SRS5401826,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.82172,,0.05893,,0.72088,,0.48241,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
54726,SRR10136106,SRX6864199,SRS5401826,SRP222275,PRJNA566103,Next Generation Sequencing to compare gene expression of PC 3M Pro4 in cell culture and in zebrafish metastasis,GSE137629,Other,We report how engrafted human prostate cancer cells respond to zebrafish microenvironment during metasatic colonization. Overall design: RNA was isolated from metastasese in zebrafish 70 fish/group  from  uninjected fish 70fish/group  and from cells in culture  in triplicate. Transcriptomics of human cancer cells were compared between in culture and in metastases. PBS injected fish was set as  control to analyze how engrafted cancer cells modulate gene expression of the host stromal cells,,pubmed:31740783,,25: Metastases1,GSM4083492,,source name:PC 3M Pro4 injected fish|tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,25: Metastases1,All RNAseq libraries 150–750 bp inserts were sequenced on an Illumina HiSeq2500 sequencer as 1 × 50 nucleotides single end reads according to the manufacturer’s protocol. Image analysis and basecalling were done using the Illumina pipeline. Total yield varied from 10 to 26 Mreads per sample. Illumina reads were aligned against the human GRCh38.p3 and zebrafish GRCz10.80 reference genome sequences using TopHat version 2.0.5. Secondary alignments of reads were excluded by filtering the files using SAMtools version 0.1.18 Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq version 0.5.3p9. To make comparisons across samples possible  these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scaling factor  library size estimates determined using the R/Bioconductor release 2.11 package DESeq were employed Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Detailed read coverage for individual genes was extracted from the TopHat alignments using SAMtools. Supplementary files format and content: tab delimited text files include gene name  ID  reads and normalized comparision between each groups,PC 3M Pro4 injected fish,,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer’s instructions Illumina  San Diego CA  USA.,PC 3M Pro4 cells were cultured in DMEM complemented with 10% Fetal Clone II. 200 400 PC 3M Pro4 cells were injected into the duct of cuvier DoC of the zebrafish embryos using a Pneumatic Picopump and a manipulator WPI. post transplantation  120 well engrafted embryos were selected using fluorescent microscope and incubated in a 34 ˚C incubator for 6 days.,tissue:Metastases at zebrafish caudal hematopoietic tissue|FISH strain:TGFli1a:EGFP|age:8 dpf,GSM4083492,GSM4083492: 25: Metastases1; Danio rerio; Homo sapiens; RNA Seq,GSM4083492,,1,Metastasis samples in zebrafish embryos and uninjected control were isolated by cutting the whole metastatic area 80 fish per group randomly chosen from >100 engrafted fish at 6dpi 8dpf with a micro dissection scissor WPI. The samples were immediately washed with cold PBS and stored in TRIzol Sigma at  80 ˚C. The whole process was finished within 30 min.  1000000 Cells in culture were lysized with TRIzol and stored at   80 ˚C. RNA isolation was further performed using RNeasy mini kit qiagen then Illumina RNAseq libraries were prepared using the Illumina TruSeq RNA Sample Prep Kit v2 according to the manufacturer's instructions Illumina  San Diego CA  USA.,GEO Accession:GSM4083492,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP222275,,,ZFG-16-03_25_19263_ACAGTG_L002_R1_001.fastq.gz,fastq,348764061.0,6838511.0,GSM4083492 r2,0:51,A:85790391;C:84069256;G:82076851;T:96714974;N:112589,51,,,,85790391,84069256,82076851,96714974,112589,SRX6864199,SRS5401826,SRA963954,GEO,"Institute of Biology, Leiden University",1,0.82119,,0.06015,,0.72299,,0.47492,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,trueseq,bulk,unknown,unknown,,Netherlands,2019-09-18,Larval,Larval,Blood,Hematopoietic System
