{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", technology = \"smartseq\" and tissue_curation = \"Blood\"", "rows": [[42501, "SRR5683317", "SRX2918465", "SRS2284474", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 14 xxx post injury Round2 cryo3", "GSM2668116", null, "source name:Mpeg 14 xxx post injury Round2 cryo3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse", "Mpeg 14 xxx post injury Round2 cryo3", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 14 xxx post injury Round2 cryo3", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse", "GSM2668116", "GSM2668116: Mpeg 14 xxx post injury Round2 cryo3; Danio rerio; RNA Seq", "GSM2668116", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668116", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "cryo3_14dpi_B_R1.fastq.gz cryo3_14dpi_B_R2.fastq.gz", "fastq fastq", 7861934638.0, 49554149.0, "GSM2668116 r1", "0:79.32 1:79.33", "A:2180198909;C:1707559679;G:1786562980;T:2185442888;N:2170182", 79, 79, null, null, 2180198909, 1707559679, 1786562980, 2185442888, 2170182, "SRX2918465", "SRS2284474", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.92041, 0.92378, 0.14221, 0.14168, 0.79799, 0.8016, 0.45038, 0.35896, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42502, "SRR5683316", "SRX2918464", "SRS2284472", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 14 xxx post injury Round2 cryo2", "GSM2668115", null, "source name:Mpeg 14 xxx post injury Round2 cryo2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse", "Mpeg 14 xxx post injury Round2 cryo2", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 14 xxx post injury Round2 cryo2", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse", "GSM2668115", "GSM2668115: Mpeg 14 xxx post injury Round2 cryo2; Danio rerio; RNA Seq", "GSM2668115", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668115", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "cryo2_14dpi_B_R1.fastq.gz cryo2_14dpi_B_R2.fastq.gz", "fastq fastq", 8095516200.0, 51058824.0, "GSM2668115 r1", "0:79.28 1:79.28", "A:2251179258;C:1721305507;G:1814673340;T:2305885309;N:2472786", 79, 79, null, null, 2251179258, 1721305507, 1814673340, 2305885309, 2472786, "SRX2918464", "SRS2284472", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.89889, 0.89756, 0.18338, 0.17899, 0.81219, 0.81525, 0.43098, 0.4397, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42503, "SRR5683314", "SRX2918463", "SRS2284471", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 14 xxx post injury Round2 cryo1 merged", "GSM2668114", null, "source name:Mpeg 14 xxx post injury Round2 cryo1 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse", "Mpeg 14 xxx post injury Round2 cryo1 merged", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 14 xxx post injury Round2 cryo1 merged", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse", "GSM2668114", "GSM2668114: Mpeg 14 xxx post injury Round2 cryo1 merged; Danio rerio; RNA Seq", "GSM2668114", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668114", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "14dpicryo1_mpeg_B_R1_May.fastq.gz 14dpicryo1_mpeg_B_R2_May.fastq.gz", "fastq fastq", 3423280266.0, 21561025.0, "GSM2668114 r1", "0:79.38 1:79.39", "A:1107875201;C:594804208;G:621478979;T:1098524417;N:597461", 79, 79, null, null, 1107875201, 594804208, 621478979, 1098524417, 597461, "SRX2918463", "SRS2284471", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.82792, 0.82592, 0.70435, 0.70409, 0.7963, 0.81209, 0.49674, 0.50012, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42504, "SRR5683315", "SRX2918463", "SRS2284471", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 14 xxx post injury Round2 cryo1 merged", "GSM2668114", null, "source name:Mpeg 14 xxx post injury Round2 cryo1 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse", "Mpeg 14 xxx post injury Round2 cryo1 merged", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 14 xxx post injury Round2 cryo1 merged", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse", "GSM2668114", "GSM2668114: Mpeg 14 xxx post injury Round2 cryo1 merged; Danio rerio; RNA Seq", "GSM2668114", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668114", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "14dpicryo1_mpeg_B_R1_June.fastq.gz 14dpicryo1_mpeg_B_R2_June.fastq.gz", "fastq fastq", 610753180.0, 3844389.0, "GSM2668114 r2", "0:79.43 1:79.44", "A:194990113;C:106753101;G:111444912;T:197419441;N:145613", 79, 79, null, null, 194990113, 106753101, 111444912, 197419441, 145613, "SRX2918463", "SRS2284471", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.83295, 0.83136, 0.71203, 0.71039, 0.79902, 0.80957, 0.50147, 0.50457, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42505, "SRR5683313", "SRX2918462", "SRS2284470", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 14 xxx post injury Round2 sham3", "GSM2668113", null, "source name:Mpeg 14 xxx post injury Round2 sham3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "Mpeg 14 xxx post injury Round2 sham3", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 14 xxx post injury Round2 sham3", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "GSM2668113", "GSM2668113: Mpeg 14 xxx post injury Round2 sham3; Danio rerio; RNA Seq", "GSM2668113", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668113", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "sham3_14dpi_B_R1.fastq.gz sham3_14dpi_B_R2.fastq.gz", "fastq fastq", 6045529728.0, 38096625.0, "GSM2668113 r1", "0:79.34 1:79.35", "A:1692396398;C:1295917589;G:1361588402;T:1694052830;N:1574509", 79, 79, null, null, 1692396398, 1295917589, 1361588402, 1694052830, 1574509, "SRX2918462", "SRS2284470", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.91926, 0.91739, 0.11828, 0.11628, 0.82223, 0.82534, 0.47847, 0.49838, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42506, "SRR5683309", "SRX2918461", "SRS2284469", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 14 xxx post injury Round1 sham3 merged", "GSM2668112", null, "source name:Mpeg 14 xxx post injury Round1 sham3 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "Mpeg 14 xxx post injury Round1 sham3 merged", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 14 xxx post injury Round1 sham3 merged", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "GSM2668112", "GSM2668112: Mpeg 14 xxx post injury Round1 sham3 merged; Danio rerio; RNA Seq", "GSM2668112", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668112", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "14dpisham3_mpeg_B_R1_May.fastq.gz 14dpisham3_mpeg_B_R2_May.fastq.gz", "fastq fastq", 3088232153.0, 19713193.0, "GSM2668112 r1", "0:78.31 1:78.34", "A:921823592;C:606907388;G:646058581;T:910627373;N:2815219", 78, 78, null, null, 921823592, 606907388, 646058581, 910627373, 2815219, "SRX2918461", "SRS2284469", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.87257, 0.87547, 0.20876, 0.20608, 0.81253, 0.81773, 0.44997, 0.46461, 80, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42507, "SRR5683311", "SRX2918461", "SRS2284469", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 14 xxx post injury Round1 sham3 merged", "GSM2668112", null, "source name:Mpeg 14 xxx post injury Round1 sham3 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "Mpeg 14 xxx post injury Round1 sham3 merged", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 14 xxx post injury Round1 sham3 merged", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "GSM2668112", "GSM2668112: Mpeg 14 xxx post injury Round1 sham3 merged; Danio rerio; RNA Seq", "GSM2668112", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668112", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "14dpisham3_mpeg_B_R1_June.fastq.gz 14dpisham3_mpeg_B_R2_June.fastq.gz", "fastq fastq", 846302505.0, 5389309.0, "GSM2668112 r2", "0:78.51 1:78.53", "A:245478169;C:167755451;G:179179261;T:253210722;N:678902", 78, 78, null, null, 245478169, 167755451, 179179261, 253210722, 678902, "SRX2918461", "SRS2284469", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.87646, 0.87747, 0.20632, 0.20462, 0.81272, 0.81897, 0.46568, 0.46082, 78, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42508, "SRR5683308", "SRX2918460", "SRS2284468", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 14 xxx post injury Round1 sham2", "GSM2668111", null, "source name:Mpeg 14 xxx post injury Round1 sham2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "Mpeg 14 xxx post injury Round1 sham2", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 14 xxx post injury Round1 sham2", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "GSM2668111", "GSM2668111: Mpeg 14 xxx post injury Round1 sham2; Danio rerio; RNA Seq", "GSM2668111", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668111", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "14dpisham2_mpeg_B_R1.fastq.gz 14dpisham2_mpeg_B_R2.fastq.gz", "fastq fastq", 6035307225.0, 38834475.0, "GSM2668111 r1", "0:77.69 1:77.73", "A:1766010265;C:1217065541;G:1295674905;T:1748007248;N:8549266", 77, 77, null, null, 1766010265, 1217065541, 1295674905, 1748007248, 8549266, "SRX2918460", "SRS2284468", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.87025, 0.87255, 0.16504, 0.16092, 0.82075, 0.8252, 0.48031, 0.38246, 80, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42509, "SRR5683307", "SRX2918459", "SRS2284467", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 14 xxx post injury Round1 sham1", "GSM2668110", null, "source name:Mpeg 14 xxx post injury Round1 sham1|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "Mpeg 14 xxx post injury Round1 sham1", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 14 xxx post injury Round1 sham1", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:14 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "GSM2668110", "GSM2668110: Mpeg 14 xxx post injury Round1 sham1; Danio rerio; RNA Seq", "GSM2668110", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668110", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "14dpisham1_mpeg_B_R1.fastq.gz 14dpisham1_mpeg_B_R2.fastq.gz", "fastq fastq", 12977926933.0, 85345256.0, "GSM2668110 r1", "0:76.00 1:76.06", "A:3815859192;C:2608097642;G:2746153398;T:3772773322;N:35043379", 76, 76, null, null, 3815859192, 2608097642, 2746153398, 3772773322, 35043379, "SRX2918459", "SRS2284467", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.84194, 0.84592, 0.19588, 0.19184, 0.82022, 0.82373, 0.49431, 0.48674, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42510, "SRR5683306", "SRX2918458", "SRS2284466", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 5 xxx post injury resec2", "GSM2668109", null, "source name:Mpeg 5 xxx post injury resec2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse", "Mpeg 5 xxx post injury resec2", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 5 xxx post injury resec2", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse", "GSM2668109", "GSM2668109: Mpeg 5 xxx post injury resec2; Danio rerio; RNA Seq", "GSM2668109", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668109", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "mpeg_5dpi_resec2_R1.fastq.gz mpeg_5dpi_resec2_R2.fastq.gz", "fastq fastq", 3383380650.0, 21264204.0, "GSM2668109 r1", "0:79.56 1:79.56", "A:1033165656;C:667727603;G:708080342;T:973980006;N:427043", 79, 79, null, null, 1033165656, 667727603, 708080342, 973980006, 427043, "SRX2918458", "SRS2284466", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.86066, 0.85477, 0.25065, 0.25874, 0.8072, 0.81586, 0.45299, 0.45757, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42511, "SRR5683305", "SRX2918457", "SRS2284465", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 5 xxx post injury resec1", "GSM2668108", null, "source name:Mpeg 5 xxx post injury resec1|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse", "Mpeg 5 xxx post injury resec1", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 5 xxx post injury