rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
33075,SRR29654109,SRX25158199,SRS21848821,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3,GSM8369980,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100,GSM8369980,GSM8369980: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3; Danio rerio; RNA Seq,GSM8369980 r1,GSM8369980,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_AMD_-016_cbc.fastq.gz,fastq,347162880.0,5786048.0,GSM8369980 r1,0:60,A:122562825;C:62219285;G:75539895;T:86775172;N:65703,60,,,,122562825,62219285,75539895,86775172,65703,SRX25158199,SRS21848821,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33076,SRR29654110,SRX25158199,SRS21848821,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3,GSM8369980,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100,GSM8369980,GSM8369980: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3; Danio rerio; RNA Seq,GSM8369980 r1,GSM8369980,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_AMD_-016_cbc.fastq.gz,fastq,340954260.0,5682571.0,GSM8369980 r2,0:60,A:120149623;C:60854408;G:75192893;T:84703966;N:53370,60,,,,120149623,60854408,75192893,84703966,53370,SRX25158199,SRS21848821,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33077,SRR29654111,SRX25158199,SRS21848821,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3,GSM8369980,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100,GSM8369980,GSM8369980: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3; Danio rerio; RNA Seq,GSM8369980 r1,GSM8369980,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_AMD_-016_cbc.fastq.gz,fastq,351749160.0,5862486.0,GSM8369980 r3,0:60,A:124352905;C:63078724;G:76291828;T:87988386;N:37317,60,,,,124352905,63078724,76291828,87988386,37317,SRX25158199,SRS21848821,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33078,SRR29654112,SRX25158199,SRS21848821,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3,GSM8369980,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100,GSM8369980,GSM8369980: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 3; Danio rerio; RNA Seq,GSM8369980 r1,GSM8369980,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_AMD_-016_cbc.fastq.gz,fastq,345225720.0,5753762.0,GSM8369980 r4,0:60,A:121803902;C:61651407;G:75900430;T:85843789;N:26192,60,,,,121803902,61651407,75900430,85843789,26192,SRX25158199,SRS21848821,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33079,SRR29654113,SRX25158198,SRS21848820,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2,GSM8369979,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100,GSM8369979,GSM8369979: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2; Danio rerio; RNA Seq,GSM8369979 r1,GSM8369979,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_AMD_-015_cbc.fastq.gz,fastq,159497640.0,2658294.0,GSM8369979 r1,0:60,A:55569742;C:28678683;G:33264744;T:41953354;N:31117,60,,,,55569742,28678683,33264744,41953354,31117,SRX25158198,SRS21848820,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33080,SRR29654114,SRX25158198,SRS21848820,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2,GSM8369979,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100,GSM8369979,GSM8369979: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2; Danio rerio; RNA Seq,GSM8369979 r1,GSM8369979,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_AMD_-015_cbc.fastq.gz,fastq,156549240.0,2609154.0,GSM8369979 r2,0:60,A:54428858;C:28027289;G:33149650;T:40918247;N:25196,60,,,,54428858,28027289,33149650,40918247,25196,SRX25158198,SRS21848820,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33081,SRR29654115,SRX25158198,SRS21848820,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2,GSM8369979,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100,GSM8369979,GSM8369979: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2; Danio rerio; RNA Seq,GSM8369979 r1,GSM8369979,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_AMD_-015_cbc.fastq.gz,fastq,161735280.0,2695588.0,GSM8369979 r3,0:60,A:56425187;C:29084972;G:33637112;T:42570603;N:17406,60,,,,56425187,29084972,33637112,42570603,17406,SRX25158198,SRS21848820,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33082,SRR29654116,SRX25158198,SRS21848820,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2,GSM8369979,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100,GSM8369979,GSM8369979: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 2; Danio rerio; RNA Seq,GSM8369979 r1,GSM8369979,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_AMD_-015_cbc.fastq.gz,fastq,158621520.0,2643692.0,GSM8369979 r4,0:60,A:55213721;C:28430013;G:33462307;T:41503213;N:12266,60,,,,55213721,28430013,33462307,41503213,12266,SRX25158198,SRS21848820,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33083,SRR29654117,SRX25158197,SRS21848819,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1,GSM8369978,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100,GSM8369978,GSM8369978: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1; Danio rerio; RNA Seq,GSM8369978 r1,GSM8369978,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_AMD_-011_cbc.fastq.gz,fastq,44363040.0,739384.0,GSM8369978 r1,0:60,A:17756825;C:7540147;G:9311367;T:9746444;N:8257,60,,,,17756825,7540147,9311367,9746444,8257,SRX25158197,SRS21848819,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33084,SRR29654118,SRX25158197,SRS21848819,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1,GSM8369978,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100,GSM8369978,GSM8369978: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1; Danio rerio; RNA Seq,GSM8369978 r1,GSM8369978,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_AMD_-011_cbc.fastq.gz,fastq,43450800.0,724180.0,GSM8369978 r2,0:60,A:17376442;C:7355139;G:9244019;T:9468455;N:6745,60,,,,17376442,7355139,9244019,9468455,6745,SRX25158197,SRS21848819,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33085,SRR29654119,SRX25158197,SRS21848819,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1,GSM8369978,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100,GSM8369978,GSM8369978: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1; Danio rerio; RNA Seq,GSM8369978 r1,GSM8369978,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_AMD_-011_cbc.fastq.gz,fastq,44795880.0,746598.0,GSM8369978 r3,0:60,A:17988707;C:7600964;G:9362568;T:9839285;N:4356,60,,,,17988707,7600964,9362568,9839285,4356,SRX25158197,SRS21848819,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33086,SRR29654120,SRX25158197,SRS21848819,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1,GSM8369978,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury AMD3100,GSM8369978,GSM8369978: Neutrophils mpx+  8 xxx post injury  AMD3100  biol rep 1; Danio rerio; RNA Seq,GSM8369978 r1,GSM8369978,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_AMD_-011_cbc.fastq.gz,fastq,44060940.0,734349.0,GSM8369978 r4,0:60,A:17608648;C:7492643;G:9327676;T:9628642;N:3331,60,,,,17608648,7492643,9327676,9628642,3331,SRX25158197,SRS21848819,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33087,SRR29654121,SRX25158196,SRS21848818,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  AMD3100  biol rep 3,GSM8369977,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  AMD3100  biol rep 3,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100,GSM8369977,GSM8369977: Neutrophils mpx+  uninjured  AMD3100  biol rep 3; Danio rerio; RNA Seq,GSM8369977 r1,GSM8369977,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_AMD_-014_cbc.fastq.gz,fastq,115048140.0,1917469.0,GSM8369977 r1,0:60,A:41373215;C:21759509;G:21832537;T:30061744;N:21135,60,,,,41373215,21759509,21832537,30061744,21135,SRX25158196,SRS21848818,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33088,SRR29654122,SRX25158196,SRS21848818,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  AMD3100  biol rep 3,GSM8369977,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  AMD3100  biol rep 3,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100,GSM8369977,GSM8369977: Neutrophils mpx+  uninjured  AMD3100  biol rep 3; Danio rerio; RNA Seq,GSM8369977 r1,GSM8369977,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_AMD_-014_cbc.fastq.gz,fastq,112845060.0,1880751.0,GSM8369977 r2,0:60,A:40482360;C:21287713;G:21750928;T:29306465;N:17594,60,,,,40482360,21287713,21750928,29306465,17594,SRX25158196,SRS21848818,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33089,SRR29654123,SRX25158196,SRS21848818,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  AMD3100  biol rep 3,GSM8369977,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  AMD3100  biol rep 3,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100,GSM8369977,GSM8369977: Neutrophils mpx+  uninjured  AMD3100  biol rep 3; Danio rerio; RNA Seq,GSM8369977 r1,GSM8369977,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_AMD_-014_cbc.fastq.gz,fastq,116696580.0,1944943.0,GSM8369977 r3,0:60,A:42022776;C:22106040;G:22075778;T:30479513;N:12473,60,,,,42022776,22106040,22075778,30479513,12473,SRX25158196,SRS21848818,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33090,SRR29654124,SRX25158196,SRS21848818,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  AMD3100  biol rep 3,GSM8369977,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  AMD3100  biol rep 3,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100,GSM8369977,GSM8369977: Neutrophils mpx+  uninjured  AMD3100  biol rep 3; Danio rerio; RNA Seq,GSM8369977 r1,GSM8369977,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_AMD_-014_cbc.fastq.gz,fastq,114334980.0,1905583.0,GSM8369977 r4,0:60,A:41132105;C:21578779;G:21934073;T:29681512;N:8511,60,,,,41132105,21578779,21934073,29681512,8511,SRX25158196,SRS21848818,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33091,SRR29654125,SRX25158195,SRS21848817,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  AMD3100  biol rep 2,GSM8369976,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  AMD3100  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100,GSM8369976,GSM8369976: Neutrophils mpx+  uninjured  AMD3100  biol rep 2; Danio rerio; RNA Seq,GSM8369976 r1,GSM8369976,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_AMD_-013_cbc.fastq.gz,fastq,354085380.0,5901423.0,GSM8369976 r1,0:60,A:124800871;C:65627966;G:72434440;T:91152029;N:70074,60,,,,124800871,65627966,72434440,91152029,70074,SRX25158195,SRS21848817,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33092,SRR29654126,SRX25158195,SRS21848817,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  AMD3100  biol rep 2,GSM8369976,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  AMD3100  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100,GSM8369976,GSM8369976: Neutrophils mpx+  uninjured  AMD3100  biol rep 2; Danio rerio; RNA Seq,GSM8369976 r1,GSM8369976,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_AMD_-013_cbc.fastq.gz,fastq,347250360.0,5787506.0,GSM8369976 r2,0:60,A:122147080;C:64042522;G:72135325;T:88869927;N:55506,60,,,,122147080,64042522,72135325,88869927,55506,SRX25158195,SRS21848817,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33093,SRR29654127,SRX25158195,SRS21848817,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  AMD3100  biol rep 2,GSM8369976,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  AMD3100  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100,GSM8369976,GSM8369976: Neutrophils mpx+  uninjured  AMD3100  biol rep 2; Danio rerio; RNA Seq,GSM8369976 r1,GSM8369976,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_AMD_-013_cbc.fastq.gz,fastq,358862580.0,5981043.0,GSM8369976 r3,0:60,A:126636264;C:66527902;G:73214426;T:92445348;N:38640,60,,,,126636264,66527902,73214426,92445348,38640,SRX25158195,SRS21848817,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33094,SRR29654128,SRX25158195,SRS21848817,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  AMD3100  biol rep 