55536,SRR10532692,SRX7216663,SRS5719129,SRP233258,PRJNA591815,Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis,PRJNA591815,Other,MicroRNAs are sequentially processed by two RNAse III enzymes  Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation  where it becomes the most abundant miRNA. However  the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.,,,,,miR 451 mutant,,isolate:Lab reared|age:2 days|sex:not applicable|tissue:peripheral blood|genotype:miR 451 / |phenotype:wild type|treatment:n1|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic profiling of peripheral blood from 2 dpf zebrafish embryos,mRNA Mut miR 451,mRNA Mut miR 451,mRNA libraries were cloned from polyA+ RNA isolated from peripheral blood of 2 dpf WT and mutant zebrafish embryos according to Illumina TruSeq protocol. Libraries were cloned and sequenced at Boston University Microarray and Sequencing core.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP233258,,,mRNA-miR-451.fastq.gz,fastq,7904410367.0,104613601.0,mRNA miR 451.fastq.gz,0:75.56 1:0,A:1795110678;C:2004074141;G:2113982350;T:1989843693;N:1399505,75,0,,,1795110678,2004074141,2113982350,1989843693,1399505,SRX7216663,SRS5719129,SRA1002853,University of East Anglia|Biological Sciences,University of East Anglia,1,0.97314,,0.03847,,0.81744,,0.4673,,75,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-26,Hatching,Embryo,Blood,Hematopoietic System
55537,SRR10532693,SRX7216662,SRS5719128,SRP233258,PRJNA591815,Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis,PRJNA591815,Other,MicroRNAs are sequentially processed by two RNAse III enzymes  Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation  where it becomes the most abundant miRNA. However  the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.,,,,,miR 144 mutant,,isolate:Lab reared|age:2 days|sex:not applicable|tissue:peripheral blood|genotype:miR 144 / |phenotype:wild type|treatment:n1|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic profiling of peripheral blood from 2 dpf zebrafish embryos,mRNA Mut miR 144,mRNA Mut miR 144,mRNA libraries were cloned from polyA+ RNA isolated from peripheral blood of 2 dpf WT and mutant zebrafish embryos according to Illumina TruSeq protocol. Libraries were cloned and sequenced at Boston University Microarray and Sequencing core.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP233258,,,mRNA-miR-144.fastq.gz,fastq,21666521349.0,286736059.0,mRNA miR 144.fastq.gz,0:75.56 1:0,A:4937891523;C:5429635867;G:5884853915;T:5410789187;N:3350857,75,0,,,4937891523,5429635867,5884853915,5410789187,3350857,SRX7216662,SRS5719128,SRA1002853,University of East Anglia|Biological Sciences,University of East Anglia,1,0.97729,,0.02379,,0.84102,,0.45517,,76,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-26,Hatching,Embryo,Blood,Hematopoietic System
55538,SRR10532694,SRX7216661,SRS5719127,SRP233258,PRJNA591815,Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis,PRJNA591815,Other,MicroRNAs are sequentially processed by two RNAse III enzymes  Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation  where it becomes the most abundant miRNA. However  the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.,,,,,wild type,,isolate:Lab reared|age:2 days|sex:not applicable|tissue:peripheral blood|genotype:wild type|phenotype:wild type|treatment:n1|BioSampleModel:Model organism or animal,,,,,,,,,Transcriptomic profiling of peripheral blood from 2 dpf zebrafish embryos,mRNA WT,mRNA WT,mRNA libraries were cloned from polyA+ RNA isolated from peripheral blood of 2 dpf WT and mutant zebrafish embryos according to Illumina TruSeq protocol. Libraries were cloned and sequenced at Boston University Microarray and Sequencing core.,,,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,SINGLE,ILLUMINA,NextSeq 500,,SRP233258,,,mRNA-WT.fastq.gz,fastq,5359234061.0,70925969.0,mRNA WT.fastq.gz,0:75.56 1:0,A:1229417939;C:1341096472;G:1448568683;T:1339375309;N:775658,75,0,,,1229417939,1341096472,1448568683,1339375309,775658,SRX7216661,SRS5719127,SRA1002853,University of East Anglia|Biological Sciences,University of East Anglia,1,0.97314,,0.02809,,0.83179,,0.40499,,75,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,trueseq,bulk,unknown,unknown,,United Kingdom,2019-11-26,Hatching,Embryo,Blood,Hematopoietic System