resec1", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse", "GSM2668108", "GSM2668108: Mpeg 5 xxx post injury resec1; Danio rerio; RNA Seq", "GSM2668108", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668108", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "mpeg_5dpi_resec1_R1.fastq.gz mpeg_5dpi_resec1_R2.fastq.gz", "fastq fastq", 6869873301.0, 43173364.0, "GSM2668108 r1", "0:79.56 1:79.56", "A:2031090336;C:1426974358;G:1499082453;T:1911947654;N:778500", 79, 79, null, null, 2031090336, 1426974358, 1499082453, 1911947654, 778500, "SRX2918457", "SRS2284465", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.89183, 0.88662, 0.13918, 0.13872, 0.81284, 0.81736, 0.39007, 0.49219, 78, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42512, "SRR5683304", "SRX2918456", "SRS2284463", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 5 xxx post injury cryo4", "GSM2668107", null, "source name:Mpeg 5 xxx post injury cryo4|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse", "Mpeg 5 xxx post injury cryo4", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 5 xxx post injury cryo4", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse", "GSM2668107", "GSM2668107: Mpeg 5 xxx post injury cryo4; Danio rerio; RNA Seq", "GSM2668107", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668107", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "mpeg_5dpi_cryo4_R1.fastq.gz mpeg_5dpi_cryo4_R2.fastq.gz", "fastq fastq", 6277247450.0, 39463081.0, "GSM2668107 r1", "0:79.53 1:79.54", "A:1929673813;C:1267115857;G:1307899881;T:1772085832;N:472067", 79, 79, null, null, 1929673813, 1267115857, 1307899881, 1772085832, 472067, "SRX2918456", "SRS2284463", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.85203, 0.8343, 0.24868, 0.25, 0.81308, 0.82647, 0.48925, 0.50311, 80, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42513, "SRR5683303", "SRX2918455", "SRS2284464", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 5 xxx post injury cryo1", "GSM2668106", null, "source name:Mpeg 5 xxx post injury cryo1|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse", "Mpeg 5 xxx post injury cryo1", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 5 xxx post injury cryo1", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse", "GSM2668106", "GSM2668106: Mpeg 5 xxx post injury cryo1; Danio rerio; RNA Seq", "GSM2668106", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668106", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "mpeg_5dpi_cryo1_R1.fastq.gz mpeg_5dpi_cryo1_R2.fastq.gz", "fastq fastq", 4027290734.0, 25319007.0, "GSM2668106 r1", "0:79.53 1:79.53", "A:1233222560;C:810894366;G:838434971;T:1144395366;N:343471", 79, 79, null, null, 1233222560, 810894366, 838434971, 1144395366, 343471, "SRX2918455", "SRS2284464", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.85923, 0.84321, 0.1985, 0.20039, 0.83625, 0.84236, 0.49381, 0.48397, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42514, "SRR5683302", "SRX2918454", "SRS2284462", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 5 xxx post injury sham3", "GSM2668105", null, "source name:Mpeg 5 xxx post injury sham3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "Mpeg 5 xxx post injury sham3", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 5 xxx post injury sham3", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "GSM2668105", "GSM2668105: Mpeg 5 xxx post injury sham3; Danio rerio; RNA Seq", "GSM2668105", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668105", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "mpeg_5dpi_sham3_R2.fastq.gz mpeg_5dpi_sham3_R1.fastq.gz", "fastq fastq", 8115490925.0, 51002382.0, "GSM2668105 r1", "0:79.56 1:79.56", "A:2440332785;C:1628963788;G:1720872185;T:2324279946;N:1042221", 79, 79, null, null, 2440332785, 1628963788, 1720872185, 2324279946, 1042221, "SRX2918454", "SRS2284462", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.85247, 0.84621, 0.27035, 0.27069, 0.85084, 0.85451, 0.45753, 0.45612, 80, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42515, "SRR5683300", "SRX2918453", "SRS2284461", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 5 xxx post injury sham2 merged", "GSM2668104", null, "source name:Mpeg 5 xxx post injury sham2 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "Mpeg 5 xxx post injury sham2 merged", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 5 xxx post injury sham2 merged", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "GSM2668104", "GSM2668104: Mpeg 5 xxx post injury sham2 merged; Danio rerio; RNA Seq", "GSM2668104", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668104", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "5dpisham2_mpeg_A_R2_April.fastq.gz 5dpisham2_mpeg_A_R1_April.fastq.gz", "fastq fastq", 3860992328.0, 24366329.0, "GSM2668104 r1", "0:79.22 1:79.23", "A:1130628484;C:798981479;G:837808724;T:1092372622;N:1201019", 79, 79, null, null, 1130628484, 798981479, 837808724, 1092372622, 1201019, "SRX2918453", "SRS2284461", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.89802, 0.89614, 0.23222, 0.22961, 0.79894, 0.8056, 0.40655, 0.416, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42516, "SRR5683301", "SRX2918453", "SRS2284461", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 5 xxx post injury sham2 merged", "GSM2668104", null, "source name:Mpeg 5 xxx post injury sham2 merged|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "Mpeg 5 xxx post injury sham2 merged", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 5 xxx post injury sham2 merged", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:5 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "GSM2668104", "GSM2668104: Mpeg 5 xxx post injury sham2 merged; Danio rerio; RNA Seq", "GSM2668104", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668104", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "5dpisham2_mpeg_A_R2_June.fastq.gz 5dpisham2_mpeg_A_R1_June.fastq.gz", "fastq fastq", 1457479078.0, 9196316.0, "GSM2668104 r2", "0:79.24 1:79.24", "A:416316844;C:300713902;G:316902348;T:423075764;N:470220", 79, 79, null, null, 416316844, 300713902, 316902348, 423075764, 470220, "SRX2918453", "SRS2284461", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.89427, 0.89319, 0.2414, 0.23951, 0.80259, 0.80842, 0.40686, 0.41528, 80, 78, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42517, "SRR5683299", "SRX2918452", "SRS2284460", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 1 xxx post injury resec4", "GSM2668103", null, "source name:Mpeg 1 xxx post injury resec4|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse", "Mpeg 1 xxx post injury resec4", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 1 xxx post injury resec4", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse", "GSM2668103", "GSM2668103: Mpeg 1 xxx post injury resec4; Danio rerio; RNA Seq", "GSM2668103", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668103", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "mpeg_1dpi_resec4_R1.fastq.gz mpeg_1dpi_resec4_R2.fastq.gz", "fastq fastq", 5609751993.0, 35249823.0, "GSM2668103 r1", "0:79.57 1:79.57", "A:1726370842;C:1096706423;G:1151202056;T:1634668514;N:804158", 79, 79, null, null, 1726370842, 1096706423, 1151202056, 1634668514, 804158, "SRX2918452", "SRS2284460", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.85046, 0.84548, 0.24214, 0.24515, 0.77538, 0.78123, 0.4936, 0.48972, 80, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42518, "SRR5683298", "SRX2918451", "SRS2284459", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg xxx post injury resec3", "GSM2668102", null, "source name:Mpeg xxx post injury resec3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse", "Mpeg xxx post injury resec3", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg xxx post injury resec3", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:resection|strand:reverse", "GSM2668102", "GSM2668102: Mpeg xxx post injury resec3; Danio rerio; RNA Seq", "GSM2668102", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668102", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "mpeg_1dpi_resec3_R2.fastq.gz mpeg_1dpi_resec3_R1.fastq.gz", "fastq fastq", 5982719209.0, 37588800.0, "GSM2668102 r1", "0:79.58 1:79.58", "A:1830395391;C:1164413802;G:1227508893;T:1759666888;N:734235", 79, 79, null, null, 1830395391, 1164413802, 1227508893, 1759666888, 734235, "SRX2918451", "SRS2284459", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.84899, 0.84538, 0.24802, 0.24928, 0.77352, 0.77958, 0.48455, 0.48731, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42519, "SRR5683297", "SRX2918450", "SRS2284458", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg xxx post injury resec2", "GSM2668101", null, "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", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "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", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for 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", null, "SRP109201", null, null, "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, null, null, 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", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42520, "SRR5683296", "SRX2918449", "SRS2284457", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 1 xxx post injury cryo3", "GSM2668100", null, "source name:Mpeg 1 xxx post injury cryo3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse", "Mpeg 1 xxx post injury cryo3", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 1 xxx post injury cryo3", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse", "GSM2668100", "GSM2668100: Mpeg 1 xxx post injury cryo3; Danio rerio; RNA Seq", "GSM2668100", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668100", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "mpeg_1dpi_cryo3_R1.fastq.gz mpeg_1dpi_cryo3_R2.fastq.gz", "fastq fastq", 11880750994.0, 75033249.0, "GSM2668100 r1", "0:79.16 1:79.18", "A:3655884756;C:2399881665;G:2467642327;T:3355036709;N:2305537", 79, 79, null, null, 3655884756, 2399881665, 2467642327, 3355036709, 2305537, "SRX2918449", "SRS2284457", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.88646, 0.87912, 0.09292, 0.08786, 0.84867, 0.85184, 0.60254, 0.60389, 80, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42521, "SRR5683295", "SRX2918448", "SRS2284456", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 1 xxx post injury cryo2", "GSM2668099", null, "source name:Mpeg 1 xxx post injury cryo2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse", "Mpeg 1 xxx post injury cryo2", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 1 xxx post injury cryo2", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:cryoinjury|strand:reverse", "GSM2668099", "GSM2668099: Mpeg 1 xxx post injury cryo2; Danio rerio; RNA Seq", "GSM2668099", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668099", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "mpeg_1dpi_cryo2_R1.fastq.gz mpeg_1dpi_cryo2_R2.fastq.gz", "fastq fastq", 8232458249.0, 51981300.0, "GSM2668099 r1", "0:79.19 1:79.19", "A:2515938515;C:1635124065;G:1691955854;T:2387623909;N:1815906", 79, 79, null, null, 2515938515, 1635124065, 1691955854, 2387623909, 1815906, "SRX2918448", "SRS2284456", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.84555, 0.8442, 0.15288, 0.14711, 0.85123, 0.85222, 0.49769, 0.49241, 80, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42522, "SRR5683294", "SRX2918447", "SRS2284455", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 1 xxx post injury sham3", "GSM2668098", null, "source name:Mpeg 1 xxx post injury sham3|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "Mpeg 1 xxx post injury sham3", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 1 xxx post injury sham3", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "GSM2668098", "GSM2668098: Mpeg 1 xxx post injury sham3; Danio rerio; RNA