2,GSM8369976,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  AMD3100  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100,GSM8369976,GSM8369976: Neutrophils mpx+  uninjured  AMD3100  biol rep 2; Danio rerio; RNA Seq,GSM8369976 r1,GSM8369976,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_AMD_-013_cbc.fastq.gz,fastq,351843120.0,5864052.0,GSM8369976 r4,0:60,A:123921807;C:64956560;G:72828989;T:90107944;N:27820,60,,,,123921807,64956560,72828989,90107944,27820,SRX25158195,SRS21848817,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33095,SRR29654129,SRX25158194,SRS21848816,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  AMD3100  biol rep 1,GSM8369975,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  AMD3100  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100,GSM8369975,GSM8369975: Neutrophils mpx+  uninjured  AMD3100  biol rep 1; Danio rerio; RNA Seq,GSM8369975 r1,GSM8369975,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_AMD_-010_cbc.fastq.gz,fastq,100732380.0,1678873.0,GSM8369975 r1,0:60,A:37215898;C:18610797;G:18111317;T:26774380;N:19988,60,,,,37215898,18610797,18111317,26774380,19988,SRX25158194,SRS21848816,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33096,SRR29654130,SRX25158194,SRS21848816,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  AMD3100  biol rep 1,GSM8369975,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  AMD3100  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100,GSM8369975,GSM8369975: Neutrophils mpx+  uninjured  AMD3100  biol rep 1; Danio rerio; RNA Seq,GSM8369975 r1,GSM8369975,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_AMD_-010_cbc.fastq.gz,fastq,98830860.0,1647181.0,GSM8369975 r2,0:60,A:36388012;C:18195984;G:18122717;T:26108692;N:15455,60,,,,36388012,18195984,18122717,26108692,15455,SRX25158194,SRS21848816,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33097,SRR29654131,SRX25158194,SRS21848816,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  AMD3100  biol rep 1,GSM8369975,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  AMD3100  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100,GSM8369975,GSM8369975: Neutrophils mpx+  uninjured  AMD3100  biol rep 1; Danio rerio; RNA Seq,GSM8369975 r1,GSM8369975,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_AMD_-010_cbc.fastq.gz,fastq,102277560.0,1704626.0,GSM8369975 r3,0:60,A:37811843;C:18928051;G:18347174;T:27179477;N:11015,60,,,,37811843,18928051,18347174,27179477,11015,SRX25158194,SRS21848816,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33098,SRR29654132,SRX25158194,SRS21848816,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  AMD3100  biol rep 1,GSM8369975,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  AMD3100  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured AMD3100,GSM8369975,GSM8369975: Neutrophils mpx+  uninjured  AMD3100  biol rep 1; Danio rerio; RNA Seq,GSM8369975 r1,GSM8369975,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_AMD_-010_cbc.fastq.gz,fastq,100371840.0,1672864.0,GSM8369975 r4,0:60,A:37032383;C:18500721;G:18308236;T:26522753;N:7747,60,,,,37032383,18500721,18308236,26522753,7747,SRX25158194,SRS21848816,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33099,SRR29654133,SRX25158193,SRS21848815,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3,GSM8369974,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO,GSM8369974,GSM8369974: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3; Danio rerio; RNA Seq,GSM8369974 r1,GSM8369974,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_DMSO_-008_cbc.fastq.gz,fastq,161717520.0,2695292.0,GSM8369974 r1,0:60,A:58227035;C:29120167;G:33153372;T:41186362;N:30584,60,,,,58227035,29120167,33153372,41186362,30584,SRX25158193,SRS21848815,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33100,SRR29654134,SRX25158193,SRS21848815,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3,GSM8369974,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO,GSM8369974,GSM8369974: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3; Danio rerio; RNA Seq,GSM8369974 r1,GSM8369974,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_DMSO_-008_cbc.fastq.gz,fastq,158810460.0,2646841.0,GSM8369974 r2,0:60,A:57059029;C:28475827;G:33090143;T:40160441;N:25020,60,,,,57059029,28475827,33090143,40160441,25020,SRX25158193,SRS21848815,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33101,SRR29654135,SRX25158193,SRS21848815,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3,GSM8369974,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO,GSM8369974,GSM8369974: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3; Danio rerio; RNA Seq,GSM8369974 r1,GSM8369974,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_DMSO_-008_cbc.fastq.gz,fastq,164136600.0,2735610.0,GSM8369974 r3,0:60,A:59164760;C:29564845;G:33567677;T:41822336;N:16982,60,,,,59164760,29564845,33567677,41822336,16982,SRX25158193,SRS21848815,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33102,SRR29654136,SRX25158193,SRS21848815,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3,GSM8369974,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO,GSM8369974,GSM8369974: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 3; Danio rerio; RNA Seq,GSM8369974 r1,GSM8369974,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_DMSO_-008_cbc.fastq.gz,fastq,160939740.0,2682329.0,GSM8369974 r4,0:60,A:57905646;C:28872433;G:33402085;T:40746636;N:12940,60,,,,57905646,28872433,33402085,40746636,12940,SRX25158193,SRS21848815,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33103,SRR29654137,SRX25158192,SRS21848814,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2,GSM8369973,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO,GSM8369973,GSM8369973: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2; Danio rerio; RNA Seq,GSM8369973 r1,GSM8369973,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_DMSO_-005_cbc.fastq.gz,fastq,294896760.0,4914946.0,GSM8369973 r1,0:60,A:113302890;C:53832811;G:54274745;T:73429183;N:57131,60,,,,113302890,53832811,54274745,73429183,57131,SRX25158192,SRS21848814,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33104,SRR29654138,SRX25158192,SRS21848814,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2,GSM8369973,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO,GSM8369973,GSM8369973: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2; Danio rerio; RNA Seq,GSM8369973 r1,GSM8369973,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_DMSO_-005_cbc.fastq.gz,fastq,289658820.0,4827647.0,GSM8369973 r2,0:60,A:111138289;C:52646716;G:54190664;T:71637241;N:45910,60,,,,111138289,52646716,54190664,71637241,45910,SRX25158192,SRS21848814,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33105,SRR29654139,SRX25158192,SRS21848814,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2,GSM8369973,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO,GSM8369973,GSM8369973: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2; Danio rerio; RNA Seq,GSM8369973 r1,GSM8369973,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_DMSO_-005_cbc.fastq.gz,fastq,299290800.0,4988180.0,GSM8369973 r3,0:60,A:115247052;C:54662821;G:54854607;T:74494831;N:31489,60,,,,115247052,54662821,54854607,74494831,31489,SRX25158192,SRS21848814,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33106,SRR29654140,SRX25158192,SRS21848814,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2,GSM8369973,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO,GSM8369973,GSM8369973: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 2; Danio rerio; RNA Seq,GSM8369973 r1,GSM8369973,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_DMSO_-005_cbc.fastq.gz,fastq,294091920.0,4901532.0,GSM8369973 r4,0:60,A:113032051;C:53520496;G:54754695;T:72762244;N:22434,60,,,,113032051,53520496,54754695,72762244,22434,SRX25158192,SRS21848814,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33107,SRR29654141,SRX25158191,SRS21848813,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1,GSM8369972,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO,GSM8369972,GSM8369972: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1; Danio rerio; RNA Seq,GSM8369972 r1,GSM8369972,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L001_8hpi_DMSO_-004_cbc.fastq.gz,fastq,79542600.0,1325710.0,GSM8369972 r1,0:60,A:29052800;C:15106261;G:15344010;T:20023888;N:15641,60,,,,29052800,15106261,15344010,20023888,15641,SRX25158191,SRS21848813,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33108,SRR29654142,SRX25158191,SRS21848813,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1,GSM8369972,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO,GSM8369972,GSM8369972: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1; Danio rerio; RNA Seq,GSM8369972 r1,GSM8369972,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L002_8hpi_DMSO_-004_cbc.fastq.gz,fastq,78150840.0,1302514.0,GSM8369972 r2,0:60,A:28490299;C:14795977;G:15298357;T:19554765;N:11442,60,,,,28490299,14795977,15298357,19554765,11442,SRX25158191,SRS21848813,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33109,SRR29654143,SRX25158191,SRS21848813,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1,GSM8369972,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO,GSM8369972,GSM8369972: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1; Danio rerio; RNA Seq,GSM8369972 r1,GSM8369972,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L003_8hpi_DMSO_-004_cbc.fastq.gz,fastq,80719140.0,1345319.0,GSM8369972 r3,0:60,A:29548150;C:15350378;G:15486892;T:20325654;N:8066,60,,,,29548150,15350378,15486892,20325654,8066,SRX25158191,SRS21848813,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33110,SRR29654144,SRX25158191,SRS21848813,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1,GSM8369972,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:8 xxx post injury DMSO,GSM8369972,GSM8369972: Neutrophils mpx+  8 xxx post injury  DMSO  biol rep 1; Danio rerio; RNA Seq,GSM8369972 r1,GSM8369972,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L004_8hpi_DMSO_-004_cbc.fastq.gz,fastq,79070760.0,1317846.0,GSM8369972 r4,0:60,A:28874779;C:14986197;G:15407453;T:19795922;N:6409,60,,,,28874779,14986197,15407453,19795922,6409,SRX25158191,SRS21848813,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33111,SRR29654145,SRX25158190,SRS21848812,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 3,GSM8369971,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 3,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369971,GSM8369971: Neutrophils mpx+  uninjured  DMSO  biol rep 3; Danio rerio; RNA Seq,GSM8369971 r1,GSM8369971,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_DMSO_-009_cbc.fastq.gz,fastq,182391600.0,3039860.0,GSM8369971 r1,0:60,A:65842196;C:33929963;G:37226765;T:45358269;N:34407,60,,,,65842196,33929963,37226765,45358269,34407,SRX25158190,SRS21848812,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33112,SRR29654146,SRX25158190,SRS21848812,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 3,GSM8369971,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 3,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369971,GSM8369971: Neutrophils mpx+  uninjured  DMSO  biol rep 3; Danio rerio; RNA Seq,GSM8369971 r1,GSM8369971,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_DMSO_-009_cbc.fastq.gz,fastq,179081640.0,2984694.0,GSM8369971 r2,0:60,A:64544585;C:33163305;G:37078756;T:44266486;N:28508,60,,,,64544585,33163305,37078756,44266486,28508,SRX25158190,SRS21848812,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33113,SRR29654147,SRX25158190,SRS21848812,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 3,GSM8369971,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 3,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369971,GSM8369971: Neutrophils mpx+  uninjured  DMSO  biol rep 3; Danio rerio; RNA Seq,GSM8369971 