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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
42519 SRR5683297 SRX2918450 SRS2284458 SRP109201 PRJNA390533 Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair GSE100029 Transcriptome Analysis Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition. Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar. Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury. Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors enhanced scar formation and induced fibrosis respectively via cell autonomous production of collagen. In zebrafish macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts. These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.   pubmed:32001677   Mpeg xxx post injury resec2 GSM2668101   source name:Mpeg xxx post injury resec2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse Mpeg xxx post injury resec2 Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10 Mpeg xxx post injury resec2   For nuclei isolation hearts were dissected at appropriate time points and washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl­2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet Invitrogen cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNAse treatment were carried out using the RNAqueous® Micro Kit Life Technologies cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories cat #’s 634888 634889 634890 634891 634892 634893 and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina cat # FC 404 1002.   strain:TgBACmpeg1:BirA Citrine;bactin:Avi Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse GSM2668101 GSM2668101: Mpeg xxx post injury resec2; Danio rerio; RNA Seq GSM2668101   1 For nuclei isolation hearts were dissected at appropriate time points and washed in hypotonic buffer H 20 mM HEPES pH 7.9 15 mM MgCl­2 10 mM KCl 1 mM DTT and 1 X Complete protease inhibitor and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B every 5 minutes for 15 minutes. Nuclei were collected by centrifugation 2000 g 4 °C and resuspended in 1 mL buffer NDP 10 mM HEPES pH 7.9 40 mM NaCl 90 mM KCl 0.5 mM EDTA 0.5 mM spermidine 0.15 mM spermine 1 mM dithiothreitol and 1 X Complete protease inhibitor. For nuclei purification nuclei were incubated with 5 mg of M 280 streptavidin coated dynabeads with rotation for 30 minutes at 4 °C. A flow based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette VWR cat # 8913 898 attached to a 1 mL micropipette tip Rainin reach pipet tip cat # RT L1000S both pre treated with NPB/BSA for 30 minutes and added to a MiniMACS separator magnet OctoMACS Separator Miltenyl Biotec cat # 130 042 109. A two way stopcock Biorad cat # 732 8102 was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing Fisher Scientific cat # 8220 and the flow rate set to 0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X 100 NPBt and added to the slow flow setup. The tip was subsequently removed from the stand and the nuclei beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow flow setup. Nuclei beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand DynaMag TM 2 magnet Invitrogen cat # 12321D. Nuclei beads were then processed for RNA extraction. RNA extraction and DNase treatment were carried out using the RNAqueous® Micro Kit Life Technologies cat # AM1931. RNA integrity was checked with a RNA pico chip Agilent Technologies cat # 5067 1513 using the Agilent 2100 Bioanalyzer. cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories cat #’s 634888 634889 634890 634891 634892 634893 and 634894. Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads 150 cycles Illumina cat # FC 404 1002. GEO Accession:GSM2668101 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP109201     mpeg_1dpi_resec2_R2.fastq.gz mpeg_1dpi_resec2_R1.fastq.gz fastq fastq 5076782892.0 31911484.0 GSM2668101 r1 0:79.54 1:79.55 A:1549105925;C:1013432083;G:1063735890;T:1449731944;N:777050 79 79     1549105925 1013432083 1063735890 1449731944 777050 SRX2918450 SRS2284458 SRA574274 GEO Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine 2 0.8623 0.85895 0.22428 0.22646 0.77378 0.78246 0.4794 0.47986 80 80 B B biological fallback assumption illumina nextseq full_length random_priming nextera sc single_cell_plate smartseq   United Kingdom 2017-06-14 Adult Adult Blood Hematopoietic System