Seq", "GSM2668098", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668098", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "mpeg_1dpi_sham3_R1.fastq.gz mpeg_1dpi_sham3_R2.fastq.gz", "fastq fastq", 8496331498.0, 53397150.0, "GSM2668098 r1", "0:79.56 1:79.56", "A:2502482113;C:1814852881;G:1898533497;T:2279486892;N:976115", 79, 79, null, null, 2502482113, 1814852881, 1898533497, 2279486892, 976115, "SRX2918447", "SRS2284455", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.91041, 0.90731, 0.06459, 0.06347, 0.87945, 0.88032, 0.49844, 0.49408, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42523, "SRR5683293", "SRX2918446", "SRS2284453", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 1 xxx post injury sham2", "GSM2668097", null, "source name:Mpeg 1 xxx post injury sham2|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "Mpeg 1 xxx post injury sham2", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 1 xxx post injury sham2", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "GSM2668097", "GSM2668097: Mpeg 1 xxx post injury sham2; Danio rerio; RNA Seq", "GSM2668097", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668097", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "mpeg_1dpi_sham2_R1.fastq.gz mpeg_1dpi_sham2_R2.fastq.gz", "fastq fastq", 14052650652.0, 88376646.0, "GSM2668097 r1", "0:79.50 1:79.50", "A:4126576983;C:3017594179;G:3122815728;T:3783988637;N:1675125", 79, 79, null, null, 4126576983, 3017594179, 3122815728, 3783988637, 1675125, "SRX2918446", "SRS2284453", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.90317, 0.90144, 0.09764, 0.10054, 0.82714, 0.83088, 0.45243, 0.46936, 80, 80, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [42524, "SRR5683292", "SRX2918445", "SRS2284454", "SRP109201", "PRJNA390533", "Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair", "GSE100029", "Transcriptome Analysis", "Canonical roles for macrophages in mediating the fibrotic response post a heart attack myocardial infarction include turnover of the extracellular matrix and activation of cardiac fibroblasts to initiate collagen deposition.  Here we reveal through studying the functional kinetics of fibrosis during zebrafish heart regeneration and mouse heart repair that macrophages can directly contribute collagen to the forming scar.  Unbiased transcriptomics revealed an up regulation of collagen isoforms in both zebrafish and mouse macrophages following injury.  Adoptive transfer of macrophages from collagen tagged transgenic zebrafish and splenic monocyte derived macrophages from adult mouse GFPtpz collagen donors  enhanced scar formation and induced fibrosis  respectively  via cell autonomous production of collagen.  In zebrafish  macrophage specific targeting of collagen 4a binding protein and cognate collagen 4a1 followed by transfer led to significantly reduced scarring in cryo injured hosts.  These findings contrast with the current model of scarring whereby collagen deposition is exclusively attributed to myofibroblasts  and implicate macrophages as direct contributors to fibrosis during heart repair. Overall design: Whole nuclear transcriptome profiling of macrohages in response to 2 types of heart injury ventricular resection and cryo injury at 3 different stages of regenerative process in the zebrafish heart.", null, "pubmed:32001677", null, "Mpeg 1 xxx post injury sham1", "GSM2668096", null, "source name:Mpeg 1 xxx post injury sham1|strain:TgBACmpeg1:BirA Citrine; bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "Mpeg 1 xxx post injury sham1 \u00a0", "Reads were mapped using STAR v.2.4.2a to danRer10 and read counts were obtained using subreads FeatureCounts Differential Expression analysis was performed using DESeq2 R package. Genome build: danRer10", "Mpeg 1 xxx post injury sham1 \u00a0", null, "For nuclei isolation  hearts were dissected at appropriate time points and  washed in hypotonic buffer H 20 mM HEPES pH 7.9  15 mM MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", null, "strain:TgBACmpeg1:BirA Citrine;bactin:Avi  Cerulean Rangapox133|development:Adult|xxx post injury:1 xxx post injury|tissue:macrophages|isolation method:In vivo Biotinylated Macrophage Nuclei|treatment:sham injury|strand:reverse", "GSM2668096", "GSM2668096: Mpeg 1 xxx post injury sham1 \u00a0; Danio rerio; RNA Seq", "GSM2668096", null, "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 MgCl\u00ad2  10 mM KCl  1 mM DTT  and 1 X Complete protease inhibitor and subsequently resuspended in 500 \u03bcL 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 \u00b0C 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 \u00b0C. 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\u00ae 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 \u2013 1 ng of input RNA using SMART seqTMv4 ultra low input kit for RNA Clontech laboratories  cat #\u2019s 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\u2122 500 High Output Kit\u00a0for the generation of 80 base pair paired end reads 150 cycles Illumina  cat # FC 404 1002.", "GEO Accession:GSM2668096", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP109201", null, null, "mpeg_1dpi_sham1_R1.fastq.gz mpeg_1dpi_sham1_R2.fastq.gz", "fastq fastq", 7915875034.0, 49807715.0, "GSM2668096 r1", "0:79.47 1:79.46", "A:2336098216;C:1599111229;G:1685489518;T:2293887279;N:1288792", 79, 79, null, null, 2336098216, 1599111229, 1685489518, 2293887279, 1288792, "SRX2918445", "SRS2284454", "SRA574274", "GEO", "Sauka-Spengler lab, University of Oxford, MRC Weatherall Institute of Molecular Medicine", 2, 0.86023, 0.86553, 0.15948, 0.1498, 0.84258, 0.8434, 0.46511, 0.46972, 80, 79, "B", "B", "biological fallback assumption", "illumina", "nextseq", "full_length", "random_priming", "nextera", "sc", "single_cell_plate", "smartseq", null, "United Kingdom", "2017-06-14", "Adult", "Adult", "Blood", "Hematopoietic System"], [51253, "SRR8632333", "SRX5431034", "SRS4411029", "SRP186864", "PRJNA524286", "The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation", "GSE127174", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 199 in neutrophils Overall design: for miRNA profiles  we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control", null, "pubmed:31451657", null, "miR 199 3", "GSM3629728", null, "source name:neutrophils overexpressing miR199|strain background:AB|gentoype/variation:overexpressing miR199|tissue:neutrophils", "miR 199 3", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter:  for Samples 1 5:  \u201c  alignEndsType EndToEnd   outFilterMismatchNmax 1   outFilterMultimapScoreRange 0   outFilterMultimapNmax 10   outSAMunmapped Within   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 16   alignSJDBoverhangMin 1000\u201d  for Samples 6 11: \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples;  for Samples 6 11  using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "neutrophils overexpressing miR199", "transgenic zebrafish lines were used to produce embryos. For miRNA profiling  transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery  transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grown to 3 dpf in embryonic media", "strain background:AB|gentoype/variation:overexpressing miR199|tissue:neutrophils", "GSM3629728", "GSM3629728: miR 199 3; Danio rerio; RNA Seq", "GSM3629728", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM3629728", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP186864", null, null, "199-3_S24_L003_R1_001.fastq.gz 199-3_S24_L003_R2_001.fastq.gz", "fastq fastq", 4220702408.0, 27767779.0, "GSM3629728 r1", "0:76 1:76", "A:1146580683;C:960484877;G:940832942;T:1172384006;N:419900", 76, 76, null, null, 1146580683, 960484877, 940832942, 1172384006, 419900, "SRX5431034", "SRS4411029", "SRA852308", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.89723, 0.89774, 0.11975, 0.12234, 0.7751, 0.77922, 0.44498, 0.44774, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "smartseq", null, "United States", "2019-02-26", "Larval", "Larval", "Blood", "Hematopoietic System"], [51254, "SRR8632332", "SRX5431033", "SRS4411028", "SRP186864", "PRJNA524286", "The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation", "GSE127174", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 199 in neutrophils Overall design: for miRNA profiles  we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control", null, "pubmed:31451657", null, "miR 199 2", "GSM3629727", null, "source name:neutrophils overexpressing miR199|strain background:AB|gentoype/variation:overexpressing miR199|tissue:neutrophils", "miR 199 2", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter:  for Samples 1 5:  \u201c  alignEndsType EndToEnd   outFilterMismatchNmax 1   outFilterMultimapScoreRange 0   outFilterMultimapNmax 10   outSAMunmapped Within   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 16   alignSJDBoverhangMin 1000\u201d  for Samples 6 11: \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples;  for Samples 6 11  using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "neutrophils overexpressing miR199", "transgenic zebrafish lines were used to produce embryos. For miRNA profiling  transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery  transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grown to 3 dpf in embryonic media", "strain background:AB|gentoype/variation:overexpressing miR199|tissue:neutrophils", "GSM3629727", "GSM3629727: miR 199 2; Danio rerio; RNA Seq", "GSM3629727", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM3629727", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP186864", null, null, "199-2_S23_L003_R1_001.fastq.gz 199-2_S23_L003_R2_001.fastq.gz", "fastq fastq", 3774196024.0, 24830237.0, "GSM3629727 r1", "0:76 1:76", "A:1021471524;C:862938363;G:846398406;T:1043017523;N:370208", 76, 76, null, null, 1021471524, 862938363, 846398406, 1043017523, 370208, "SRX5431033", "SRS4411028", "SRA852308", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.89642, 0.89638, 0.09057, 0.09272, 0.77512, 0.78058, 0.44281, 0.44275, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "smartseq", null, "United States", "2019-02-26", "Larval", "Larval", "Blood", "Hematopoietic System"], [51255, "SRR8632331", "SRX5431032", "SRS4411027", "SRP186864", "PRJNA524286", "The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation", "GSE127174", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 199 in neutrophils Overall design: for miRNA profiles  we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control", null, "pubmed:31451657", null, "miR 199 1", "GSM3629726", null, "source name:neutrophils overexpressing miR199|strain background:AB|gentoype/variation:overexpressing miR199|tissue:neutrophils", "miR 199 1", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter:  for Samples 1 5:  \u201c  alignEndsType EndToEnd   outFilterMismatchNmax 1   outFilterMultimapScoreRange 0   outFilterMultimapNmax 10   outSAMunmapped Within   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 16   alignSJDBoverhangMin 1000\u201d  for Samples 6 11: \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples;  for Samples 6 11  using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "neutrophils overexpressing miR199", "transgenic zebrafish lines were used to produce embryos. For miRNA profiling  transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery  transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grown to 3 dpf in embryonic media", "strain background:AB|gentoype/variation:overexpressing miR199|tissue:neutrophils", "GSM3629726", "GSM3629726: miR 199 1; Danio rerio; RNA Seq", "GSM3629726", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM3629726", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP186864", null, null, "199-1_S22_L003_R1_001.fastq.gz 199-1_S22_L003_R2_001.fastq.gz", "fastq fastq", 4421886720.0, 29091360.0, "GSM3629726 r1", "0:76 1:76", "A:1191230633;C:1016736078;G:997138231;T:1216372578;N:409200", 76, 76, null, null, 1191230633, 1016736078, 997138231, 1216372578, 