55539,SRR10532695,SRX7216660,SRS5719128,SRP233258,PRJNA591815,Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis,PRJNA591815,Other,MicroRNAs are sequentially processed by two RNAse III enzymes  Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation  where it becomes the most abundant miRNA. However  the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.,,,,,miR 144 mutant,,isolate:Lab reared|age:2 days|sex:not applicable|tissue:peripheral blood|genotype:miR 144 / |phenotype:wild type|treatment:n1|BioSampleModel:Model organism or animal,,,,,,,,,Small RNA from peripheral blood from 2 dpf zebrafish embryos  miR 451 mutant,sRNA Mut miR 144,sRNA Mut miR 144,Small RNA libraries were prepared from total RNA 0.5 g isolated from peripheral blood of wild type WT and miR 144 /  embryos at 48 hpf Small RNAs were size selected in 10% denaturing polyacrylamide gel in 1X TBE in range from 18 to 75 bp. RNA extraction from the gel was achieved by incubation in 0.3 M NaCl overnight at 4C with following precipitation with isopropanol. Pre adenylated 3 custom adaptor WT: /5PHOS/N*NCACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/; miR 144 / :/5PHOS/N*NAGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/ were ligated to small RNAs by T4 RNA ligase for 2 h at 22 C. post ligated products were size selected by gel from non ligated adaptor. Reverse transcription was performed by SuperScript III Reverse Transcription kit Thermo Fisher using custom RT Cloning Primer /5PHOS/NNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC SPC18 GGATCC SPC18 GTGACTGGAGTTCAGACGTGTGCTC. Then cDNA products were isolated by gel selection and then circularized by CircLigase ssDNA Ligase Epicentre. cDNA libraries were amplified in reactions containing forward and reverse Illumina index primers.,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP233258,,,sRNA-miR-144.fastq.gz,fastq,284208421.0,7813754.0,sRNA miR 144.fastq.gz,0:36.37,A:63063755;C:66933795;G:92235682;T:61966771;N:8418,36,,,,63063755,66933795,92235682,61966771,8418,SRX7216660,SRS5719128,SRA1002853,University of East Anglia|Biological Sciences,University of East Anglia,1,0.02041,,0.00444,,0.98512,,0.44771,,28,,B,,usable mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United Kingdom,2019-11-26,Hatching,Embryo,Blood,Hematopoietic System
55540,SRR10532696,SRX7216659,SRS5719127,SRP233258,PRJNA591815,Ago2 dependent processing allows miR 451 to evade the global microRNA turnover elicited during erythropoiesis,PRJNA591815,Other,MicroRNAs are sequentially processed by two RNAse III enzymes  Drosha and Dicer. miR 451 is the only known miRNA whose processing bypasses Dicer and instead relies on the slicer activity of Argonaute 2 Ago2. MiR 451 is highly conserved in vertebrates and regulates erythrocyte maturation  where it becomes the most abundant miRNA. However  the basis for the non canonical biogenesis of miR 451 is unclear. In this study we tested the hypothesis that miR 144 represses Dicer in a negative feedback loop during erythropoiesis and enhances miR 451 biogenesis. Loss of miR 144 mediated Dicer repression in zebrafish embryos and human cells leads to increased canonical miRNA production and impaired miR 451 maturation.,,,,,wild type,,isolate:Lab reared|age:2 days|sex:not applicable|tissue:peripheral blood|genotype:wild type|phenotype:wild type|treatment:n1|BioSampleModel:Model organism or animal,,,,,,,,,Small RNA from peripheral blood from 2 dpf zebrafish embryos  wild type,sRNA WT,sRNA WT,Small RNA libraries were prepared from total RNA 0.5 g isolated from peripheral blood of wild type WT and miR 144 /  embryos at 48 hpf Small RNAs were size selected in 10% denaturing polyacrylamide gel in 1X TBE in range from 18 to 75 bp. RNA extraction from the gel was achieved by incubation in 0.3 M NaCl overnight at 4C with following precipitation with isopropanol. Pre adenylated 3 custom adaptor WT: /5PHOS/N*NCACAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/; miR 144 / :/5PHOS/N*NAGAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3ddC/ were ligated to small RNAs by T4 RNA ligase for 2 h at 22 C. post ligated products were size selected by gel from non ligated adaptor. Reverse transcription was performed by SuperScript III Reverse Transcription kit Thermo Fisher using custom RT Cloning Primer /5PHOS/NNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC SPC18 GGATCC SPC18 GTGACTGGAGTTCAGACGTGTGCTC. Then cDNA products were isolated by gel selection and then circularized by CircLigase ssDNA Ligase Epicentre. cDNA libraries were amplified in reactions containing forward and reverse Illumina index primers.,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,ILLUMINA,NextSeq 500,,SRP233258,,,sRNA-WT.fastq.gz,fastq,294275059.0,8550051.0,sRNA WT.fastq.gz,0:34.42,A:65237071;C:85092331;G:80441993;T:63494506;N:9158,34,,,,65237071,85092331,80441993,63494506,9158,SRX7216659,SRS5719127,SRA1002853,University of East Anglia|Biological Sciences,University of East Anglia,1,0.00854,,0.00213,,0.99184,,0.55467,,31,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,size_fractionation,unknown,bulk,unknown,unknown,,United Kingdom,2019-11-26,Hatching,Embryo,Blood,Hematopoietic System