r1,GSM8369971,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_DMSO_-009_cbc.fastq.gz,fastq,185068740.0,3084479.0,GSM8369971 r3,0:60,A:66919946;C:34450944;G:37652300;T:46025841;N:19709,60,,,,66919946,34450944,37652300,46025841,19709,SRX25158190,SRS21848812,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33114,SRR29654148,SRX25158190,SRS21848812,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 3,GSM8369971,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 3,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369971,GSM8369971: Neutrophils mpx+  uninjured  DMSO  biol rep 3; Danio rerio; RNA Seq,GSM8369971 r1,GSM8369971,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_DMSO_-009_cbc.fastq.gz,fastq,181507740.0,3025129.0,GSM8369971 r4,0:60,A:65513514;C:33675079;G:37432606;T:44872485;N:14056,60,,,,65513514,33675079,37432606,44872485,14056,SRX25158190,SRS21848812,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33115,SRR29654149,SRX25158189,SRS21848811,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 2,GSM8369970,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369970,GSM8369970: Neutrophils mpx+  uninjured  DMSO  biol rep 2; Danio rerio; RNA Seq,GSM8369970 r1,GSM8369970,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_DMSO_-006_cbc.fastq.gz,fastq,45794760.0,763246.0,GSM8369970 r1,0:60,A:16928569;C:8492491;G:9006326;T:11358172;N:9202,60,,,,16928569,8492491,9006326,11358172,9202,SRX25158189,SRS21848811,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33116,SRR29654150,SRX25158189,SRS21848811,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 2,GSM8369970,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369970,GSM8369970: Neutrophils mpx+  uninjured  DMSO  biol rep 2; Danio rerio; RNA Seq,GSM8369970 r1,GSM8369970,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_DMSO_-006_cbc.fastq.gz,fastq,45009960.0,750166.0,GSM8369970 r2,0:60,A:16608407;C:8309766;G:8990622;T:11094414;N:6751,60,,,,16608407,8309766,8990622,11094414,6751,SRX25158189,SRS21848811,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33117,SRR29654151,SRX25158189,SRS21848811,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 2,GSM8369970,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369970,GSM8369970: Neutrophils mpx+  uninjured  DMSO  biol rep 2; Danio rerio; RNA Seq,GSM8369970 r1,GSM8369970,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_DMSO_-006_cbc.fastq.gz,fastq,46565880.0,776098.0,GSM8369970 r3,0:60,A:17217451;C:8640544;G:9146095;T:11557146;N:4644,60,,,,17217451,8640544,9146095,11557146,4644,SRX25158189,SRS21848811,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33118,SRR29654152,SRX25158189,SRS21848811,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 2,GSM8369970,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 2,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369970,GSM8369970: Neutrophils mpx+  uninjured  DMSO  biol rep 2; Danio rerio; RNA Seq,GSM8369970 r1,GSM8369970,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_DMSO_-006_cbc.fastq.gz,fastq,45624660.0,760411.0,GSM8369970 r4,0:60,A:16852187;C:8431444;G:9090234;T:11246907;N:3888,60,,,,16852187,8431444,9090234,11246907,3888,SRX25158189,SRS21848811,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33119,SRR29654153,SRX25158188,SRS21848810,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 1,GSM8369969,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369969,GSM8369969: Neutrophils mpx+  uninjured  DMSO  biol rep 1; Danio rerio; RNA Seq,GSM8369969 r1,GSM8369969,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L001_Uninjured_DMSO_-003_cbc.fastq.gz,fastq,55867380.0,931123.0,GSM8369969 r1,0:60,A:20680346;C:10254613;G:10895370;T:14026951;N:10100,60,,,,20680346,10254613,10895370,14026951,10100,SRX25158188,SRS21848810,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33120,SRR29654154,SRX25158188,SRS21848810,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 1,GSM8369969,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369969,GSM8369969: Neutrophils mpx+  uninjured  DMSO  biol rep 1; Danio rerio; RNA Seq,GSM8369969 r1,GSM8369969,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L002_Uninjured_DMSO_-003_cbc.fastq.gz,fastq,54889080.0,914818.0,GSM8369969 r2,0:60,A:20264110;C:10026239;G:10861715;T:13728039;N:8977,60,,,,20264110,10026239,10861715,13728039,8977,SRX25158188,SRS21848810,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33121,SRR29654155,SRX25158188,SRS21848810,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 1,GSM8369969,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369969,GSM8369969: Neutrophils mpx+  uninjured  DMSO  biol rep 1; Danio rerio; RNA Seq,GSM8369969 r1,GSM8369969,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L003_Uninjured_DMSO_-003_cbc.fastq.gz,fastq,56764440.0,946074.0,GSM8369969 r3,0:60,A:21036899;C:10416984;G:11027830;T:14275499;N:7228,60,,,,21036899,10416984,11027830,14275499,7228,SRX25158188,SRS21848810,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
33122,SRR29654156,SRX25158188,SRS21848810,SRP517033,PRJNA1129880,Neutrophil immune profile guides spinal cord regeneration in zebrafish,GSE271113,Transcriptome Analysis,Spinal cord injury triggers a strong innate inflammatory response in both non regenerative mammals and regenerative zebrafish. Neutrophils are the first immune population to be recruited to the injury site. Yet  their role in the repair process  particularly in a regenerative context  remains largely unknown. Here  we show that  promoting neutrophil inflammation resolution by inhibiting Cxcr4 boosts cellular and functional regeneration. Neutrophil specific RNA seq analysis reveals an enhanced activation state that correlates with a transient increase in tnf a expression in macrophage/microglia populations. Conversely  blocking neutrophil recruitment through Cxcr1/2 inhibition diminishes the presence of macrophage/microglia at the injury site and impairs spinal cord regeneration. Altogether  these findings provide new insights into the role of neutrophils in spinal cord regeneration  emphasizing the significant impact of their immune profile on the outcome of the repair process. Overall design: To understand the biological mechanisms promoted by neutrophils that improve spinal cord regeneration upon Cxcr4 inhibition  we sorted mpx:GFP+ cells from the injury site of lesioned larvae and from the same region of age matched uninjured controls and performed Bulk RNA sequencing analysis in AMD3100  and DMSO treated samples. Grant ID: 2022.02766.PTDC Grant title: Improving Spinal Cord Regeneration by modulating Neutrophil inflammation: lessons from a Zebrafish perspective Funding agency: Fundaçåo para a Ciência e Tecnologia FCT  Portugal,,pubmed:38925414,,Neutrophils mpx+  uninjured  DMSO  biol rep 1,GSM8369969,,tissue:Neutrophils mpx:GFP+|cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO|geo loc name:missing|collection date:missing,Neutrophils mpx+  uninjured  DMSO  biol rep 1,Libraries were paired end sequenced on a Nextseq 500 Illumina  high output  with a 1x75 bp Illumina Kit Read 1: 26 cycles  index read: 6 cycles  Read 2: 60 cycles. Read 1 was used to identify the Illumina library index and CEL Seq sample barcode and read 2 was aligned to the GRCz11 reference transcriptome using Burrow Wheeler aligner BWA MEM. Reads that mapped equally well to multiple locations were discarded.  Mapping and generation of count tables was done using the MapAndGo script. Normalization and differential gene expression analyses were conducted using DESeq2 v1.38 Assembly: GRCz11 zebrafish Supplementary files format and content: counts table generated using the MapAndGo script,Neutrophils mpx:GFP+,At 3 dpf  larvae were anesthetized in 0.5 mM tricaine. Subsequenclty  the spinal cord was fully transected at the level of the anal pore using the tip of a 30G needle. Next  larvae were randomly distributed into different conditions and incubated with 25 uM AMD3100 supplemented with 0.1% DMSO from 4 xxx post injury hpi until 8 hpi.,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,Zebrafish embryos were raised at 28.5ºC in E3 media with Methylene blue,cell type:Neutrophils mpx:GFP+|treatment:uninjured DMSO,GSM8369969,GSM8369969: Neutrophils mpx+  uninjured  DMSO  biol rep 1; Danio rerio; RNA Seq,GSM8369969 r1,GSM8369969,1,Trunks containing the lesion site and same region of age matched uninjured controls were dissociated in a solution containing 2.5 mg/ml collagenase IV  15 mM HEPES  25 mM D Glucose  2% goat serum in HBSS without xxx and calcium  incubated at 28.5ºC shaking at 300 rpm  and vigorously dissociated using a pipette. Next they were filtered and stained with DAPI 1ul/ml for 10 min at 4C. Single cell suspensions were used to sort GFP+ cells directly into TRIzol using a FACSAria III BD Biosciences. All Samples were processed in less than two hours. Bulk RNA Sequencing was performed at Single Cell Discoveries. Total RNA was extracted from 2500 4800 GFP+ cells using the standard TRIzol protocol. mRNA was processed following an adapted version of CEL seq. Samples were barcoded with CEL seq primers during the reverse transcription and pooled post second strand synthesis TruSeq small RNA primers Illumina,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP517033,,,IMM-CT-b001_HW5F2BGXN_S6_L004_Uninjured_DMSO_-003_cbc.fastq.gz,fastq,55531080.0,925518.0,GSM8369969 r4,0:60,A:20538193;C:10150017;G:10949669;T:13888674;N:4527,60,,,,20538193,10150017,10949669,13888674,4527,SRX25158188,SRS21848810,SRA1913211,Instituto de Medicina Molecular,Instituto de Medicina Molecular,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Portugal,2024-06-29,Larval,Larval,Blood,Hematopoietic System
47869,SRR6908743,SRX3856808,SRS3100400,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM9 eosinophils,GSM3070146,,tissue:WKM9 eosinophils|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM9 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM9 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070146,GSM3070146: WKM9 eosinophils; Danio rerio; RNA Seq,GSM3070146,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070146,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_eosinophils_L001_R1_001.fastq.gz WKM9_eosinophils_L001_R2_001.fastq.gz,fastq fastq,1378279915.0,9133302.0,GSM3070146 r1,0:75.43 1:75.48,A:398409215;C:214050926;G:243007260;T:522806293;N:6221,75,75,,,398409215,214050926,243007260,522806293,6221,SRX3856808,SRS3100400,SRA675960,GEO,Hubrecht Institute,2,0.32967,0.72245,0.27664,0.49284,0.96217,0.88688,0.44743,0.5676,76,73,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47870,SRR6908744,SRX3856808,SRS3100400,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM9 eosinophils,GSM3070146,,tissue:WKM9 eosinophils|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM9 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM9 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070146,GSM3070146: WKM9 eosinophils; Danio rerio; RNA Seq,GSM3070146,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070146,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_eosinophils_L002_R1_001.fastq.gz WKM9_eosinophils_L002_R2_001.fastq.gz,fastq fastq,1347027331.0,8926023.0,GSM3070146 r2,0:75.43 1:75.48,A:386373331;C:208319487;G:242442973;T:509887930;N:3610,75,75,,,386373331,208319487,242442973,509887930,3610,SRX3856808,SRS3100400,SRA675960,GEO,Hubrecht Institute,2,0.32008,0.72405,0.26859,0.48848,0.96512,0.88791,0.46692,0.55937,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47871,SRR6908745,SRX3856808,SRS3100400,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM9 eosinophils,GSM3070146,,tissue:WKM9 eosinophils|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM9 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM9 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070146,GSM3070146: WKM9 eosinophils; Danio rerio; RNA Seq,GSM3070146,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070146,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_eosinophils_L003_R1_001.fastq.gz