409200, "SRX5431032", "SRS4411027", "SRA852308", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.89934, 0.89871, 0.09142, 0.09283, 0.77534, 0.77908, 0.43477, 0.43856, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "smartseq", null, "United States", "2019-02-26", "Larval", "Larval", "Blood", "Hematopoietic System"], [51256, "SRR8632330", "SRX5431031", "SRS4411026", "SRP186864", "PRJNA524286", "The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation", "GSE127174", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 199 in neutrophils Overall design: for miRNA profiles  we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control", null, "pubmed:31451657", null, "vector  3", "GSM3629725", null, "source name:neutrophils vector|strain background:AB|gentoype/variation:overexpressing vector|tissue:neutrophils", "vector  3", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter:  for Samples 1 5:  \u201c  alignEndsType EndToEnd   outFilterMismatchNmax 1   outFilterMultimapScoreRange 0   outFilterMultimapNmax 10   outSAMunmapped Within   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 16   alignSJDBoverhangMin 1000\u201d  for Samples 6 11: \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples;  for Samples 6 11  using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "neutrophils vector", "transgenic zebrafish lines were used to produce embryos. For miRNA profiling  transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery  transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grown to 3 dpf in embryonic media", "strain background:AB|gentoype/variation:overexpressing vector|tissue:neutrophils", "GSM3629725", "GSM3629725: vector  3; Danio rerio; RNA Seq", "GSM3629725", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM3629725", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP186864", null, null, null, null, 4424857712.0, 29110906.0, "GSM3629725 r1", "0:76 1:76", "A:1191316852;C:1019584233;G:996921889;T:1216588857;N:445881", 76, 76, null, null, 1191316852, 1019584233, 996921889, 1216588857, 445881, "SRX5431031", "SRS4411026", "SRA852308", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.88192, 0.88119, 0.09054, 0.09305, 0.78748, 0.79293, 0.43612, 0.44321, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "smartseq", null, "United States", "2019-02-26", "Larval", "Larval", "Blood", "Hematopoietic System"], [51257, "SRR8632328", "SRX5431029", "SRS4411024", "SRP186864", "PRJNA524286", "The miR 199 CDK2 axis modulates neutrophil migration and systemic inflammation", "GSE127174", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 199 in neutrophils Overall design: for miRNA profiles  we compared the miRNA present in zebrafish neutrophils and keratinocytes to the whole embryo. for miR 199 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR199 or vector control", null, "pubmed:31451657", null, "vector  1", "GSM3629723", null, "source name:neutrophils vector|strain background:AB|gentoype/variation:overexpressing vector|tissue:neutrophils", "vector  1", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000 for Samples 6 11. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter:  for Samples 1 5:  \u201c  alignEndsType EndToEnd   outFilterMismatchNmax 1   outFilterMultimapScoreRange 0   outFilterMultimapNmax 10   outSAMunmapped Within   outFilterScoreMinOverLread 0   outFilterMatchNminOverLread 0   outFilterMatchNmin 16   alignSJDBoverhangMin 1000\u201d  for Samples 6 11: \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered: for Samples 1 5 using read count > 10 in more than 1 of the samples;  for Samples 6 11  using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "neutrophils vector", "transgenic zebrafish lines were used to produce embryos. For miRNA profiling  transgenic lines expressing GFP in either neutrophils or apical keratincyes were used. For miR 199 target discovery  transgenic lines expressing miR 199 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grown to 3 dpf in embryonic media", "strain background:AB|gentoype/variation:overexpressing vector|tissue:neutrophils", "GSM3629723", "GSM3629723: vector  1; Danio rerio; RNA Seq", "GSM3629723", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM3629723", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP186864", null, null, null, null, 5150699360.0, 33886180.0, "GSM3629723 r1", "0:76 1:76", "A:1387770699;C:1183384663;G:1159850071;T:1419171313;N:522614", 76, 76, null, null, 1387770699, 1183384663, 1159850071, 1419171313, 522614, "SRX5431029", "SRS4411024", "SRA852308", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.88412, 0.88386, 0.09124, 0.09316, 0.78405, 0.78817, 0.44964, 0.44745, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "smartseq", null, "United States", "2019-02-26", "Larval", "Larval", "Blood", "Hematopoietic System"], [56668, "SRR13842886", "SRX10221255", "SRS8374674", "SRP247522", "PRJNA605187", "miR 99 overexpression modulates neutrophil migration", "GSE144873", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 99 in neutrophils Overall design: For miR 99 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR1 99 or vector control **Please note that the duplicated vector* sample records of GSE127174 samples have been created as the samples have been re used in the current study and for the convenient retrieval of the complete raw data from SRA.", null, null, null, "Vector  2", "GSM5129846", null, "tissue:neutrophils|cell type:neutrophils|genotype/variation:overexpressing vector", "Vector  2", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: \u201c p \u2013Q 10\u201d The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "neutrophils", "transgenic zebrafish lines were used to produce embryos. For miR 99 target discovery  transgenic lines expressing miR 99 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grow to 3 dpf in embryonic media", "cell type:neutrophils|genotype/variation:overexpressing vector", "GSM5129846", "GSM5129846: Vector  2; Danio rerio; RNA Seq", "GSM5129846", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM5129846", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP247522", null, null, "V-2_S14_L003_R1_001.fastq.gz V-2_S14_L003_R2_001.fastq.gz", "fastq fastq", 3757553544.0, 24720747.0, "GSM5129846 r1", "0:76 1:76", "A:1012476170;C:864162299;G:843777361;T:1036759305;N:378409", 76, 76, null, null, 1012476170, 864162299, 843777361, 1036759305, 378409, "SRX10221255", "SRS8374674", "SRA1039054", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.90022, 0.90123, 0.10428, 0.10723, 0.79498, 0.79882, 0.43947, 0.42403, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-03-03", "Larval", "Larval", "Blood", "Hematopoietic System"], [56669, "SRR11035191", "SRX7687418", "SRS6113888", "SRP247522", "PRJNA605187", "miR 99 overexpression modulates neutrophil migration", "GSE144873", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 99 in neutrophils Overall design: For miR 99 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR1 99 or vector control **Please note that the duplicated vector* sample records of GSE127174 samples have been created as the samples have been re used in the current study and for the convenient retrieval of the complete raw data from SRA.", null, null, null, "vector  3 [re used]", "GSM4299825", null, "tissue:vector neutrophils|genotype/variation:overexpressing vector|cell type:neutrophils", "vector  3 [re used]", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "vector neutrophils", "transgenic zebrafish lines were used to produce embryos. For miR 99 target discovery  transgenic lines expressing miR 99 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grow to 3 dpf in embryonic media", "genotype/variation:overexpressing vector|cell type:neutrophils", "GSM4299825", "GSM4299825: vector  3 [re used]; Danio rerio; RNA Seq", "GSM4299825", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM4299825", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP247522", null, null, "V-3_S15_L003_R1_001.fastq V-3_S15_L003_R2_001.fastq", "fastq fastq", 4424857712.0, 29110906.0, "GSM4299825 r1", "0:76 1:76", "A:1191316852;C:1019584233;G:996921889;T:1216588857;N:445881", 76, 76, null, null, 1191316852, 1019584233, 996921889, 1216588857, 445881, "SRX7687418", "SRS6113888", "SRA1039054", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.88198, 0.88112, 0.09061, 0.09281, 0.78778, 0.79251, 0.43625, 0.44314, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-02-06", "Larval", "Larval", "Blood", "Hematopoietic System"], [56670, "SRR11035190", "SRX7687417", "SRS6113887", "SRP247522", "PRJNA605187", "miR 99 overexpression modulates neutrophil migration", "GSE144873", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 99 in neutrophils Overall design: For miR 99 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR1 99 or vector control **Please note that the duplicated vector* sample records of GSE127174 samples have been created as the samples have been re used in the current study and for the convenient retrieval of the complete raw data from SRA.", null, null, null, "vector  1 [re used]", "GSM4299824", null, "tissue:vector neutrophils|genotype/variation:overexpressing vector|cell type:neutrophils", "vector  1 [re used]", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "vector neutrophils", "transgenic zebrafish lines were used to produce embryos. For miR 99 target discovery  transgenic lines expressing miR 99 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grow to 3 dpf in embryonic media", "genotype/variation:overexpressing vector|cell type:neutrophils", "GSM4299824", "GSM4299824: vector  1 [re used]; Danio rerio; RNA Seq", "GSM4299824", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM4299824", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP247522", null, null, "V-1_S13_L003_R2_001.fastq V-1_S13_L003_R1_001.fastq", "fastq fastq", 5150699360.0, 33886180.0, "GSM4299824 r1", "0:76 1:76", "A:1387770699;C:1183384663;G:1159850071;T:1419171313;N:522614", 76, 76, null, null, 1387770699, 1183384663, 1159850071, 1419171313, 522614, "SRX7687417", "SRS6113887", "SRA1039054", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.88408, 0.88384, 0.09123, 0.09313, 0.78374, 0.78837, 0.45017, 0.44717, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-02-06", "Larval", "Larval", "Blood", "Hematopoietic System"], [56671, "SRR11035189", "SRX7687416", "SRS6113886", "SRP247522", "PRJNA605187", "miR 99 overexpression modulates neutrophil migration", "GSE144873", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 99 in neutrophils Overall design: For miR 99 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR1 99 or vector control **Please note that the duplicated vector* sample records of GSE127174 samples have been created as the samples have been re used in the current study and for the convenient retrieval of the complete raw data from SRA.", null, null, null, "miR 99 3", "GSM4299823", null, "tissue:miR 99 neutrophils|genotype/variation:overexpressing miR 99|cell type:neutrophils", "miR 99 3", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "miR 99 neutrophils", "transgenic zebrafish lines were used to produce embryos. For miR 99 target discovery  transgenic lines expressing miR 99 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grow to 3 dpf in embryonic media", "genotype/variation:overexpressing miR 99|cell type:neutrophils", "GSM4299823", "GSM4299823: miR 99 3; Danio rerio; RNA Seq", "GSM4299823", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM4299823", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP247522", null, null, "99-3_S21_L003_R2_001.fastq.gz 99-3_S21_L003_R1_001.fastq.gz", "fastq fastq", 4537032344.0, 29848897.0, "GSM4299823 r1", "0:76 1:76", "A:1221509254;C:1042930118;G:1023047713;T:1249089866;N:455393", 76, 76, null, null, 1221509254, 1042930118, 1023047713, 1249089866, 455393, "SRX7687416", "SRS6113886", "SRA1039054", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.90318, 0.90222, 0.09091, 0.09217, 