59146,SRR11700449,SRX8259900,SRS6601868,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep3,GSM4518498,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518498,GSM4518498: cxcr3.2wt rep3; Danio rerio; RNA Seq,GSM4518498,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518498,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt3_1.fastq.gz,fastq,173026017.0,3392667.0,GSM4518498 r1,0:51,A:50003437;C:34139662;G:34317418;T:54513188;N:52312,51,,,,50003437,34139662,34317418,54513188,52312,SRX8259900,SRS6601868,SRA1072497,GEO,LSHTM,1,0.80078,,0.22125,,0.78788,,0.53444,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59147,SRR11700450,SRX8259900,SRS6601868,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep3,GSM4518498,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518498,GSM4518498: cxcr3.2wt rep3; Danio rerio; RNA Seq,GSM4518498,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518498,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt3_2.fastq.gz,fastq,173719362.0,3406262.0,GSM4518498 r2,0:51,A:50217431;C:34289412;G:34447800;T:54729217;N:35502,51,,,,50217431,34289412,34447800,54729217,35502,SRX8259900,SRS6601868,SRA1072497,GEO,LSHTM,1,0.8033,,0.2226,,0.78498,,0.53485,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59148,SRR11700451,SRX8259900,SRS6601868,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep3,GSM4518498,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518498,GSM4518498: cxcr3.2wt rep3; Danio rerio; RNA Seq,GSM4518498,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518498,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt3_3.fastq.gz,fastq,117503031.0,2303981.0,GSM4518498 r3,0:51,A:33926847;C:22984117;G:23302421;T:37279310;N:10336,51,,,,33926847,22984117,23302421,37279310,10336,SRX8259900,SRS6601868,SRA1072497,GEO,LSHTM,1,0.76501,,0.22042,,0.79912,,0.54263,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59149,SRR11700452,SRX8259900,SRS6601868,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep3,GSM4518498,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518498,GSM4518498: cxcr3.2wt rep3; Danio rerio; RNA Seq,GSM4518498,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518498,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt3_4.fastq.gz,fastq,114086745.0,2236995.0,GSM4518498 r4,0:51,A:32945373;C:22224999;G:22487321;T:36409257;N:19795,51,,,,32945373,22224999,22487321,36409257,19795,SRX8259900,SRS6601868,SRA1072497,GEO,LSHTM,1,0.74509,,0.21675,,0.80653,,0.54624,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59150,SRR11700447,SRX8259899,SRS6601867,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2mu rep3,GSM4518497,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,cxcr3.2mu rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,GSM4518497,GSM4518497: cxcr3.2mu rep3; Danio rerio; RNA Seq,GSM4518497,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518497,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,mu3_1.fastq.gz,fastq,425713881.0,8347331.0,GSM4518497 r1,0:51,A:122037955;C:83276458;G:83884392;T:136385789;N:129287,51,,,,122037955,83276458,83884392,136385789,129287,SRX8259899,SRS6601867,SRA1072497,GEO,LSHTM,1,0.79761,,0.24807,,0.78031,,0.55233,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59151,SRR11700448,SRX8259899,SRS6601867,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2mu rep3,GSM4518497,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,cxcr3.2mu rep3,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,GSM4518497,GSM4518497: cxcr3.2mu rep3; Danio rerio; RNA Seq,GSM4518497,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518497,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,mu3_2.fastq.gz,fastq,432332151.0,8477101.0,GSM4518497 