WKM9_eosinophils_L003_R2_001.fastq.gz,fastq fastq,1241011911.0,8223327.0,GSM3070146 r3,0:75.44 1:75.48,A:356514159;C:192418351;G:221034567;T:471023588;N:21246,75,75,,,356514159,192418351,221034567,471023588,21246,SRX3856808,SRS3100400,SRA675960,GEO,Hubrecht Institute,2,0.31504,0.71934,0.26517,0.48722,0.96932,0.89499,0.47715,0.56814,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47872,SRR6908746,SRX3856808,SRS3100400,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM9 eosinophils,GSM3070146,,tissue:WKM9 eosinophils|FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM9 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM9 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM9|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070146,GSM3070146: WKM9 eosinophils; Danio rerio; RNA Seq,GSM3070146,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070146,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM9_eosinophils_L004_R1_001.fastq.gz WKM9_eosinophils_L004_R2_001.fastq.gz,fastq fastq,1199788386.0,7950347.0,GSM3070146 r4,0:75.44 1:75.47,A:343966384;C:184985849;G:216629920;T:454187010;N:19223,75,75,,,343966384,184985849,216629920,454187010,19223,SRX3856808,SRS3100400,SRA675960,GEO,Hubrecht Institute,2,0.32136,0.71802,0.27107,0.48741,0.97098,0.90057,0.4616,0.56009,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47917,SRR6908693,SRX3856796,SRS3100388,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM4 eosinophils,GSM3070134,,tissue:WKM4 eosinophils|FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM4 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM4 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070134,GSM3070134: WKM4 eosinophils; Danio rerio; RNA Seq,GSM3070134,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070134,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM4_eosinophils_L001_R1_001.fastq.gz WKM4_eosinophils_L001_R2_001.fastq.gz,fastq fastq,1044383799.0,6918578.0,GSM3070134 r1,0:75.49 1:75.46,A:293266328;C:159927306;G:179144897;T:412003143;N:42125,75,75,,,293266328,159927306,179144897,412003143,42125,SRX3856796,SRS3100388,SRA675960,GEO,Hubrecht Institute,2,0.38953,0.76677,0.33438,0.55076,0.94775,0.83664,0.47684,0.51667,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47918,SRR6908694,SRX3856796,SRS3100388,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM4 eosinophils,GSM3070134,,tissue:WKM4 eosinophils|FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM4 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM4 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070134,GSM3070134: WKM4 eosinophils; Danio rerio; RNA Seq,GSM3070134,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070134,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM4_eosinophils_L002_R1_001.fastq.gz WKM4_eosinophils_L002_R2_001.fastq.gz,fastq fastq,1065518294.0,7059081.0,GSM3070134 r2,0:75.49 1:75.45,A:299578147;C:162208243;G:185866185;T:417812882;N:52837,75,75,,,299578147,162208243,185866185,417812882,52837,SRX3856796,SRS3100388,SRA675960,GEO,Hubrecht Institute,2,0.36825,0.75817,0.3148,0.55624,0.95061,0.84794,0.47713,0.52081,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47919,SRR6908695,SRX3856796,SRS3100388,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM4 eosinophils,GSM3070134,,tissue:WKM4 eosinophils|FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM4 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM4 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070134,GSM3070134: WKM4 eosinophils; Danio rerio; RNA Seq,GSM3070134,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070134,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM4_eosinophils_L003_R1_001.fastq.gz WKM4_eosinophils_L003_R2_001.fastq.gz,fastq fastq,1020526841.0,6760661.0,GSM3070134 r3,0:75.50 1:75.45,A:287644655;C:155831653;G:174910820;T:402133481;N:6232,75,75,,,287644655,155831653,174910820,402133481,6232,SRX3856796,SRS3100388,SRA675960,GEO,Hubrecht Institute,2,0.38266,0.76495,0.32861,0.55487,0.94909,0.84502,0.47881,0.50844,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47920,SRR6908696,SRX3856796,SRS3100388,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM4 eosinophils,GSM3070134,,tissue:WKM4 eosinophils|FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM4 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM4 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM4|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070134,GSM3070134: WKM4 eosinophils; Danio rerio; RNA Seq,GSM3070134,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070134,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM4_eosinophils_L004_R2_001.fastq.gz WKM4_eosinophils_L004_R1_001.fastq.gz,fastq fastq,1036249497.0,6864317.0,GSM3070134 r4,0:75.50 1:75.46,A:290241796;C:157806083;G:180760457;T:407436042;N:5119,75,75,,,290241796,157806083,180760457,407436042,5119,SRX3856796,SRS3100388,SRA675960,GEO,Hubrecht Institute,2,0.38456,0.76284,0.32829,0.54843,0.9497,0.84668,0.48302,0.51789,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47925,SRR6908685,SRX3856794,SRS3100386,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM3 eosinophils,GSM3070132,,tissue:WKM3 eosinophils|FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM3 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM3 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070132,GSM3070132: WKM3 eosinophils; Danio rerio; RNA Seq,GSM3070132,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070132,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM3_eosinophils_L001_R1_001.fastq.gz WKM3_eosinophils_L001_R2_001.fastq.gz,fastq fastq,1288630538.0,8538558.0,GSM3070132 r1,0:75.44 1:75.48,A:384649233;C:189860338;G:186795029;T:527108032;N:217906,75,75,,,384649233,189860338,186795029,527108032,217906,SRX3856794,SRS3100386,SRA675960,GEO,Hubrecht Institute,2,0.38213,0.80648,0.32,0.39443,0.96749,0.92997,0.49763,0.55351,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47926,SRR6908686,SRX3856794,SRS3100386,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM3 eosinophils,GSM3070132,,tissue:WKM3 eosinophils|FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM3 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM3 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070132,GSM3070132: WKM3 eosinophils; Danio rerio; RNA Seq,GSM3070132,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070132,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM3_eosinophils_L002_R1_001.fastq.gz WKM3_eosinophils_L002_R2_001.fastq.gz,fastq fastq,1176806695.0,7797829.0,GSM3070132 r2,0:75.44 1:75.48,A:349406324;C:172751257;G:173925861;T:480558924;N:164329,75,75,,,349406324,172751257,173925861,480558924,164329,SRX3856794,SRS3100386,SRA675960,GEO,Hubrecht Institute,2,0.3792,0.81293,0.31911,0.39312,0.96834,0.93176,0.52878,0.54431,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47927,SRR6908687,SRX3856794,SRS3100386,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM3 eosinophils,GSM3070132,,tissue:WKM3 eosinophils|FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM3 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM3 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070132,GSM3070132: WKM3 eosinophils; Danio rerio; RNA Seq,GSM3070132,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070132,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM3_eosinophils_L003_R1_001.fastq.gz WKM3_eosinophils_L003_R2_001.fastq.gz,fastq fastq,1341470236.0,8888024.0,GSM3070132 r3,0:75.45 1:75.48,A:395746232;C:196893713;G:196590339;T:552105050;N:134902,75,75,,,395746232,196893713,196590339,552105050,134902,SRX3856794,SRS3100386,SRA675960,GEO,Hubrecht Institute,2,0.38231,0.81774,0.3205,0.39891,0.97279,0.92817,0.47656,0.53862,75,74,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47928,SRR6908688,SRX3856794,SRS3100386,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM3 eosinophils,GSM3070132,,tissue:WKM3 eosinophils|FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM3 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM3 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070132,GSM3070132: WKM3 eosinophils; Danio rerio; RNA Seq,GSM3070132,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070132,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM3_eosinophils_L004_R1_001.fastq.gz WKM3_eosinophils_L004_R2_001.fastq.gz,fastq fastq,1280409546.0,8484656.0,GSM3070132 r4,0:75.44 1:75.47,A:378449241;C:186686350;G:189951619;T:525218711;N:103625,75,75,,,378449241,186686350,189951619,525218711,103625,SRX3856794,SRS3100386,SRA675960,GEO,Hubrecht Institute,2,0.36531,0.80793,0.30661,0.38147,0.97492,0.94401,0.47223,0.55437,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47929,SRR6908681,SRX3856793,SRS3100385,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM3 classicalgate eosinophils,GSM3070131,,tissue:WKM3 classicalgate eosinophils|FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:classicalgate eosinophils,WKM3 classicalgate eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM3 classicalgate eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:classicalgate eosinophils,GSM3070131,GSM3070131: WKM3 classicalgate eosinophils; Danio rerio; RNA Seq,GSM3070131,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070131,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM3_classicalgate-eosinophils_L001_R1_001.fastq.gz WKM3_classicalgate-eosinophils_L001_R2_001.fastq.gz,fastq fastq,1462702668.0,9694435.0,GSM3070131 r1,0:75.42 1:75.46,A:445709472;C:205316750;G:205641600;T:605784979;N:249867,75,75,,,445709472,205316750,205641600,605784979,249867,SRX3856793,SRS3100385,SRA675960,GEO,Hubrecht Institute,2,0.39724,0.82292,0.32577,0.36062,0.9713,0.9301,0.46129,0.54716,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47930,SRR6908682,SRX3856793,SRS3100385,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM3 classicalgate eosinophils,GSM3070131,,tissue:WKM3 classicalgate eosinophils|FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:classicalgate eosinophils,WKM3 classicalgate eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM3 classicalgate eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:classicalgate eosinophils,GSM3070131,GSM3070131: WKM3 classicalgate eosinophils; Danio rerio; RNA Seq,GSM3070131,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070131,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM3_classicalgate-eosinophils_L002_R2_001.fastq.gz WKM3_classicalgate-eosinophils_L002_R1_001.fastq.gz,fastq fastq,1331127146.0,8822708.0,GSM3070131 r2,0:75.42 1:75.45,A:403738285;C:185977311;G:190160316;T:551055048;N:196186,75,75,,,403738285,185977311,190160316,551055048,196186,SRX3856793,SRS3100385,SRA675960,GEO,Hubrecht Institute,2,0.39004,0.81794,0.32291,0.35472,0.97228,0.93626,0.48683,0.54607,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47931,SRR6908683,SRX3856793,SRS3100385,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM3 classicalgate eosinophils,GSM3070131,,tissue:WKM3 classicalgate eosinophils|FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:classicalgate eosinophils,WKM3 classicalgate eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM3 classicalgate eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:classicalgate eosinophils,GSM3070131,GSM3070131: WKM3 classicalgate eosinophils; Danio rerio; RNA Seq,GSM3070131,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070131,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM3_classicalgate-eosinophils_L003_R2_001.fastq.gz WKM3_classicalgate-eosinophils_L003_R1_001.fastq.gz,fastq fastq,1530092022.0,10140266.0,GSM3070131 r3,0:75.43 1:75.46,A:460384140;C:214158501;G:217473146;T:637914633;N:161602,75,75,,,460384140,214158501,217473146,637914633,161602,SRX3856793,SRS3100385,SRA675960,GEO,Hubrecht