0.79411, 0.79793, 0.41754, 0.42183, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-02-06", "Larval", "Larval", "Blood", "Hematopoietic System"], [56672, "SRR11035188", "SRX7687415", "SRS6113885", "SRP247522", "PRJNA605187", "miR 99 overexpression modulates neutrophil migration", "GSE144873", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 99 in neutrophils Overall design: For miR 99 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR1 99 or vector control **Please note that the duplicated vector* sample records of GSE127174 samples have been created as the samples have been re used in the current study and for the convenient retrieval of the complete raw data from SRA.", null, null, null, "miR 99 2", "GSM4299822", null, "tissue:miR 99 neutrophils|genotype/variation:overexpressing miR 99|cell type:neutrophils", "miR 99 2", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "miR 99 neutrophils", "transgenic zebrafish lines were used to produce embryos. For miR 99 target discovery  transgenic lines expressing miR 99 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grow to 3 dpf in embryonic media", "genotype/variation:overexpressing miR 99|cell type:neutrophils", "GSM4299822", "GSM4299822: miR 99 2; Danio rerio; RNA Seq", "GSM4299822", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM4299822", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP247522", null, null, "99-2_S20_L003_R2_001.fastq.gz 99-2_S20_L003_R1_001.fastq.gz", "fastq fastq", 3758474512.0, 24726806.0, "GSM4299822 r1", "0:76 1:76", "A:1012736859;C:862863675;G:847135976;T:1035362742;N:375260", 76, 76, null, null, 1012736859, 862863675, 847135976, 1035362742, 375260, "SRX7687415", "SRS6113885", "SRA1039054", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.90422, 0.90394, 0.09824, 0.10019, 0.79295, 0.79644, 0.41246, 0.42006, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-02-06", "Larval", "Larval", "Blood", "Hematopoietic System"], [56673, "SRR11035187", "SRX7687414", "SRS6113884", "SRP247522", "PRJNA605187", "miR 99 overexpression modulates neutrophil migration", "GSE144873", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 99 in neutrophils Overall design: For miR 99 target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR1 99 or vector control **Please note that the duplicated vector* sample records of GSE127174 samples have been created as the samples have been re used in the current study and for the convenient retrieval of the complete raw data from SRA.", null, null, null, "miR 99 1", "GSM4299821", null, "tissue:miR 99 neutrophils|genotype/variation:overexpressing miR 99|cell type:neutrophils", "miR 99 1", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina HiSeq 2500 for Samples 1 5 in Illumina HiSeq 4000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "miR 99 neutrophils", "transgenic zebrafish lines were used to produce embryos. For miR 99 target discovery  transgenic lines expressing miR 99 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grow to 3 dpf in embryonic media", "genotype/variation:overexpressing miR 99|cell type:neutrophils", "GSM4299821", "GSM4299821: miR 99 1; Danio rerio; RNA Seq", "GSM4299821", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM4299821", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP247522", null, null, "99-1_S19_L003_R1_001.fastq.gz 99-1_S19_L003_R2_001.fastq.gz", "fastq fastq", 4160704056.0, 27373053.0, "GSM4299821 r1", "0:76 1:76", "A:1121170591;C:955488866;G:936977987;T:1146641997;N:424615", 76, 76, null, null, 1121170591, 955488866, 936977987, 1146641997, 424615, "SRX7687414", "SRS6113884", "SRA1039054", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.9007, 0.89892, 0.10574, 0.10747, 0.79312, 0.79768, 0.42626, 0.42782, 76, 76, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2020-02-06", "Larval", "Larval", "Blood", "Hematopoietic System"], [63408, "SRR13785103", "SRX10170285", "SRS8320380", "SRP308232", "PRJNA704949", "miRNA overexpression modulates neutrophil migration", "GSE167554", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 31  miRNA 190 and miRNA 375  in neutrophils Overall design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR 31  190  375 or vector control", null, null, null, "miR 375 2", "GSM5107441", null, "tissue:neutrophils|transgenic line:miR 375", "miR 375 2", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina NovaSeq 6000 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: \u201c s 0  p \u2013Q 10\u201d The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "neutrophils", "transgenic zebrafish lines were used to produce embryos. For miRNA target discovery  transgenic lines expressing miR 31  190  375 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grow to 3 dpf in embryonic media", "transgenic line:miR 375", "GSM5107441", "GSM5107441: miR 375 2; Danio rerio; RNA Seq", "GSM5107441", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM5107441", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP308232", null, null, "11_S27_R1_001.fastq.gz 11_S27_R2_001.fastq.gz", "fastq fastq", 6029914928.0, 29851064.0, "GSM5107441 r1", "0:101 1:101", "A:1615847350;C:1389005627;G:1392538803;T:1632327057;N:196091", 101, 101, null, null, 1615847350, 1389005627, 1392538803, 1632327057, 196091, "SRX10170285", "SRS8320380", "SRA1200205", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.70139, 0.70178, 0.12251, 0.1232, 0.84997, 0.84956, 0.64095, 0.63987, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-02-25", "Larval", "Larval", "Blood", "Hematopoietic System"], [63409, "SRR13785102", "SRX10170284", "SRS8320379", "SRP308232", "PRJNA704949", "miRNA overexpression modulates neutrophil migration", "GSE167554", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 31  miRNA 190 and miRNA 375  in neutrophils Overall design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR 31  190  375 or vector control", null, null, null, "miR 375 1", "GSM5107440", null, "tissue:neutrophils|transgenic line:miR 375", "miR 375 1", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina NovaSeq 6000 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: \u201c s 0  p \u2013Q 10\u201d The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "neutrophils", "transgenic zebrafish lines were used to produce embryos. For miRNA target discovery  transgenic lines expressing miR 31  190  375 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grow to 3 dpf in embryonic media", "transgenic line:miR 375", "GSM5107440", "GSM5107440: miR 375 1; Danio rerio; RNA Seq", "GSM5107440", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM5107440", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP308232", null, null, "10_S26_R1_001.fastq.gz 10_S26_R2_001.fastq.gz", "fastq fastq", 4592486968.0, 22735084.0, "GSM5107440 r1", "0:101 1:101", "A:1227339030;C:1060646304;G:1065493203;T:1238859749;N:148682", 101, 101, null, null, 1227339030, 1060646304, 1065493203, 1238859749, 148682, "SRX10170284", "SRS8320379", "SRA1200205", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.60112, 0.60106, 0.11798, 0.11738, 0.85202, 0.85352, 0.63903, 0.63997, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-02-25", "Larval", "Larval", "Blood", "Hematopoietic System"], [63410, "SRR13785101", "SRX10170283", "SRS8320378", "SRP308232", "PRJNA704949", "miRNA overexpression modulates neutrophil migration", "GSE167554", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 31  miRNA 190 and miRNA 375  in neutrophils Overall design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR 31  190  375 or vector control", null, null, null, "miR 190 2", "GSM5107439", null, "tissue:neutrophils|transgenic line:miR 190", "miR 190 2", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina NovaSeq 6000 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: \u201c s 0  p \u2013Q 10\u201d The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "neutrophils", "transgenic zebrafish lines were used to produce embryos. For miRNA target discovery  transgenic lines expressing miR 31  190  375 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grow to 3 dpf in embryonic media", "transgenic line:miR 190", "GSM5107439", "GSM5107439: miR 190 2; Danio rerio; RNA Seq", "GSM5107439", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM5107439", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP308232", null, null, "8_S24_R1_001.fastq.gz 8_S24_R2_001.fastq.gz", "fastq fastq", 8568406306.0, 42417853.0, "GSM5107439 r1", "0:101 1:101", "A:2236090427;C:2041198943;G:2027464666;T:2263375416;N:276854", 101, 101, null, null, 2236090427, 2041198943, 2027464666, 2263375416, 276854, "SRX10170283", "SRS8320378", "SRA1200205", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.60667, 0.60632, 0.10166, 0.1014, 0.84141, 0.84001, 0.59118, 0.58516, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-02-25", "Larval", "Larval", "Blood", "Hematopoietic System"], [63411, "SRR13785100", "SRX10170282", "SRS8320377", "SRP308232", "PRJNA704949", "miRNA overexpression modulates neutrophil migration", "GSE167554", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 31  miRNA 190 and miRNA 375  in neutrophils Overall design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR 31  190  375 or vector control", null, null, null, "miR 190 1", "GSM5107438", null, "tissue:neutrophils|transgenic line:miR 190", "miR 190 1", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina NovaSeq 6000 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: \u201c s 0  p \u2013Q 10\u201d The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "neutrophils", "transgenic zebrafish lines were used to produce embryos. For miRNA target discovery  transgenic lines expressing miR 31  190  375 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grow to 3 dpf in embryonic media", "transgenic line:miR 190", "GSM5107438", "GSM5107438: miR 190 1; Danio rerio; RNA Seq", "GSM5107438", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM5107438", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP308232", null, null, "7_S23_R1_001.fastq.gz 7_S23_R2_001.fastq.gz", "fastq fastq", 7761570230.0, 38423615.0, "GSM5107438 r1", "0:101 1:101", "A:2071933936;C:1799567237;G:1808478605;T:2081344958;N:245494", 101, 101, null, null, 2071933936, 1799567237, 1808478605, 2081344958, 245494, "SRX10170282", "SRS8320377", "SRA1200205", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.70893, 0.70785, 0.10171, 0.10088, 0.81749, 0.81649, 0.47376, 0.47584, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-02-25", "Larval", "Larval", "Blood", "Hematopoietic System"], [63412, "SRR13785099", "SRX10170281", "SRS8320376", "SRP308232", "PRJNA704949", "miRNA overexpression modulates neutrophil migration", "GSE167554", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 31  miRNA 190 and miRNA 375  in neutrophils Overall design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR 31  190  375 or vector control", null, null, null, "miR 31 3", "GSM5107437", null, "tissue:neutrophils|transgenic line:miR 31", "miR 31 3", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina NovaSeq 6000 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: \u201c s 0  p \u2013Q 10\u201d The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "neutrophils", "transgenic zebrafish lines were used to produce embryos. For miRNA target discovery  transgenic lines expressing miR 31  190  375 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grow to 3 dpf in embryonic media", "transgenic line:miR 31", "GSM5107437", "GSM5107437: miR 31 3; Danio rerio; RNA Seq", "GSM5107437", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM5107437", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP308232", null, null, "6_S22_R1_001.fastq.gz 6_S22_R2_001.fastq.gz", "fastq fastq", 8612291816.0, 42635108.0, "GSM5107437 r1", "0:101 1:101", "A:2355744610;C:1928543523;G:1934674106;T:2393044749;N:284828", 101, 101, null, null, 2355744610, 1928543523, 1934674106, 2393044749, 