r2,0:51,A:124004077;C:84578395;G:85238663;T:138421813;N:89203,51,,,,124004077,84578395,85238663,138421813,89203,SRX8259899,SRS6601867,SRA1072497,GEO,LSHTM,1,0.79871,,0.25156,,0.77962,,0.54833,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59152,SRR11700445,SRX8259898,SRS6601866,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep2,GSM4518496,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt rep2,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518496,GSM4518496: cxcr3.2wt rep2; Danio rerio; RNA Seq,GSM4518496,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518496,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt2_1.fastq.gz,fastq,338884596.0,6644796.0,GSM4518496 r1,0:51,A:95060797;C:69418429;G:69712092;T:104594793;N:98485,51,,,,95060797,69418429,69712092,104594793,98485,SRX8259898,SRS6601866,SRA1072497,GEO,LSHTM,1,0.82037,,0.19262,,0.78573,,0.50787,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59153,SRR11700446,SRX8259898,SRS6601866,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep2,GSM4518496,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt rep2,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518496,GSM4518496: cxcr3.2wt rep2; Danio rerio; RNA Seq,GSM4518496,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518496,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt2_2.fastq.gz,fastq,340274448.0,6672048.0,GSM4518496 r2,0:51,A:95520411;C:69702700;G:69990821;T:104992786;N:67730,51,,,,95520411,69702700,69990821,104992786,67730,SRX8259898,SRS6601866,SRA1072497,GEO,LSHTM,1,0.8231,,0.19334,,0.78644,,0.5196,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59154,SRR11700443,SRX8259897,SRS6601865,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2mu rep2,GSM4518495,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,cxcr3.2mu rep2,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,GSM4518495,GSM4518495: cxcr3.2mu rep2; Danio rerio; RNA Seq,GSM4518495,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518495,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,mu2_1.fastq.gz,fastq,289744005.0,5681255.0,GSM4518495 r1,0:51,A:83941467;C:56685263;G:57155798;T:91875606;N:85871,51,,,,83941467,56685263,57155798,91875606,85871,SRX8259897,SRS6601865,SRA1072497,GEO,LSHTM,1,0.797,,0.19874,,0.77948,,0.54924,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59155,SRR11700444,SRX8259897,SRS6601865,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2mu rep2,GSM4518495,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,cxcr3.2mu rep2,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,GSM4518495,GSM4518495: cxcr3.2mu rep2; Danio rerio; RNA Seq,GSM4518495,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518495,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,mu2_2.fastq.gz,fastq,292004937.0,5725587.0,GSM4518495 r2,0:51,A:84614504;C:57133336;G:57626820;T:92570322;N:59955,51,,,,84614504,57133336,57626820,92570322,59955,SRX8259897,SRS6601865,SRA1072497,GEO,LSHTM,1,0.79923,,0.19835,,0.77855,,0.53966,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59156,SRR11700441,SRX8259896,SRS6601864,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep1,GSM4518494,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt rep1,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518494,GSM4518494: cxcr3.2wt rep1; Danio rerio; RNA Seq,GSM4518494,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518494,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt1_1.fastq.gz,fastq,365558718.0,7167818.0,GSM4518494 r1,0:51,A:106749458;C:71670361;G:72075682;T:114952902;N:110315,51,,,,106749458,71670361,72075682,114952902,110315,SRX8259896,SRS6601864,SRA1072497,GEO,LSHTM,1,0.80168,,0.20934,,0.78336,,0.55284,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59157,SRR11700442,SRX8259896,SRS6601864,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2wt rep1,GSM4518494,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,cxcr3.2wt rep1,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2+/+,GSM4518494,GSM4518494: cxcr3.2wt rep1; Danio rerio; RNA Seq,GSM4518494,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518494,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,wt1_2.fastq.gz,fastq,369956805.0,7254055.0,GSM4518494 