Institute,2,0.39487,0.82643,0.32278,0.35403,0.97555,0.92989,0.49836,0.55498,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47932,SRR6908684,SRX3856793,SRS3100385,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM3 classicalgate eosinophils,GSM3070131,,tissue:WKM3 classicalgate eosinophils|FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:classicalgate eosinophils,WKM3 classicalgate eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM3 classicalgate eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM3|cell type:whole kidney marrow single cells|cell subtype:classicalgate eosinophils,GSM3070131,GSM3070131: WKM3 classicalgate eosinophils; Danio rerio; RNA Seq,GSM3070131,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070131,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM3_classicalgate-eosinophils_L004_R1_001.fastq.gz WKM3_classicalgate-eosinophils_L004_R2_001.fastq.gz,fastq fastq,1434145773.0,9505626.0,GSM3070131 r4,0:75.43 1:75.45,A:431807112;C:200115802;G:205473991;T:596630601;N:118267,75,75,,,431807112,200115802,205473991,596630601,118267,SRX3856793,SRS3100385,SRA675960,GEO,Hubrecht Institute,2,0.38268,0.82073,0.31346,0.34043,0.97678,0.94172,0.45791,0.5661,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47937,SRR6908673,SRX3856790,SRS3100384,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM2 eosinophils,GSM3070129,,tissue:WKM2 eosinophils|FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM2 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM2 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070129,GSM3070129: WKM2 eosinophils; Danio rerio; RNA Seq,GSM3070129,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070129,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM2_eosinophils_L001_R1_001.fastq.gz WKM2_eosinophils_L001_R2_001.fastq.gz,fastq fastq,1444176720.0,9566997.0,GSM3070129 r1,0:75.46 1:75.50,A:432764637;C:224282941;G:222436448;T:564444426;N:248268,75,75,,,432764637,224282941,222436448,564444426,248268,SRX3856790,SRS3100384,SRA675960,GEO,Hubrecht Institute,2,0.37168,0.75194,0.32262,0.52753,0.95915,0.94073,0.51621,0.55453,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47938,SRR6908674,SRX3856790,SRS3100384,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM2 eosinophils,GSM3070129,,tissue:WKM2 eosinophils|FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM2 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM2 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070129,GSM3070129: WKM2 eosinophils; Danio rerio; RNA Seq,GSM3070129,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070129,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM2_eosinophils_L002_R1_001.fastq.gz WKM2_eosinophils_L002_R2_001.fastq.gz,fastq fastq,1320784826.0,8749678.0,GSM3070129 r2,0:75.45 1:75.50,A:392835077;C:204358703;G:208201633;T:515202839;N:186574,75,75,,,392835077,204358703,208201633,515202839,186574,SRX3856790,SRS3100384,SRA675960,GEO,Hubrecht Institute,2,0.36921,0.73955,0.32271,0.52168,0.96047,0.94643,0.49733,0.53116,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47939,SRR6908675,SRX3856790,SRS3100384,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM2 eosinophils,GSM3070129,,tissue:WKM2 eosinophils|FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM2 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM2 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070129,GSM3070129: WKM2 eosinophils; Danio rerio; RNA Seq,GSM3070129,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070129,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM2_eosinophils_L003_R2_001.fastq.gz WKM2_eosinophils_L003_R1_001.fastq.gz,fastq fastq,1500143635.0,9937133.0,GSM3070129 r3,0:75.46 1:75.50,A:445152171;C:231621688;G:233127317;T:590090278;N:152181,75,75,,,445152171,231621688,233127317,590090278,152181,SRX3856790,SRS3100384,SRA675960,GEO,Hubrecht Institute,2,0.36533,0.75138,0.31769,0.52682,0.96731,0.94209,0.50569,0.54346,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47940,SRR6908676,SRX3856790,SRS3100384,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM2 eosinophils,GSM3070129,,tissue:WKM2 eosinophils|FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:eosinophils,WKM2 eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM2 eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:eosinophils,GSM3070129,GSM3070129: WKM2 eosinophils; Danio rerio; RNA Seq,GSM3070129,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070129,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM2_eosinophils_L004_R1_001.fastq.gz WKM2_eosinophils_L004_R2_001.fastq.gz,fastq fastq,1428668507.0,9464755.0,GSM3070129 r4,0:75.46 1:75.49,A:423108347;C:219338398;G:226517917;T:559587502;N:116343,75,75,,,423108347,219338398,226517917,559587502,116343,SRX3856790,SRS3100384,SRA675960,GEO,Hubrecht Institute,2,0.35962,0.7405,0.31464,0.51805,0.96962,0.95747,0.48862,0.53364,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47941,SRR6908669,SRX3856789,SRS3100381,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM2 classicalgate eosinophils,GSM3070128,,tissue:WKM2 classicalgate eosinophils|FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:classicalgate eosinophils,WKM2 classicalgate eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM2 classicalgate eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:classicalgate eosinophils,GSM3070128,GSM3070128: WKM2 classicalgate eosinophils; Danio rerio; RNA Seq,GSM3070128,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070128,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM2_classicalgate-eosinophils_L001_R2_001.fastq.gz WKM2_classicalgate-eosinophils_L001_R1_001.fastq.gz,fastq fastq,880478792.0,5834816.0,GSM3070128 r1,0:75.43 1:75.47,A:267072322;C:127440559;G:126304290;T:359512123;N:149498,75,75,,,267072322,127440559,126304290,359512123,149498,SRX3856789,SRS3100381,SRA675960,GEO,Hubrecht Institute,2,0.3788,0.812,0.28918,0.38972,0.96595,0.92904,0.5376,0.55651,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47942,SRR6908670,SRX3856789,SRS3100381,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM2 classicalgate eosinophils,GSM3070128,,tissue:WKM2 classicalgate eosinophils|FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:classicalgate eosinophils,WKM2 classicalgate eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM2 classicalgate eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:classicalgate eosinophils,GSM3070128,GSM3070128: WKM2 classicalgate eosinophils; Danio rerio; RNA Seq,GSM3070128,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070128,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM2_classicalgate-eosinophils_L002_R1_001.fastq.gz WKM2_classicalgate-eosinophils_L002_R2_001.fastq.gz,fastq fastq,806110283.0,5342262.0,GSM3070128 r2,0:75.42 1:75.47,A:243426891;C:116100169;G:117840212;T:328625621;N:117390,75,75,,,243426891,116100169,117840212,328625621,117390,SRX3856789,SRS3100381,SRA675960,GEO,Hubrecht Institute,2,0.38141,0.80952,0.29221,0.37995,0.96546,0.93381,0.54149,0.55378,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47943,SRR6908671,SRX3856789,SRS3100381,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM2 classicalgate eosinophils,GSM3070128,,tissue:WKM2 classicalgate eosinophils|FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:classicalgate eosinophils,WKM2 classicalgate eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM2 classicalgate eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:classicalgate eosinophils,GSM3070128,GSM3070128: WKM2 classicalgate eosinophils; Danio rerio; RNA Seq,GSM3070128,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070128,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM2_classicalgate-eosinophils_L003_R1_001.fastq.gz WKM2_classicalgate-eosinophils_L003_R2_001.fastq.gz,fastq fastq,924045470.0,6123105.0,GSM3070128 r3,0:75.44 1:75.47,A:276824263;C:133108077;G:134012420;T:380008370;N:92340,75,75,,,276824263,133108077,134012420,380008370,92340,SRX3856789,SRS3100381,SRA675960,GEO,Hubrecht Institute,2,0.3819,0.81801,0.29161,0.38224,0.97124,0.92809,0.53982,0.54629,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
47944,SRR6908672,SRX3856789,SRS3100381,SRP136633,PRJNA446034,Cell type purification by single cell transcriptome trained sorting,GSE112438,Other,Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID  a computational method that combines single cell transcriptomics  for unbiased cell type identification  with FACS index sorting  to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell  we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort  while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.,,pubmed:31585086,,WKM2 classicalgate eosinophils,GSM3070128,,tissue:WKM2 classicalgate eosinophils|FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:classicalgate eosinophils,WKM2 classicalgate eosinophils,In transcriptome libraries  first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9  ensemble 74  extended with ERCC92 Supplementary files format and content: Tabular separated files  with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz  1st column represents index of the cell specific barcode  and the second column is the barcode,WKM2 classicalgate eosinophils,,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,,FISHid:WKM2|cell type:whole kidney marrow single cells|cell subtype:classicalgate eosinophils,GSM3070128,GSM3070128: WKM2 classicalgate eosinophils; Danio rerio; RNA Seq,GSM3070128,,1,post organ isolation  live single cells are sorted into 384 well plates containing mineral oil  uniquely barcoded cell specific primers for mRNA detection  Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters,GEO Accession:GSM3070128,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP136633,,,WKM2_classicalgate-eosinophils_L004_R1_001.fastq.gz WKM2_classicalgate-eosinophils_L004_R2_001.fastq.gz,fastq fastq,867397884.0,5748519.0,GSM3070128 r4,0:75.43 1:75.46,A:260294749;C:124376674;G:127341359;T:355314902;N:70200,75,75,,,260294749,124376674,127341359,355314902,70200,SRX3856789,SRS3100381,SRA675960,GEO,Hubrecht Institute,2,0.37148,0.80708,0.28632,0.3846,0.97299,0.94474,0.5375,0.54419,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,trueseq,sc,single_cell_plate,celseq,,Netherlands,2018-03-28,Undetermined,Undetermined,Blood,Hematopoietic System