284828, "SRX10170281", "SRS8320376", "SRA1200205", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.74244, 0.74121, 0.12601, 0.12659, 0.82572, 0.8268, 0.54597, 0.54943, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-02-25", "Larval", "Larval", "Blood", "Hematopoietic System"], [63413, "SRR13785098", "SRX10170280", "SRS8320375", "SRP308232", "PRJNA704949", "miRNA overexpression modulates neutrophil migration", "GSE167554", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 31  miRNA 190 and miRNA 375  in neutrophils Overall design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR 31  190  375 or vector control", null, null, null, "miR 31 1", "GSM5107436", null, "tissue:neutrophils|transgenic line:miR 31", "miR 31 1", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina NovaSeq 6000 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: \u201c s 0  p \u2013Q 10\u201d The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "neutrophils", "transgenic zebrafish lines were used to produce embryos. For miRNA target discovery  transgenic lines expressing miR 31  190  375 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grow to 3 dpf in embryonic media", "transgenic line:miR 31", "GSM5107436", "GSM5107436: miR 31 1; Danio rerio; RNA Seq", "GSM5107436", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM5107436", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP308232", null, null, "4_S20_R1_001.fastq.gz 4_S20_R2_001.fastq.gz", "fastq fastq", 7552914936.0, 37390668.0, "GSM5107436 r1", "0:101 1:101", "A:2067021378;C:1693130222;G:1700053633;T:2092462203;N:247500", 101, 101, null, null, 2067021378, 1693130222, 1700053633, 2092462203, 247500, "SRX10170280", "SRS8320375", "SRA1200205", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.77601, 0.77589, 0.12034, 0.1199, 0.80975, 0.81097, 0.51737, 0.51695, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-02-25", "Larval", "Larval", "Blood", "Hematopoietic System"], [63414, "SRR13785097", "SRX10170279", "SRS8320374", "SRP308232", "PRJNA704949", "miRNA overexpression modulates neutrophil migration", "GSE167554", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 31  miRNA 190 and miRNA 375  in neutrophils Overall design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR 31  190  375 or vector control", null, null, null, "vector 3", "GSM5107435", null, "tissue:neutrophils|transgenic line:vector", "vector 3", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina NovaSeq 6000 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: \u201c s 0  p \u2013Q 10\u201d The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "neutrophils", "transgenic zebrafish lines were used to produce embryos. For miRNA target discovery  transgenic lines expressing miR 31  190  375 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grow to 3 dpf in embryonic media", "transgenic line:vector", "GSM5107435", "GSM5107435: vector 3; Danio rerio; RNA Seq", "GSM5107435", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM5107435", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP308232", null, null, "3_S19_R1_001.fastq.gz 3_S19_R2_001.fastq.gz", "fastq fastq", 7965811218.0, 39434709.0, "GSM5107435 r1", "0:101 1:101", "A:2094197021;C:1873715430;G:1876832073;T:2120806043;N:260651", 101, 101, null, null, 2094197021, 1873715430, 1876832073, 2120806043, 260651, "SRX10170279", "SRS8320374", "SRA1200205", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.54804, 0.5496, 0.08633, 0.08617, 0.83465, 0.83473, 0.56095, 0.56097, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-02-25", "Larval", "Larval", "Blood", "Hematopoietic System"], [63415, "SRR13785096", "SRX10170278", "SRS8320373", "SRP308232", "PRJNA704949", "miRNA overexpression modulates neutrophil migration", "GSE167554", "Transcriptome Analysis", "We performed RNAseq to identify miRNAs that were specifically down regulated in neutrophils  and RNAseq for identification of mRNA targets of  miRNA 31  miRNA 190 and miRNA 375  in neutrophils Overall design: For miRNA target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing miR 31  190  375 or vector control", null, null, null, "vector 2", "GSM5107434", null, "tissue:neutrophils|transgenic line:vector", "vector 2", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina NovaSeq 6000 The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: \u201c s 0  p \u2013Q 10\u201d The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts", "neutrophils", "transgenic zebrafish lines were used to produce embryos. For miRNA target discovery  transgenic lines expressing miR 31  190  375 or a vector control together with a GFP reporter were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish embryos were grow to 3 dpf in embryonic media", "transgenic line:vector", "GSM5107434", "GSM5107434: vector 2; Danio rerio; RNA Seq", "GSM5107434", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from 3dpf zebrafish embryos using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM5107434", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP308232", null, null, "2_S18_R1_001.fastq.gz 2_S18_R2_001.fastq.gz", "fastq fastq", 7624486566.0, 37744983.0, "GSM5107434 r1", "0:101 1:101", "A:2037049856;C:1759511498;G:1765364446;T:2062311110;N:249656", 101, 101, null, null, 2037049856, 1759511498, 1765364446, 2062311110, 249656, "SRX10170278", "SRS8320373", "SRA1200205", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.63672, 0.63646, 0.11973, 0.12018, 0.83339, 0.83414, 0.45361, 0.55503, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-02-25", "Larval", "Larval", "Blood", "Hematopoietic System"], [63869, "SRR14144778", "SRX10514122", "SRS8637874", "SRP313536", "PRJNA719817", "RORa is required for neutrophil migration", "GSE171501", "Transcriptome Analysis", "We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control", null, null, null, "RORaDN 3", "GSM5226363", null, "tissue:neutrophils|cell type:neutrophils|genotype:RORa dominant negative", "RORaDN 3", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis", "neutrophils", "Transgenic lines expressing RORa dominant negative or mcherry were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish were grow in circulating system", "cell type:neutrophils|genotype:RORa dominant negative", "GSM5226363", "GSM5226363: RORaDN 3; Danio rerio; RNA Seq", "GSM5226363", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM5226363", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP313536", null, "loader:fastq load.py", "roraDN-3_S24_R1_001.fastq.gz roraDN-3_S24_R2_001.fastq.gz", "fastq fastq", 9541970758.0, 47237479.0, "GSM5226363 r1", "0:101 1:101", "A:2556115286;C:2215951997;G:2229754627;T:2539986639;N:162209", 101, 101, null, null, 2556115286, 2215951997, 2229754627, 2539986639, 162209, "SRX10514122", "SRS8637874", "SRA1215296", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.94352, 0.93947, 0.09023, 0.08984, 0.79224, 0.79523, 0.45486, 0.45588, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-04-05", "Adult", "Adult", "Blood", "Hematopoietic System"], [63870, "SRR14144777", "SRX10514121", "SRS8637873", "SRP313536", "PRJNA719817", "RORa is required for neutrophil migration", "GSE171501", "Transcriptome Analysis", "We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control", null, null, null, "RORaDN 2", "GSM5226362", null, "tissue:neutrophils|cell type:neutrophils|genotype:RORa dominant negative", "RORaDN 2", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis", "neutrophils", "Transgenic lines expressing RORa dominant negative or mcherry were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish were grow in circulating system", "cell type:neutrophils|genotype:RORa dominant negative", "GSM5226362", "GSM5226362: RORaDN 2; Danio rerio; RNA Seq", "GSM5226362", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM5226362", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP313536", null, "loader:fastq load.py", "roraDN-2_S23_R1_001.fastq.gz roraDN-2_S23_R2_001.fastq.gz", "fastq fastq", 7807589466.0, 38651433.0, "GSM5226362 r1", "0:101 1:101", "A:2096919144;C:1807670571;G:1821028016;T:2081836449;N:135286", 101, 101, null, null, 2096919144, 1807670571, 1821028016, 2081836449, 135286, "SRX10514121", "SRS8637873", "SRA1215296", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.94042, 0.93784, 0.09122, 0.09133, 0.80192, 0.80405, 0.44224, 0.446, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-04-05", "Adult", "Adult", "Blood", "Hematopoietic System"], [63871, "SRR14144776", "SRX10514120", "SRS8637872", "SRP313536", "PRJNA719817", "RORa is required for neutrophil migration", "GSE171501", "Transcriptome Analysis", "We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control", null, null, null, "RORaDN 1", "GSM5226361", null, "tissue:neutrophils|cell type:neutrophils|genotype:RORa dominant negative", "RORaDN 1", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis", "neutrophils", "Transgenic lines expressing RORa dominant negative or mcherry were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish were grow in circulating system", "cell type:neutrophils|genotype:RORa dominant negative", "GSM5226361", "GSM5226361: RORaDN 1; Danio rerio; RNA Seq", "GSM5226361", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM5226361", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP313536", null, "loader:fastq load.py", "roraDN-1_S22_R1_001.fastq.gz roraDN-1_S22_R2_001.fastq.gz", "fastq fastq", 10197330670.0, 50481835.0, "GSM5226361 r1", "0:101 1:101", "A:2788946417;C:2302836921;G:2316790438;T:2788574338;N:182556", 101, 101, null, null, 2788946417, 2302836921, 2316790438, 2788574338, 182556, "SRX10514120", "SRS8637872", "SRA1215296", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.92564, 0.92366, 0.09078, 0.09026, 0.81381, 0.81542, 0.50301, 0.49369, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-04-05", "Adult", "Adult", "Blood", "Hematopoietic System"], [63872, "SRR14144775", "SRX10514119", "SRS8637871", "SRP313536", "PRJNA719817", "RORa is required for neutrophil migration", "GSE171501", "Transcriptome Analysis", "We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control", null, null, null, "mCherry 3", "GSM5226360", null, "tissue:neutrophils|cell type:neutrophils|genotype:control", "mCherry 3", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis", "neutrophils", "Transgenic lines expressing RORa dominant negative or mcherry were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish were grow in circulating system", "cell type:neutrophils|genotype:control", "GSM5226360", "GSM5226360: mCherry 3; Danio rerio; RNA Seq", "GSM5226360", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM5226360", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP313536", null, "loader:fastq load.py", "ctrl_mcherry-3_S21_R1_001.fastq.gz ctrl_mcherry-3_S21_R2_001.fastq.gz", "fastq fastq", 8880772036.0, 43964218.0, "GSM5226360 r1", "0:101 1:101", "A:2381825109;C:2057122621;G:2068743076;T:2372921245;N:159985", 101, 101, null, null, 2381825109, 2057122621, 2068743076, 2372921245, 159985, "SRX10514119", "SRS8637871", "SRA1215296", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.93299, 0.93061, 0.09615, 0.09601, 0.80004, 0.8017, 0.43695, 0.43475, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-04-05", "Adult", "Adult", "Blood", "Hematopoietic System"], [63873, "SRR14144774", "SRX10514118", "SRS8637870", "SRP313536", "PRJNA719817", "RORa is required for neutrophil migration", "GSE171501", "Transcriptome Analysis", "We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control", null, null, null, "mCherry 2", "GSM5226359", null, "tissue:neutrophils|cell type:neutrophils|genotype:control", "mCherry 2", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis", "neutrophils", "Transgenic lines expressing RORa dominant negative or mcherry were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish were grow in circulating system", "cell type:neutrophils|genotype:control", "GSM5226359", "GSM5226359: mCherry 