r2,0:51,A:108102133;C:72565792;G:72967269;T:116246235;N:75376,51,,,,108102133,72565792,72967269,116246235,75376,SRX8259896,SRS6601864,SRA1072497,GEO,LSHTM,1,0.80058,,0.21005,,0.78303,,0.54972,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59158,SRR11700439,SRX8259895,SRS6601863,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2mu rep1,GSM4518493,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,cxcr3.2mu rep1,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,GSM4518493,GSM4518493: cxcr3.2mu rep1; Danio rerio; RNA Seq,GSM4518493,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518493,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,mu1_1.fastq.gz,fastq,413105049.0,8100099.0,GSM4518493 r1,0:51,A:117770136;C:83069765;G:83597140;T:128544513;N:123495,51,,,,117770136,83069765,83597140,128544513,123495,SRX8259895,SRS6601863,SRA1072497,GEO,LSHTM,1,0.74703,,0.18405,,0.79072,,0.52251,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System
59159,SRR11700440,SRX8259895,SRS6601863,SRP260213,PRJNA630667,RNAseq expression analysis of FACS sorted macrophages from cxcr3.2 mutant and wt zebrafish larvae,GSE149942,Transcriptome Analysis,The zebrafish Cxcr3.2 is a functional homolog of the human chemokine receptor CXCR3. Zebrafish macrophages lacking this receptor have impaired motility and a rounded shape compared to their wildtype counterparts. To investigate the effects of cxcr3.2 mutation on the transcriptional profile of macrophages  we sorted macrophages from zebrafish larvae lacking a functional cxcr3.2 and compared their transcriptome to that of macrophages from wildtype larvae. Mutant and wildtype macrophages could be clearly distinguished based on the overall differential expression profiles. Classification of genes by compartment showed that peroxisomal  lysosomal and Golgi related genes were most frequently up regulated. Moreover  lysosomal and Golgi related terms were significantly differentially represented in Gene Ontology and KEGG enrichment analysis. Of note  several lysosomal markers  including acidic hydrolases and voltage ATPases were consistently upregulated in cxcr3.2 mutant macrophages  indicating that cxcr3.2 mediated chemokine signaling is tightly connected to the regulation of lysosomal function. Overall design: 3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted  retrotranscribed into cDNA and amplified using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech  prior Illumina sequencing.,,pubmed:33852860,,cxcr3.2mu rep1,GSM4518493,,tissue:FACS mpeg1: mCherryF positive cells|age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,cxcr3.2mu rep1,Image analysis and base calling was done by the Illumina HCS version 1.15.1 Quality trimmed reads were aligned to the Ensembl zebrafish genome GRCz10 using Bowtie Reads were mapped to zebrafish transcripts using TopHat Genome build: GRCz10 Supplementary files format and content: tab separated value files of read counts for each sample,FACS mpeg1: mCherryF positive cells,,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers’ instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer’s guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,,age:6 dpf type:macrophage|strain:mpeg1: mCherryF|genotype:cxcr3.2 / ,GSM4518493,GSM4518493: cxcr3.2mu rep1; Danio rerio; RNA Seq,GSM4518493,,1,3 independent groups of 150 200 5dpf Tg mpeg1: mCherryF cxcr3.2 /  and cxcr3.2+/+ larvae were dissociated and red fluorescent macrophages were FACS sorted. RNA was extracted using the miRNeasy mini kit Qiagen according to the manufacturers' instructions. cDNA synthesis and amplification was done using the SMARTer® Universal Low Input RNA Kit for Sequencing Clontech following the manufacturer's guidelines. Approximately 10 Mreads were obtained  using Illimuna Single Read runs. Reads were then aligned to GRCz10 Danio rerio genome.,GEO Accession:GSM4518493,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2000,,SRP260213,,,mu1_2.fastq.gz,fastq,417048216.0,8177416.0,GSM4518493 r2,0:51,A:119015831;C:83862032;G:84384304;T:129702704;N:83345,51,,,,119015831,83862032,84384304,129702704,83345,SRX8259895,SRS6601863,SRA1072497,GEO,LSHTM,1,0.74816,,0.18628,,0.78782,,0.52889,,51,,B,,usable mapping rate,illumina,hiseq_era,full_length,cdna_unspecified,smarter,bulk,unknown,unknown,,United Kingdom,2020-05-06,Larval,Larval,Blood,Hematopoietic System