62567,SRR13238450,SRX9670474,SRS7869376,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN8 4dpf uninjured mpeg1 mcherry R2,GSM4969715,,tissue:mpeg1 expressing macrophages|development stage:4 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:uninjured|xxx post injury:n/a,PN8 4dpf uninjured mpeg1 mcherry R2,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:4 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:uninjured|xxx post injury:n/a,GSM4969715,GSM4969715: PN8 4dpf uninjured mpeg1 mcherry R2; Danio rerio; RNA Seq,GSM4969715,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969715,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN8_R1_cat.fastq.gz PN8_R2_cat.fastq.gz,fastq fastq,12597661755.0,83472446.0,GSM4969715 r1,0:75.48 1:75.44,A:3580107664;C:1794661271;G:2126218655;T:5095225054;N:1449111,75,75,,,3580107664,1794661271,2126218655,5095225054,1449111,SRX9670474,SRS7869376,SRA1169931,GEO,The University of Melbourne,2,0.24621,0.75686,0.17058,0.19967,0.99198,0.83075,0.4368,0.53942,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62568,SRR13238446,SRX9670473,SRS7869375,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN7 3dpi mpeg1 mcherry R2,GSM4969714,,tissue:mpeg1 expressing macrophages|development stage:7 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:3,PN7 3dpi mpeg1 mcherry R2,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:7 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:3,GSM4969714,GSM4969714: PN7 3dpi mpeg1 mcherry R2; Danio rerio; RNA Seq,GSM4969714,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969714,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN7_L001_R1_001.fastq.gz PN7_L001_R2_001.fastq.gz,fastq fastq,6533788395.0,43286860.0,GSM4969714 r1,0:75.49 1:75.45,A:1875974034;C:979457427;G:1120952137;T:2556380216;N:1024581,75,75,,,1875974034,979457427,1120952137,2556380216,1024581,SRX9670473,SRS7869375,SRA1169931,GEO,The University of Melbourne,2,0.18309,0.71892,0.15278,0.43253,0.99178,0.84682,0.46869,0.53212,75,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62569,SRR13238447,SRX9670473,SRS7869375,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN7 3dpi mpeg1 mcherry R2,GSM4969714,,tissue:mpeg1 expressing macrophages|development stage:7 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:3,PN7 3dpi mpeg1 mcherry R2,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:7 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:3,GSM4969714,GSM4969714: PN7 3dpi mpeg1 mcherry R2; Danio rerio; RNA Seq,GSM4969714,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969714,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN7_L002_R1_001.fastq.gz PN7_L002_R2_001.fastq.gz,fastq fastq,6528184943.0,43245004.0,GSM4969714 r2,0:75.50 1:75.46,A:1862291360;C:977585295;G:1137753556;T:2549421996;N:1132736,75,75,,,1862291360,977585295,1137753556,2549421996,1132736,SRX9670473,SRS7869375,SRA1169931,GEO,The University of Melbourne,2,0.19676,0.71816,0.16378,0.43047,0.98938,0.84559,0.4879,0.53494,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62570,SRR13238448,SRX9670473,SRS7869375,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN7 3dpi mpeg1 mcherry R2,GSM4969714,,tissue:mpeg1 expressing macrophages|development stage:7 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:3,PN7 3dpi mpeg1 mcherry R2,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:7 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:3,GSM4969714,GSM4969714: PN7 3dpi mpeg1 mcherry R2; Danio rerio; RNA Seq,GSM4969714,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969714,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN7_L003_R1_001.fastq.gz PN7_L003_R2_001.fastq.gz,fastq fastq,6312954721.0,41820466.0,GSM4969714 r3,0:75.49 1:75.46,A:1801851943;C:946692024;G:1087319440;T:2476657942;N:433372,75,75,,,1801851943,946692024,1087319440,2476657942,433372,SRX9670473,SRS7869375,SRA1169931,GEO,The University of Melbourne,2,0.19676,0.71745,0.16319,0.42904,0.99295,0.84822,0.47188,0.52687,76,73,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62571,SRR13238449,SRX9670473,SRS7869375,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN7 3dpi mpeg1 mcherry R2,GSM4969714,,tissue:mpeg1 expressing macrophages|development stage:7 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:3,PN7 3dpi mpeg1 mcherry R2,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:7 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:3,GSM4969714,GSM4969714: PN7 3dpi mpeg1 mcherry R2; Danio rerio; RNA Seq,GSM4969714,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969714,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN7_L004_R1_001.fastq.gz PN7_L004_R2_001.fastq.gz,fastq fastq,6302598305.0,41751846.0,GSM4969714 r4,0:75.49 1:75.46,A:1794933968;C:941128970;G:1101536340;T:2464462858;N:536169,75,75,,,1794933968,941128970,1101536340,2464462858,536169,SRX9670473,SRS7869375,SRA1169931,GEO,The University of Melbourne,2,0.20948,0.71708,0.17441,0.42976,0.99137,0.84729,0.45996,0.53153,74,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62572,SRR13238442,SRX9670472,SRS7869374,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN5 1dpi mpeg1 mcherry R2,GSM4969713,,tissue:mpeg1 expressing macrophages|development stage:5 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:1,PN5 1dpi mpeg1 mcherry R2,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:5 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:1,GSM4969713,GSM4969713: PN5 1dpi mpeg1 mcherry R2; Danio rerio; RNA Seq,GSM4969713,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969713,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN5_L001_R1_001.fastq.gz PN5_L001_R2_001.fastq.gz,fastq fastq,2804071552.0,18580299.0,GSM4969713 r1,0:75.46 1:75.46,A:780538559;C:397784495;G:463784341;T:1161529955;N:434202,75,75,,,780538559,397784495,463784341,1161529955,434202,SRX9670472,SRS7869374,SRA1169931,GEO,The University of Melbourne,2,0.15961,0.76669,0.0903,0.2248,0.9903,0.85979,0.49059,0.54085,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62573,SRR13238443,SRX9670472,SRS7869374,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN5 1dpi mpeg1 mcherry R2,GSM4969713,,tissue:mpeg1 expressing macrophages|development stage:5 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:1,PN5 1dpi mpeg1 mcherry R2,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:5 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:1,GSM4969713,GSM4969713: PN5 1dpi mpeg1 mcherry R2; Danio rerio; RNA Seq,GSM4969713,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969713,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN5_L002_R1_001.fastq.gz PN5_L002_R2_001.fastq.gz,fastq fastq,2817528079.0,18667012.0,GSM4969713 r2,0:75.47 1:75.46,A:777879955;C:399565496;G:475237777;T:1164353068;N:491783,75,75,,,777879955,399565496,475237777,1164353068,491783,SRX9670472,SRS7869374,SRA1169931,GEO,The University of Melbourne,2,0.16708,0.7689,0.09701,0.22575,0.98963,0.86087,0.49215,0.54034,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62574,SRR13238444,SRX9670472,SRS7869374,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN5 1dpi mpeg1 mcherry R2,GSM4969713,,tissue:mpeg1 expressing macrophages|development stage:5 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:1,PN5 1dpi mpeg1 mcherry R2,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:5 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:1,GSM4969713,GSM4969713: PN5 1dpi mpeg1 mcherry R2; Danio rerio; RNA Seq,GSM4969713,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969713,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN5_L003_R1_001.fastq.gz PN5_L003_R2_001.fastq.gz,fastq fastq,2709779117.0,17953752.0,GSM4969713 r3,0:75.47 1:75.46,A:747919461;C:385238024;G:450429962;T:1126007119;N:184551,75,75,,,747919461,385238024,450429962,1126007119,184551,SRX9670472,SRS7869374,SRA1169931,GEO,The University of Melbourne,2,0.16104,0.7674,0.09406,0.22591,0.99235,0.86005,0.52979,0.51658,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62575,SRR13238445,SRX9670472,SRS7869374,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN5 1dpi mpeg1 mcherry R2,GSM4969713,,tissue:mpeg1 expressing macrophages|development stage:5 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:1,PN5 1dpi mpeg1 mcherry R2,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:5 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:1,GSM4969713,GSM4969713: PN5 1dpi mpeg1 mcherry R2; Danio rerio; RNA Seq,GSM4969713,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969713,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN5_L004_R1_001.fastq.gz PN5_L004_R2_001.fastq.gz,fastq fastq,2712637937.0,17972560.0,GSM4969713 r4,0:75.47 1:75.47,A:746503332;C:383902822;G:458791789;T:1123213585;N:226409,75,75,,,746503332,383902822,458791789,1123213585,226409,SRX9670472,SRS7869374,SRA1169931,GEO,The University of Melbourne,2,0.16976,0.76668,0.09686,0.22439,0.99054,0.86052,0.47154,0.53536,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62576,SRR13238438,SRX9670471,SRS7869373,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN4 3dpi mpeg1 mcherry R1,GSM4969712,,tissue:mpeg1 expressing macrophages|development stage:7 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:3,PN4 3dpi mpeg1 mcherry R1,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:7 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:3,GSM4969712,GSM4969712: PN4 3dpi mpeg1 mcherry R1; Danio rerio; RNA Seq,GSM4969712,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969712,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN4_L001_R1_001.fastq.gz PN4_L001_R2_001.fastq.gz,fastq fastq,1188135797.0,13884556.0,GSM4969712 r1,0:26 1:59.57,A:315958963;C:231575226;G:212680418;T:392625872;N:35295318,26,59,,,315958963,231575226,212680418,392625872,35295318,SRX9670471,SRS7869373,SRA1169931,GEO,The University of Melbourne,2,0.09037,0.64724,0.08438,0.52624,0.99046,0.94712,0.45562,0.48233,26,59,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62577,SRR13238439,SRX9670471,SRS7869373,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN4 3dpi mpeg1 mcherry R1,GSM4969712,,tissue:mpeg1 expressing macrophages|development stage:7 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:3,PN4 3dpi mpeg1 mcherry R1,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:7 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:3,GSM4969712,GSM4969712: PN4 3dpi mpeg1 mcherry R1; Danio rerio; RNA Seq,GSM4969712,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969712,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN4_L002_R1_001.fastq.gz PN4_L002_R2_001.fastq.gz,fastq fastq,1144513224.0,13373871.0,GSM4969712 r2,0:26 1:59.58,A:301945874;C:221045328;G:212388479;T:374986241;N:34147302,26,59,,,301945874,221045328,212388479,374986241,34147302,SRX9670471,SRS7869373,SRA1169931,GEO,The University of Melbourne,2,0.08887,0.6406,0.08286,0.52058,0.9907,0.94903,0.44936,0.4831,26,57,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62578,SRR13238440,SRX9670471,SRS7869373,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN4 3dpi mpeg1 mcherry R1,GSM4969712,,tissue:mpeg1 expressing macrophages|development stage:7 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:3,PN4 3dpi mpeg1 mcherry R1,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:7 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:3,GSM4969712,GSM4969712: PN4 3dpi mpeg1 mcherry R1; Danio rerio; RNA Seq,GSM4969712,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969712,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN4_L003_R1_001.fastq.gz PN4_L003_R2_001.fastq.gz,fastq fastq,1173422430.0,13712474.0,GSM4969712 r3,0:26 1:59.57,A:312225339;C:228926320;G:209623486;T:387242633;N:35404652,26,59,,,312225339,228926320,209623486,387242633,35404652,SRX9670471,SRS7869373,SRA1169931,GEO,The University of Melbourne,2,0.08927,0.64246,0.08325,0.52118,0.99076,0.94805,0.44477,0.48419,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62579,SRR13238441,SRX9670471,SRS7869373,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN4 3dpi mpeg1 mcherry R1,GSM4969712,,tissue:mpeg1 expressing macrophages|development stage:7 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:3,PN4 3dpi mpeg1 mcherry R1,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:7 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:3,GSM4969712,GSM4969712: PN4 3dpi mpeg1 mcherry R1; Danio rerio; RNA Seq,GSM4969712,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969712,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN4_L004_R1_001.fastq.gz PN4_L004_R2_001.fastq.gz,fastq fastq,1147622587.0,13410181.0,GSM4969712 r4,0:26 1:59.58,A:303224338;C:221709862;G:212063267;T:376057151;N:34567969,26,59,,,303224338,221709862,212063267,376057151,34567969,SRX9670471,SRS7869373,SRA1169931,GEO,The University of Melbourne,2,0.08878,0.63849,0.08271,0.51688,0.99066,0.9486,0.43689,0.47686,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62580,SRR13238434,SRX9670470,SRS7869372,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN3 2dpi mpeg1 mcherry R1,GSM4969711,,tissue:mpeg1 expressing macrophages|development stage:6 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:2,PN3 2dpi mpeg1 mcherry R1,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:6 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:2,GSM4969711,GSM4969711: PN3 2dpi mpeg1 mcherry R1; Danio rerio; RNA Seq,GSM4969711,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969711,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN3_L001_R1_001.fastq.gz PN3_L001_R2_001.fastq.gz,fastq