2; Danio rerio; RNA Seq", "GSM5226359", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM5226359", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP313536", null, "loader:fastq load.py", "ctrl_mcherry-2_S20_R1_001.fastq.gz ctrl_mcherry-2_S20_R2_001.fastq.gz", "fastq fastq", 9245210942.0, 45768371.0, "GSM5226359 r1", "0:101 1:101", "A:2490401320;C:2130041068;G:2145686856;T:2478916438;N:165260", 101, 101, null, null, 2490401320, 2130041068, 2145686856, 2478916438, 165260, "SRX10514118", "SRS8637870", "SRA1215296", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.93171, 0.92876, 0.08782, 0.08787, 0.79699, 0.79886, 0.44448, 0.44757, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-04-05", "Adult", "Adult", "Blood", "Hematopoietic System"], [63874, "SRR14144773", "SRX10514117", "SRS8637869", "SRP313536", "PRJNA719817", "RORa is required for neutrophil migration", "GSE171501", "Transcriptome Analysis", "We performed RNAseq to identify mRNAs that were specifically down regulated in neutrophils when RORa function is inhibited Overall design: For RORa target identification we sequenced messenger RNAs in zebrafish neutrophils over expressing a dominant RORa or mcherry control", null, null, null, "mCherry 1", "GSM5226358", null, "tissue:neutrophils|cell type:neutrophils|genotype:control", "mCherry 1", "Base calling and quality scoreing were performed by Real Time Analysis RTA v2 in Illumina Novaseq 6000. The bcl2fastq2 Conversion software were used to convert base call bcl files to FASTQ files  and trim adapter sequence at the same time. The reads were mapped to the zebrafish genome using STAR v2.5 RNA seq aligner with the following parameter \u201c  outSAMmapqUnique 60\u201d. Uniquely mapped sequencing reads were assigned to genes using featureCounts from subread v1.5.1 with the following parameters: for Samples 1 5:  \u201c s 1 \u2013Q 10\u201d  for Samples 6 11  \" p  Q 10\". The data was filtered using read count per million CPM > 0.5 in more than 3 of the samples  normalized using TMM trimmed mean of M values method and subjected to differential expression analysis using edgeR v3.20.8. Genome build: GRCz11 Supplementary files format and content: Raw counts and differential analysis", "neutrophils", "Transgenic lines expressing RORa dominant negative or mcherry were used.", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "zebrafish were grow in circulating system", "cell type:neutrophils|genotype:control", "GSM5226358", "GSM5226358: mCherry 1; Danio rerio; RNA Seq", "GSM5226358", null, "1", "tissue specific isolation: cells were labeled with fluorescent reporters and isolated from adult zebrafish whole kidney marrow using FACS. mRNA was extracted using Qiagen RNeasy Mini Kit  and total RNA was extracted using Invirtogen mirVANA kit for miRNA sequencing. miRNA sequencing library were constructed using Illumina TruSeq Small RNA Preparation and 145 160bp band are excised for sequencing.  mRNA sequencing library were constructed withSMART Seq v4 Ultra Low Input RNA Kit for Sequencing Takara Clontech Laboratories  Inc..", "GEO Accession:GSM5226358", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP313536", null, "loader:fastq load.py", "ctrl_mcherry-1_S19_R1_001.fastq.gz ctrl_mcherry-1_S19_R2_001.fastq.gz", "fastq fastq", 8133040958.0, 40262579.0, "GSM5226358 r1", "0:101 1:101", "A:2181019795;C:1885103754;G:1889273889;T:2177502095;N:141425", 101, 101, null, null, 2181019795, 1885103754, 1889273889, 2177502095, 141425, "SRX10514117", "SRS8637869", "SRA1215296", "GEO", "Department of Biological Sciences, Purdue University", 2, 0.9318, 0.93011, 0.09874, 0.09885, 0.79239, 0.79488, 0.42603, 0.44023, 101, 101, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "small_rna", "trueseq", "sc", "single_cell_plate", "smartseq", null, "United States", "2021-04-05", "Adult", "Adult", "Blood", "Hematopoietic System"], [68662, "SRR18124522", "SRX14274937", "SRS12093628", "SRP361285", "PRJNA809951", "A lysosomal regulatory circuit essential for the development and function of microglia", "GSE197349", "Transcriptome Analysis", "We performed Illumina NovaSeq on macrophages isolated from zebrafish Overall design: Cells of the macrophage lineage tagged with mpeg:GFP were isolated from rraga mutants and their wildtype siblings by FACS  RNA was extracted  and sequencing was performed.", "parent bioproject:PRJNA809950", "pubmed:36044568", null, "rraga wildtype sibling macrophage sample biological replicate 4", "GSM5914979", null, "tissue:Macrophages|genotype:rraga wild type|strain:TL|developmental stage:6 dpf type:Macrophages", "rraga wildtype sibling macrophage sample biological replicate 4", "Raw data of FASTQ format were processed through Novogene in house PERL scripts Clean reads were obtained by removing reads containing adapter  reads containing poly N and low quality reads from raw data Q20  Q30  and GC content of all clean data were calculated Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome. Mapped reads of each sample were assembled by StringTie v1.3.3b featureCount v1.5.0 was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2R package 1.20.0 Genome build: GRCz11 Supplementary files format and content: text file contains gene counts  normalized FPKM reads for genes identified by gene name and ENSEMBL ID", "Macrophages", "Embryos were scored as mutant or wildtype using a confocal microscope at 4 dpf and 5 dpf Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS.", "RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit", "Zebrafish embryos were raised at 28.5 \u00baC in embryo water with methylene blue and PTU", "genotype:rraga wild type|strain:TL|developmental stage:6 dpf type:Macrophages", "GSM5914979", "GSM5914979: rraga wildtype sibling macrophage sample biological replicate 4; Danio rerio; RNA Seq", "GSM5914979 r1", "GSM5914979", "1", "RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP361285", null, "loader:fastq load.py", "WT5_S62_1.fq.gz WT5_S62_2.fq.gz", "fastq fastq", 14242695000.0, 47475650.0, "GSM5914979 r1", "0:150 1:150", "A:3803830606;C:3323851570;G:3342727186;T:3772146235;N:139403", 150, 150, null, null, 3803830606, 3323851570, 3342727186, 3772146235, 139403, "SRX14274937", "SRS12093628", "SRA1377812", "Talbot, Developmental Biology, Stanford University", "Talbot, Developmental Biology, Stanford University", 2, 0.94344, 0.94256, 0.06598, 0.06609, 0.74732, 0.74933, 0.48975, 0.48907, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-02-24", "Larval", "Larval", "Blood", "Hematopoietic System"], [68663, "SRR18124523", "SRX14274936", "SRS12093627", "SRP361285", "PRJNA809951", "A lysosomal regulatory circuit essential for the development and function of microglia", "GSE197349", "Transcriptome Analysis", "We performed Illumina NovaSeq on macrophages isolated from zebrafish Overall design: Cells of the macrophage lineage tagged with mpeg:GFP were isolated from rraga mutants and their wildtype siblings by FACS  RNA was extracted  and sequencing was performed.", "parent bioproject:PRJNA809950", "pubmed:36044568", null, "rraga wildtype sibling macrophage sample biological replicate 3", "GSM5914978", null, "tissue:Macrophages|genotype:rraga wild type|strain:TL|developmental stage:6 dpf type:Macrophages", "rraga wildtype sibling macrophage sample biological replicate 3", "Raw data of FASTQ format were processed through Novogene in house PERL scripts Clean reads were obtained by removing reads containing adapter  reads containing poly N and low quality reads from raw data Q20  Q30  and GC content of all clean data were calculated Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome. Mapped reads of each sample were assembled by StringTie v1.3.3b featureCount v1.5.0 was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2R package 1.20.0 Genome build: GRCz11 Supplementary files format and content: text file contains gene counts  normalized FPKM reads for genes identified by gene name and ENSEMBL ID", "Macrophages", "Embryos were scored as mutant or wildtype using a confocal microscope at 4 dpf and 5 dpf Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS.", "RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit", "Zebrafish embryos were raised at 28.5 \u00baC in embryo water with methylene blue and PTU", "genotype:rraga wild type|strain:TL|developmental stage:6 dpf type:Macrophages", "GSM5914978", "GSM5914978: rraga wildtype sibling macrophage sample biological replicate 3; Danio rerio; RNA Seq", "GSM5914978 r1", "GSM5914978", "1", "RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP361285", null, "loader:fastq load.py", "WT4_S60_1.fq.gz WT4_S60_2.fq.gz", "fastq fastq", 13192857000.0, 43976190.0, "GSM5914978 r1", "0:150 1:150", "A:3525239825;C:3077994139;G:3094731575;T:3494762519;N:128942", 150, 150, null, null, 3525239825, 3077994139, 3094731575, 3494762519, 128942, "SRX14274936", "SRS12093627", "SRA1377812", "Talbot, Developmental Biology, Stanford University", "Talbot, Developmental Biology, Stanford University", 2, 0.94452, 0.94349, 0.06316, 0.06336, 0.75939, 0.75986, 0.48896, 0.48863, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-02-24", "Larval", "Larval", "Blood", "Hematopoietic System"], [68664, "SRR18124524", "SRX14274935", "SRS12093626", "SRP361285", "PRJNA809951", "A lysosomal regulatory circuit essential for the development and function of microglia", "GSE197349", "Transcriptome Analysis", "We performed Illumina NovaSeq on macrophages isolated from zebrafish Overall design: Cells of the macrophage lineage tagged with mpeg:GFP were isolated from rraga mutants and their wildtype siblings by FACS  RNA was extracted  and sequencing was performed.", "parent bioproject:PRJNA809950", "pubmed:36044568", null, "rraga wildtype sibling macrophage sample biological replicate 2", "GSM5914977", null, "tissue:Macrophages|genotype:rraga wild type|strain:TL|developmental stage:6 dpf type:Macrophages", "rraga wildtype sibling macrophage sample biological replicate 2", "Raw data of FASTQ format were processed through Novogene in house PERL scripts Clean reads were obtained by removing reads containing adapter  reads containing poly N and low quality reads from raw data Q20  Q30  and GC content of all clean data were calculated Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome. Mapped reads of each sample were assembled by StringTie v1.3.3b featureCount v1.5.0 was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2R package 1.20.0 Genome build: GRCz11 Supplementary files format and content: text file contains gene counts  normalized FPKM reads for genes identified by gene name and ENSEMBL ID", "Macrophages", "Embryos were scored as mutant or wildtype using a confocal microscope at 4 dpf and 5 dpf Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS.", "RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit", "Zebrafish embryos were raised at 28.5 \u00baC in embryo water with methylene blue and PTU", "genotype:rraga wild type|strain:TL|developmental stage:6 dpf type:Macrophages", "GSM5914977", "GSM5914977: rraga wildtype sibling macrophage sample biological replicate 2; Danio rerio; RNA Seq", "GSM5914977 r1", "GSM5914977", "1", "RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP361285", null, "loader:fastq load.py", "WT2_S58_1.fq.gz WT2_S58_2.fq.gz", "fastq fastq", 14306259300.0, 47687531.0, "GSM5914977 r1", "0:150 1:150", "A:3835681757;C:3324696461;G:3339727926;T:3806013274;N:139882", 150, 150, null, null, 3835681757, 3324696461, 3339727926, 3806013274, 139882, "SRX14274935", "SRS12093626", "SRA1377812", "Talbot, Developmental Biology, Stanford University", "Talbot, Developmental Biology, Stanford University", 2, 0.946, 0.94382, 0.07547, 0.07591, 0.7529, 0.75404, 0.4827, 0.48954, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-02-24", "Larval", "Larval", "Blood", "Hematopoietic System"], [68665, "SRR18124525", "SRX14274934", "SRS12093625", "SRP361285", "PRJNA809951", "A lysosomal regulatory circuit essential for the development and function