fastq,3045940998.0,20182475.0,GSM4969711 r1,0:75.46 1:75.46,A:861591362;C:472200330;G:548416371;T:1163271404;N:461531,75,75,,,861591362,472200330,548416371,1163271404,461531,SRX9670470,SRS7869372,SRA1169931,GEO,The University of Melbourne,2,0.22646,0.71156,0.13481,0.24351,0.98184,0.85178,0.4659,0.56773,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62581,SRR13238435,SRX9670470,SRS7869372,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN3 2dpi mpeg1 mcherry R1,GSM4969711,,tissue:mpeg1 expressing macrophages|development stage:6 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:2,PN3 2dpi mpeg1 mcherry R1,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:6 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:2,GSM4969711,GSM4969711: PN3 2dpi mpeg1 mcherry R1; Danio rerio; RNA Seq,GSM4969711,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969711,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN3_L002_R1_001.fastq.gz PN3_L002_R2_001.fastq.gz,fastq fastq,3058134810.0,20261124.0,GSM4969711 r2,0:75.47 1:75.47,A:859026588;C:473360269;G:558456557;T:1166762411;N:528985,75,75,,,859026588,473360269,558456557,1166762411,528985,SRX9670470,SRS7869372,SRA1169931,GEO,The University of Melbourne,2,0.23705,0.71418,0.143,0.24407,0.9779,0.85224,0.49099,0.56732,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62582,SRR13238436,SRX9670470,SRS7869372,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN3 2dpi mpeg1 mcherry R1,GSM4969711,,tissue:mpeg1 expressing macrophages|development stage:6 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:2,PN3 2dpi mpeg1 mcherry R1,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:6 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:2,GSM4969711,GSM4969711: PN3 2dpi mpeg1 mcherry R1; Danio rerio; RNA Seq,GSM4969711,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969711,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN3_L003_R1_001.fastq.gz PN3_L003_R2_001.fastq.gz,fastq fastq,2937750186.0,19464119.0,GSM4969711 r3,0:75.46 1:75.47,A:826799903;C:453565630;G:532874749;T:1124319105;N:190799,75,75,,,826799903,453565630,532874749,1124319105,190799,SRX9670470,SRS7869372,SRA1169931,GEO,The University of Melbourne,2,0.22661,0.71083,0.13025,0.24386,0.98388,0.85214,0.48448,0.56575,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62583,SRR13238437,SRX9670470,SRS7869372,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN3 2dpi mpeg1 mcherry R1,GSM4969711,,tissue:mpeg1 expressing macrophages|development stage:6 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:2,PN3 2dpi mpeg1 mcherry R1,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:6 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:2,GSM4969711,GSM4969711: PN3 2dpi mpeg1 mcherry R1; Danio rerio; RNA Seq,GSM4969711,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969711,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN3_L004_R1_001.fastq.gz PN3_L004_R2_001.fastq.gz,fastq fastq,2947338266.0,19527523.0,GSM4969711 r4,0:75.46 1:75.47,A:826921712;C:453009451;G:543071709;T:1124092188;N:243206,75,75,,,826921712,453009451,543071709,1124092188,243206,SRX9670470,SRS7869372,SRA1169931,GEO,The University of Melbourne,2,0.23443,0.71193,0.13859,0.24106,0.98202,0.85202,0.44751,0.55877,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62584,SRR13238430,SRX9670469,SRS7869371,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN2 1dpi mpeg1 mcherry R1,GSM4969710,,tissue:mpeg1 expressing macrophages|development stage:5 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:1,PN2 1dpi mpeg1 mcherry R1,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:5 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:1,GSM4969710,GSM4969710: PN2 1dpi mpeg1 mcherry R1; Danio rerio; RNA Seq,GSM4969710,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969710,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN2_L001_R1_001.fastq.gz PN2_L001_R2_001.fastq.gz,fastq fastq,1737466730.0,20301987.0,GSM4969710 r1,0:26 1:59.58,A:422780101;C:341883160;G:323452885;T:619204653;N:30145931,26,59,,,422780101,341883160,323452885,619204653,30145931,SRX9670469,SRS7869371,SRA1169931,GEO,The University of Melbourne,2,0.01965,0.91425,0.01776,0.64626,0.9948,0.9124,0.50147,0.52977,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62585,SRR13238431,SRX9670469,SRS7869371,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN2 1dpi mpeg1 mcherry R1,GSM4969710,,tissue:mpeg1 expressing macrophages|development stage:5 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:1,PN2 1dpi mpeg1 mcherry R1,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:5 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:1,GSM4969710,GSM4969710: PN2 1dpi mpeg1 mcherry R1; Danio rerio; RNA Seq,GSM4969710,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969710,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN2_L002_R1_001.fastq.gz PN2_L002_R2_001.fastq.gz,fastq fastq,1683950505.0,19675642.0,GSM4969710 r2,0:26 1:59.59,A:406617443;C:329099407;G:322324098;T:596755074;N:29154483,26,59,,,406617443,329099407,322324098,596755074,29154483,SRX9670469,SRS7869371,SRA1169931,GEO,The University of Melbourne,2,0.0185,0.9085,0.01676,0.64398,0.99502,0.91364,0.50788,0.53846,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62586,SRR13238432,SRX9670469,SRS7869371,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN2 1dpi mpeg1 mcherry R1,GSM4969710,,tissue:mpeg1 expressing macrophages|development stage:5 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:1,PN2 1dpi mpeg1 mcherry R1,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:5 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:1,GSM4969710,GSM4969710: PN2 1dpi mpeg1 mcherry R1; Danio rerio; RNA Seq,GSM4969710,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969710,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN2_L003_R1_001.fastq.gz PN2_L003_R2_001.fastq.gz,fastq fastq,1715335402.0,20043345.0,GSM4969710 r3,0:26 1:59.58,A:417485809;C:337845935;G:318495667;T:611426599;N:30081392,26,59,,,417485809,337845935,318495667,611426599,30081392,SRX9670469,SRS7869371,SRA1169931,GEO,The University of Melbourne,2,0.01941,0.91463,0.01744,0.64848,0.9946,0.91313,0.47058,0.53898,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
62587,SRR13238433,SRX9670469,SRS7869371,SRP297552,PRJNA684129,Skeletal muscle injury responsive macrophage subsets in larval zebrafish,GSE162979,Transcriptome Analysis,Single cell RNA sequencing scRNA seq  was applied to identify and characterise macrophage subsets that responded to larval zebrafish muscle injury. The Tgmpeg1:mCherry transgenic zebrafish line was utilised to isolate mCherry expressing macrophages by FACS. Following needle stab muscle injury of a 4 dpf dpf larvae  the wound site was dissected out at 1  2  and 3 xxx post injury dpi for macrophage isolation. Macrophages isolated from 4 dpf uninjured larvae were also included. This analysis led to the identification of 8 discrete clusters of macrophages  one of which corresponded to uninjured macrophages. The 7 wound present macrophage subsets highlighted greater macrophage heterogeneity than previously described in an in vivo skeletal muscle injury context. Overall design: Total of 4 different time points were assayed  including a 4 dpf uninjured control and 3 time points during injury resolution 1 3 dpi.,,pubmed:33568815,,PN2 1dpi mpeg1 mcherry R1,GSM4969710,,tissue:mpeg1 expressing macrophages|development stage:5 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:1,PN2 1dpi mpeg1 mcherry R1,Paired reads were mapped against the zebrafish reference assembly version 9 Zv9 using bwa with a transcriptome dataset with improved 3’ UTR annotations to increase the mapability of transcripts. Read 1 was used for assigning reads to correct cells and libraries R1: 6 nt UMI + 8 nt cell barcode  while read 2 was mapped to gene models. The scripts to generate the count files can be found here https://github.com/vertesy/TheCorvinas/tree/master/Python/MapAndGo2 with the readme files found here https://github.com/vertesy/TheCorvinas/blob/master/Python/MapAndGo/Readme MapAndGo.md. Read counts were first corrected for UMI barcode by removing duplicate reads that had an identical combination of library  cellular and molecular barcodes that were mapped to the same gene. Transcript counts were then adjusted to the expected number of molecules based on counts  4096 possible UMI’s and Poissonian counting statistics. Genome build: Zv9 Supplementary files format and content: Each sample's cell transcript counts matrices are gzipped TSV files.  The sequencing facility did not provide cell barcode sequences for each cell ID.,mpeg1 expressing macrophages,4dpf larvae were anaesthetized in 0.01% tricaine in Ringer’s solution. Mechanical injures were targeted to the dorsal myotome above the cloaca when the larvae is oriented dorsal to the top  anterior to the left. The myotome was subjected to a single 30 gauge needle puncture that generates an extensive injury with many damaged muscle fibres.,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,All procedures involving animals at the Hubrecht Institute were approved by the local animal experiments committees and performed in compliance with animal welfare laws  guidelines and policies  according to national and European law. Staging and husbandry were performed using standard established and approved protocols. All embryos were maintained in Ringer’s solution at 28.5°C and treated with 0.003% 1 phenyl 2 thiourea PTU Sigma Aldrich from 8 hpf.,development stage:5 dpf|strain:TL|transgenic line:Tgmpeg1:mCherry|cell type:macrophages|treatment:injured muscle|xxx post injury:1,GSM4969710,GSM4969710: PN2 1dpi mpeg1 mcherry R1; Danio rerio; RNA Seq,GSM4969710,,1,Muscle injury region was dissected out and tissue dissociated into a single cell suspension. Whole larva were utilised for uninjured time point. Cells were sorted using a FACS Aria II BD biosciences. Live individual macrophages based on mCherry fluorescence  DAPI exclusion and forward and side scatter properties were sorted into pre prepared 384 well plates containing 100 200 nl of CEL seq primers  dNTPs and synthetic mRNA Spike Ins contained in 5 μl of Vapor Lock Qiagen. Immediately following sorting  plates were spun down and frozen at  80°C until sequencing. Single cell RNA sequencing libraries were prepared using the SORT seq platform. Here the Cel Seq2 protocol is followed with the aid of robotic liquid handlers. This protocol results in each cell being barcoded  and generating single cell transcriptomes of all isolated macrophages.,GEO Accession:GSM4969710,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP297552,,,PN2_L004_R1_001.fastq.gz PN2_L004_R2_001.fastq.gz,fastq fastq,1687227882.0,19713999.0,GSM4969710 r4,0:26 1:59.59,A:408029041;C:330002530;G:321413836;T:598268431;N:29514044,26,59,,,408029041,330002530,321413836,598268431,29514044,SRX9670469,SRS7869371,SRA1169931,GEO,The University of Melbourne,2,0.01885,0.90779,0.01704,0.64337,0.99492,0.91534,0.51524,0.54086,26,59,T,B,sc-like readlen,illumina,nextseq,unknown,random_priming,unknown,sc,single_cell_plate,celseq,,Australia,2020-12-10,Larval,Larval,Blood,Hematopoietic System
63272,SRR13724975,SRX10113008,SRS8268904,SRP306756,PRJNA702191,Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells,GSE166900,Transcriptome Analysis,Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated  using FACS sorting HSPCs were isolated and single cell RNA seq was performed.,,pubmed:33714985,,SBF 23,GSM5087787,,tissue:Caudal Hematopoietic Tissue|developmental stage:5dpf,SBF 23,"Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24   B1 to B24   until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing  Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode  cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber  2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün  Dominic  Lennart Kester  and Alexander Van Oudenaarden. ""Validation of noise models for single cell transcriptomics."" Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads  *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio",Caudal Hematopoietic Tissue,,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,,developmental stage:5dpf|sort day see plate layout:13|genotype or treatment see plate layout:LY294002 treated,GSM5087787,GSM5087787: SBF 23; Danio rerio; RNA Seq,GSM5087787,,1,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5087787,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306756,,,HUB-SF-023_HM5N7BGXC_S5_L001_R1_001.fastq.gz HUB-SF-023_HM5N7BGXC_S5_L001_R2_001.fastq.gz,fastq fastq,497476718.0,5784613.0,GSM5087787 r1,0:26 1:60,A:119810734;C:98970597;G:101956236;T:176037139;N:702012,26,60,,,119810734,98970597,101956236,176037139,702012,SRX10113008,SRS8268904,SRA1196923,GEO,Hubrecht Institute,2,0.09006,0.8442,0.08375,0.19753,0.99253,0.84589,0.68372,0.57253,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2021-02-16,Larval,Larval,Blood,Hematopoietic System
63273,SRR13724976,SRX10113008,SRS8268904,SRP306756,PRJNA702191,Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells,GSE166900,Transcriptome Analysis,Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated  using FACS sorting HSPCs were isolated and single cell RNA seq was performed.,,pubmed:33714985,,SBF 23,GSM5087787,,tissue:Caudal Hematopoietic Tissue|developmental stage:5dpf,SBF 23,"Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24   B1 to B24   until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing  Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode  cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber  2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün  Dominic  Lennart Kester  and Alexander Van Oudenaarden. ""Validation of noise models for single cell transcriptomics."" Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads  *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio",Caudal Hematopoietic Tissue,,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,,developmental stage:5dpf|sort day see plate layout:13|genotype or treatment see plate layout:LY294002 treated,GSM5087787,GSM5087787: SBF 23; Danio rerio; RNA Seq,GSM5087787,,1,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5087787,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306756,,,HUB-SF-023_HM5N7BGXC_S5_L002_R1_001.fastq.gz HUB-SF-023_HM5N7BGXC_S5_L002_R2_001.fastq.gz,fastq fastq,485306600.0,5643100.0,GSM5087787 r2,0:26 1:60,A:115996506;C:95759572;G:102194588;T:170746790;N:609144,26,60,,,115996506,95759572,102194588,170746790,609144,SRX10113008,SRS8268904,SRA1196923,GEO,Hubrecht Institute,2,0.09067,0.83684,0.08385,0.19289,0.9919,0.8477,0.67154,0.57449,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2021-02-16,Larval,Larval,Blood,Hematopoietic System
63274,SRR13724977,SRX10113008,SRS8268904,SRP306756,PRJNA702191,Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells,GSE166900,Transcriptome Analysis,Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated  using FACS sorting HSPCs were isolated and single cell RNA seq was performed.,,pubmed:33714985,,SBF 23,GSM5087787,,tissue:Caudal Hematopoietic Tissue|developmental stage:5dpf,SBF 23,"Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24   B1 to B24   until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing  Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode  cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber  2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün  Dominic  Lennart Kester  and Alexander Van Oudenaarden. ""Validation of noise models for single cell transcriptomics."" Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads  *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio",Caudal Hematopoietic Tissue,,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,,developmental stage:5dpf|sort day see plate layout:13|genotype or treatment see plate layout:LY294002 treated,GSM5087787,GSM5087787: SBF 23; Danio rerio; RNA Seq,GSM5087787,,1,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5087787,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306756,,,HUB-SF-023_HM5N7BGXC_S5_L003_R1_001.fastq.gz HUB-SF-023_HM5N7BGXC_S5_L003_R2_001.fastq.gz,fastq fastq,500039776.0,5814416.0,GSM5087787 r3,0:26 1:60,A:120392168;C:99507866;G:102641157;T:177069144;N:429441,26,60,,,120392168,99507866,102641157,177069144,429441,SRX10113008,SRS8268904,SRA1196923,GEO,Hubrecht Institute,2,0.09148,0.84686,0.0847,0.19685,0.99141,0.84753,0.65939,0.57293,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2021-02-16,Larval,Larval,Blood,Hematopoietic System
63275,SRR13724978,SRX10113008,SRS8268904,SRP306756,PRJNA702191,Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells,GSE166900,Transcriptome Analysis,Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated  using FACS sorting HSPCs were isolated and single cell RNA seq was performed.,,pubmed:33714985,,SBF 23,GSM5087787,,tissue:Caudal Hematopoietic Tissue|developmental stage:5dpf,SBF 23,"Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24   B1 to B24   until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing  Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode  cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber  2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün  Dominic  Lennart Kester  and Alexander Van Oudenaarden. ""Validation of noise models for single cell transcriptomics."" Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads  *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio",Caudal Hematopoietic Tissue,,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,,developmental stage:5dpf|sort day see plate layout:13|genotype or treatment see plate layout:LY294002 treated,GSM5087787,GSM5087787: SBF 23; Danio rerio; RNA Seq,GSM5087787,,1,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5087787,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306756,,,HUB-SF-023_HM5N7BGXC_S5_L004_R1_001.fastq.gz HUB-SF-023_HM5N7BGXC_S5_L004_R2_001.fastq.gz,fastq fastq,492861184.0,5730944.0,GSM5087787 r4,0:26 1:60,A:117758138;C:97299695;G:103802938;T:173573965;N:426448,26,60,,,117758138,97299695,103802938,173573965,426448,SRX10113008,SRS8268904,SRA1196923,GEO,Hubrecht Institute,2,0.09041,0.83933,0.0839,0.19275,0.99267,0.84723,0.63166,0.57545,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2021-02-16,Larval,Larval,Blood,Hematopoietic System
63276,SRR13724971,SRX10113007,SRS8268903,SRP306756,PRJNA702191,Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells,GSE166900,Transcriptome Analysis,Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated  using FACS sorting HSPCs were isolated and single cell RNA seq was performed.,,pubmed:33714985,,SBF 22,GSM5087786,,tissue:Caudal Hematopoietic Tissue|developmental stage:5dpf,SBF 22,"Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24   B1 to B24   until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing  Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode  cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber  2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün  Dominic  Lennart Kester  and Alexander Van Oudenaarden. ""Validation of noise models for single cell transcriptomics."" Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads  *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio",Caudal Hematopoietic Tissue,,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,,developmental stage:5dpf|sort day see plate layout:13|genotype or treatment see plate layout:LY294002 treated,GSM5087786,GSM5087786: SBF 22; Danio rerio; RNA Seq,GSM5087786,,1,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5087786,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306756,,,HUB-SF-022_HM5N7BGXC_S4_L001_R1_001.fastq.gz HUB-SF-022_HM5N7BGXC_S4_L001_R2_001.fastq.gz,fastq fastq,692152252.0,8048282.0,GSM5087786 r1,0:26 1:60,A:163624673;C:136146319;G:138410010;T:253002242;N:969008,26,60,,,163624673,136146319,138410010,253002242,969008,SRX10113007,SRS8268903,SRA1196923,GEO,Hubrecht Institute,2,0.1078,0.88463,0.09968,0.20723,0.9903,0.82254,0.61429,0.54857,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2021-02-16,Larval,Larval,Blood,Hematopoietic System
63277,SRR13724972,SRX10113007,SRS8268903,SRP306756,PRJNA702191,Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells,GSE166900,Transcriptome Analysis,Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated  using FACS sorting HSPCs were isolated and single cell RNA seq was performed.,,pubmed:33714985,,SBF 22,GSM5087786,,tissue:Caudal Hematopoietic Tissue|developmental stage:5dpf,SBF 22,"Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24   B1 to B24   until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing  Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode  cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber  2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün  Dominic  Lennart Kester  and Alexander Van Oudenaarden. ""Validation of noise models for single cell transcriptomics."" Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads  *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio",Caudal Hematopoietic Tissue,,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,,developmental stage:5dpf|sort day see plate layout:13|genotype or treatment see plate layout:LY294002 treated,GSM5087786,GSM5087786: SBF 22; Danio rerio; RNA Seq,GSM5087786,,1,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5087786,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306756,,,HUB-SF-022_HM5N7BGXC_S4_L002_R1_001.fastq.gz HUB-SF-022_HM5N7BGXC_S4_L002_R2_001.fastq.gz,fastq fastq,671222346.0,7804911.0,GSM5087786 r2,0:26 1:60,A:157709930;C:131021057;G:137587478;T:244048639;N:855242,26,60,,,157709930,131021057,137587478,244048639,855242,SRX10113007,SRS8268903,SRA1196923,GEO,Hubrecht Institute,2,0.10866,0.87439,0.10052,0.20141,0.9904,0.82546,0.61794,0.56015,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2021-02-16,Larval,Larval,Blood,Hematopoietic System
63278,SRR13724973,SRX10113007,SRS8268903,SRP306756,PRJNA702191,Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells,GSE166900,Transcriptome Analysis,Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated  using FACS sorting HSPCs were isolated and single cell RNA seq was performed.,,pubmed:33714985,,SBF 22,GSM5087786,,tissue:Caudal Hematopoietic Tissue|developmental stage:5dpf,SBF 22,"Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24   B1 to B24   until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing  Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode  cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber  2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün  Dominic  Lennart Kester  and Alexander Van Oudenaarden. ""Validation of noise models for single cell transcriptomics."" Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads  *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio",Caudal Hematopoietic Tissue,,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,,developmental stage:5dpf|sort day see plate layout:13|genotype or treatment see plate layout:LY294002 treated,GSM5087786,GSM5087786: SBF 22; Danio rerio; RNA Seq,GSM5087786,,1,Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols,GEO Accession:GSM5087786,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP306756,,,HUB-SF-022_HM5N7BGXC_S4_L003_R1_001.fastq.gz HUB-SF-022_HM5N7BGXC_S4_L003_R2_001.fastq.gz,fastq fastq,695196652.0,8083682.0,GSM5087786 r3,0:26 1:60,A:164311022;C:136759406;G:139356369;T:254166382;N:603473,26,60,,,164311022,136759406,139356369,254166382,603473,SRX10113007,SRS8268903,SRA1196923,GEO,Hubrecht Institute,2,0.10819,0.8846,0.1002,0.20578,0.99066,0.82343,0.62859,0.57036,26,60,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,celseq,,Netherlands,2021-02-16,Larval,Larval,Blood,Hematopoietic System