of microglia", "GSE197349", "Transcriptome Analysis", "We performed Illumina NovaSeq on macrophages isolated from zebrafish Overall design: Cells of the macrophage lineage tagged with mpeg:GFP were isolated from rraga mutants and their wildtype siblings by FACS  RNA was extracted  and sequencing was performed.", "parent bioproject:PRJNA809950", "pubmed:36044568", null, "rraga wildtype sibling macrophage sample biological replicate 1", "GSM5914976", null, "tissue:Macrophages|genotype:rraga wild type|strain:TL|developmental stage:6 dpf type:Macrophages", "rraga wildtype sibling macrophage sample biological replicate 1", "Raw data of FASTQ format were processed through Novogene in house PERL scripts Clean reads were obtained by removing reads containing adapter  reads containing poly N and low quality reads from raw data Q20  Q30  and GC content of all clean data were calculated Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome. Mapped reads of each sample were assembled by StringTie v1.3.3b featureCount v1.5.0 was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2R package 1.20.0 Genome build: GRCz11 Supplementary files format and content: text file contains gene counts  normalized FPKM reads for genes identified by gene name and ENSEMBL ID", "Macrophages", "Embryos were scored as mutant or wildtype using a confocal microscope at 4 dpf and 5 dpf Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS.", "RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit", "Zebrafish embryos were raised at 28.5 \u00baC in embryo water with methylene blue and PTU", "genotype:rraga wild type|strain:TL|developmental stage:6 dpf type:Macrophages", "GSM5914976", "GSM5914976: rraga wildtype sibling macrophage sample biological replicate 1; Danio rerio; RNA Seq", "GSM5914976 r1", "GSM5914976", "1", "RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. 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Mapped reads of each sample were assembled by StringTie v1.3.3b featureCount v1.5.0 was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2R package 1.20.0 Genome build: GRCz11 Supplementary files format and content: text file contains gene counts  normalized FPKM reads for genes identified by gene name and ENSEMBL ID", "Macrophages", "Embryos were scored as mutant or wildtype using a confocal microscope at 4 dpf and 5 dpf Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS.", "RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit", "Zebrafish embryos were raised at 28.5 \u00baC in embryo water with methylene blue and PTU", "genotype:rraga mutant|strain:TL|developmental stage:6 dpf type:Macrophages", "GSM5914975", "GSM5914975: rraga mutant macrophage sample biological replicate 4; Danio rerio; RNA Seq", "GSM5914975 r1", "GSM5914975", "1", "RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP361285", null, "loader:fastq load.py", "RRGA5_S63_1.fq.gz RRGA5_S63_2.fq.gz", "fastq fastq", 16056097500.0, 53520325.0, "GSM5914975 r1", "0:150 1:150", "A:4294601650;C:3737735522;G:3760015896;T:4263588285;N:156147", 150, 150, null, null, 4294601650, 3737735522, 3760015896, 4263588285, 156147, "SRX14274933", "SRS12093624", "SRA1377812", "Talbot, Developmental Biology, Stanford University", "Talbot, Developmental Biology, Stanford University", 2, 0.94205, 0.93992, 0.04764, 0.04795, 0.76278, 0.76512, 0.48852, 0.48702, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-02-24", "Larval", "Larval", "Blood", "Hematopoietic System"], [68667, "SRR18124527", "SRX14274932", "SRS12093623", "SRP361285", "PRJNA809951", "A lysosomal regulatory circuit essential for the development and function of microglia", "GSE197349", "Transcriptome Analysis", "We performed Illumina NovaSeq on macrophages isolated from zebrafish Overall design: Cells of the macrophage lineage tagged with mpeg:GFP were isolated from rraga mutants and their wildtype siblings by FACS  RNA was extracted  and sequencing was performed.", "parent bioproject:PRJNA809950", "pubmed:36044568", null, "rraga mutant macrophage sample biological replicate 3", "GSM5914974", null, "tissue:Macrophages|genotype:rraga mutant|strain:TL|developmental stage:6 dpf type:Macrophages", "rraga mutant macrophage sample biological replicate 3", "Raw data of FASTQ format were processed through Novogene in house PERL scripts Clean reads were obtained by removing reads containing adapter  reads containing poly N and low quality reads from raw data Q20  Q30  and GC content of all clean data were calculated Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome. Mapped reads of each sample were assembled by StringTie v1.3.3b featureCount v1.5.0 was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2R package 1.20.0 Genome build: GRCz11 Supplementary files format and content: text file contains gene counts  normalized FPKM reads for genes identified by gene name and ENSEMBL ID", "Macrophages", "Embryos were scored as mutant or wildtype using a confocal microscope at 4 dpf and 5 dpf Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS.", "RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit", "Zebrafish embryos were raised at 28.5 \u00baC in embryo water with methylene blue and PTU", "genotype:rraga mutant|strain:TL|developmental stage:6 dpf type:Macrophages", "GSM5914974", "GSM5914974: rraga mutant macrophage sample biological replicate 3; Danio rerio; RNA Seq", "GSM5914974 r1", "GSM5914974", "1", "RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP361285", null, "loader:fastq load.py", "RRGA4_S61_1.fq.gz RRGA4_S61_2.fq.gz", "fastq fastq", 13800732900.0, 46002443.0, "GSM5914974 r1", "0:150 1:150", "A:3681710812;C:3222984593;G:3240482342;T:3655419422;N:135731", 150, 150, null, null, 3681710812, 3222984593, 3240482342, 3655419422, 135731, "SRX14274932", "SRS12093623", "SRA1377812", "Talbot, Developmental Biology, Stanford University", "Talbot, Developmental Biology, Stanford University", 2, 0.94451, 0.94367, 0.03979, 0.04074, 0.7754, 0.77654, 0.49111, 0.48192, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-02-24", "Larval", "Larval", "Blood", "Hematopoietic System"], [68668, "SRR18124528", "SRX14274931", "SRS12093622", "SRP361285", "PRJNA809951", "A lysosomal regulatory circuit essential for the development and function of microglia", "GSE197349", "Transcriptome Analysis", "We performed Illumina NovaSeq on macrophages isolated from zebrafish Overall design: Cells of the macrophage lineage tagged with mpeg:GFP were isolated from rraga mutants and their wildtype siblings by FACS  RNA was extracted  and sequencing was performed.", "parent bioproject:PRJNA809950", "pubmed:36044568", null, "rraga mutant macrophage sample biological replicate 2", "GSM5914973", null, "tissue:Macrophages|genotype:rraga mutant|strain:TL|developmental stage:6 dpf type:Macrophages", "rraga mutant macrophage sample biological replicate 2", "Raw data of FASTQ format were processed through Novogene in house PERL scripts Clean reads were obtained by removing reads containing adapter  reads containing poly N and low quality reads from raw data Q20  Q30  and GC content of all clean data were calculated Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome. Mapped reads of each sample were assembled by StringTie v1.3.3b featureCount v1.5.0 was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2R package 1.20.0 Genome build: GRCz11 Supplementary files format and content: text file contains gene counts  normalized FPKM reads for genes identified by gene name and ENSEMBL ID", "Macrophages", "Embryos were scored as mutant or wildtype using a confocal microscope at 4 dpf and 5 dpf Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS.", "RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit", "Zebrafish embryos were raised at 28.5 \u00baC in embryo water with methylene blue and PTU", "genotype:rraga mutant|strain:TL|developmental stage:6 dpf type:Macrophages", "GSM5914973", "GSM5914973: rraga mutant macrophage sample biological replicate 2; Danio rerio; RNA Seq", "GSM5914973 r1", "GSM5914973", "1", "RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP361285", null, "loader:fastq load.py", "RRGA2_S59_1.fq.gz RRGA2_S59_2.fq.gz", "fastq fastq", 13029428100.0, 43431427.0, "GSM5914973 r1", "0:150 1:150", "A:3511989568;C:3007102768;G:3023337404;T:3486872579;N:125781", 150, 150, null, null, 3511989568, 3007102768, 3023337404, 3486872579, 125781, "SRX14274931", "SRS12093622", "SRA1377812", "Talbot, Developmental Biology, Stanford University", "Talbot, Developmental Biology, Stanford University", 2, 0.94027, 0.93791, 0.05191, 0.05248, 0.77759, 0.77908, 0.48627, 0.49588, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-02-24", "Larval", "Larval", "Blood", "Hematopoietic System"], [68669, "SRR18124529", "SRX14274930", "SRS12093621", "SRP361285", "PRJNA809951", "A lysosomal regulatory circuit essential for the development and function of microglia", "GSE197349", "Transcriptome Analysis", "We performed Illumina NovaSeq on macrophages isolated from zebrafish Overall design: Cells of the macrophage lineage tagged with mpeg:GFP were isolated from rraga mutants and their wildtype siblings by FACS  RNA was extracted  and sequencing was performed.", "parent bioproject:PRJNA809950", "pubmed:36044568", null, "rraga mutant macrophage sample biological replicate 1", "GSM5914972", null, "tissue:Macrophages|genotype:rraga mutant|strain:TL|developmental stage:6 dpf type:Macrophages", "rraga mutant macrophage sample biological replicate 1", "Raw data of FASTQ format were processed through Novogene in house PERL scripts Clean reads were obtained by removing reads containing adapter  reads containing poly N and low quality reads from raw data Q20  Q30  and GC content of all clean data were calculated Index of reference genome GRCz11 was built using Hisat2 v2.0.5 and paired end clean reads were aligned to reference genome. Mapped reads of each sample were assembled by StringTie v1.3.3b featureCount v1.5.0 was used to count the read numbers mapped to each gene. Differential expression analysis was performed using the DESeq2R package 1.20.0 Genome build: GRCz11 Supplementary files format and content: text file contains gene counts  normalized FPKM reads for genes identified by gene name and ENSEMBL ID", "Macrophages", "Embryos were scored as mutant or wildtype using a confocal microscope at 4 dpf and 5 dpf Larvae were dissociated at 6 dpf and GFP+ macrophages were isolated using FACS.", "RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit", "Zebrafish embryos were raised at 28.5 \u00baC in embryo water with methylene blue and PTU", "genotype:rraga mutant|strain:TL|developmental stage:6 dpf type:Macrophages", "GSM5914972", "GSM5914972: rraga mutant macrophage sample biological replicate 1; Danio rerio; RNA Seq", "GSM5914972 r1", "GSM5914972", "1", "RNA was extracted using the Qiagen RNeasy Micro kit using the manufacturer's instructions. Takara SMART Seq v4 Ultra Low Input RNA Kit", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP361285", null, "loader:fastq load.py", "RRGA1_S57_1.fq.gz RRGA1_S57_2.fq.gz", "fastq fastq", 15238446600.0, 50794822.0, "GSM5914972 r1", "0:150 1:150", "A:4094568173;C:3530048869;G:3550699321;T:4062982708;N:147529", 150, 150, null, null, 4094568173, 3530048869, 3550699321, 4062982708, 147529, "SRX14274930", "SRS12093621", "SRA1377812", "Talbot, Developmental Biology, Stanford University", "Talbot, Developmental Biology, Stanford University", 2, 0.94164, 0.9408, 0.04872, 0.04897, 0.76999, 0.77029, 0.47856, 0.48556, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "smartseq", null, "United States", "2022-02-24", "Larval", "Larval", "Blood", "Hematopoietic System"]], "truncated": false, "filtered_table_rows_count": 57, "expanded_columns": [], "expandable_columns": [], "columns": ["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", 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[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, 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