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
11130,ERR9979395,ERX9520370,ERS12499848,ERP139765,PRJEB54901,Single cell RNA sequencing of germ free zebrafish embryos,E-MTAB-11984,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,,Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 2 WT GO+BA,SAMEA110401656,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401656|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 2 WT GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 2 WT GO+BA|sex:not available|stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,E MTAB 11984:Sample 2 WT GO+BA p,Sample 2 WT GO+BA p,Single cell RNA sequencing of germ free zebrafish embryos,The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139765,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,P22202_7002_S2_L002_R1_001.fastq.gz P22202_7002_S2_L002_R2_001.fastq.gz,fastq fastq,18144406998.0,153766161.0,E MTAB 11984:P22202 7002 S2 L002,0:28 1:90,A:5277424121;C:3880928155;G:4118706097;T:4866649878;N:698747,28,90,,,5277424121,3880928155,4118706097,4866649878,698747,ERX9520370,ERS12499848,ERA16483151,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.0109,0.90145,0.0053,0.21373,0.98746,0.79423,0.41198,0.54447,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-22,Multi-stage,Embryo,Whole Organism,All anatomical structures
11131,ERR9979394,ERX9520370,ERS12499848,ERP139765,PRJEB54901,Single cell RNA sequencing of germ free zebrafish embryos,E-MTAB-11984,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,,Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 2 WT GO+BA,SAMEA110401656,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401656|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 2 WT GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 2 WT GO+BA|sex:not available|stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,E MTAB 11984:Sample 2 WT GO+BA p,Sample 2 WT GO+BA p,Single cell RNA sequencing of germ free zebrafish embryos,The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139765,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,P22202_7002_S2_L001_R1_001.fastq.gz P22202_7002_S2_L001_R2_001.fastq.gz,fastq fastq,18458951574.0,156431793.0,E MTAB 11984:P22202 7002 S2 L001,0:28 1:90,A:5372920926;C:3946687814;G:4185647697;T:4953205454;N:489683,28,90,,,5372920926,3946687814,4185647697,4953205454,489683,ERX9520370,ERS12499848,ERA16483151,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.01037,0.90168,0.0048,0.21246,0.98752,0.79297,0.42601,0.54996,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-22,Multi-stage,Embryo,Whole Organism,All anatomical structures
11132,ERR9979392,ERX9520369,ERS12499847,ERP139765,PRJEB54901,Single cell RNA sequencing of germ free zebrafish embryos,E-MTAB-11984,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,,Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 1 WT control,SAMEA110401655,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401655|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 1 WT control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 1 WT control|sex:not available|stimulus:n1|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,E MTAB 11984:Sample 1 WT control p,Sample 1 WT control p,Single cell RNA sequencing of germ free zebrafish embryos,The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:n1,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139765,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,P22202_7001_S1_L001_R1_001.fastq.gz P22202_7001_S1_L001_R2_001.fastq.gz,fastq fastq,19396994226.0,164381307.0,E MTAB 11984:P22202 7001 S1 L001,0:28 1:90,A:5665199484;C:4091196594;G:4415211076;T:5224866754;N:520318,28,90,,,5665199484,4091196594,4415211076,5224866754,520318,ERX9520369,ERS12499847,ERA16483151,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.01093,0.89238,0.00557,0.232,0.98764,0.79444,0.40806,0.54781,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-22,Multi-stage,Embryo,Whole Organism,All anatomical structures
11133,ERR9979393,ERX9520369,ERS12499847,ERP139765,PRJEB54901,Single cell RNA sequencing of germ free zebrafish embryos,E-MTAB-11984,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,,Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 1 WT control,SAMEA110401655,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401655|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 1 WT control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 1 WT control|sex:not available|stimulus:n1|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,E MTAB 11984:Sample 1 WT control p,Sample 1 WT control p,Single cell RNA sequencing of germ free zebrafish embryos,The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:n1,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139765,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,P22202_7001_S1_L002_R1_001.fastq.gz P22202_7001_S1_L002_R2_001.fastq.gz,fastq fastq,19063958224.0,161558968.0,E MTAB 11984:P22202 7001 S1 L002,0:28 1:90,A:5563588848;C:4022930643;G:4344549562;T:5132136743;N:752428,28,90,,,5563588848,4022930643,4344549562,5132136743,752428,ERX9520369,ERS12499847,ERA16483151,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.01118,0.89308,0.00573,0.23128,0.98737,0.79354,0.39264,0.54552,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-22,Multi-stage,Embryo,Whole Organism,All anatomical structures
11134,ERR9981089,ERX9522049,ERS12503451,ERP139797,PRJEB54930,Single cell RNA sequencing of lck GFP transgenic zebrafish,E-MTAB-11991,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,,Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 1 lck control,SAMEA110406305,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406305|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 1 lck control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 1 lck control|strain:Tglck:GFP,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,E MTAB 11991:Sample 1 lck control p,Sample 1 lck control p,Single cell RNA sequencing of lck GFP transgenic zebrafish,The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °,Experimental Factor: stimulus:n1,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139797,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,P25452_2002_S2_L001_R1_001.fastq.gz P25452_2002_S2_L001_R2_001.fastq.gz,fastq fastq,60177283876.0,509976982.0,E MTAB 11991:P25452 2002 S2 L001,0:28 1:90,A:17254566438;C:13547211711;G:14188233429;T:15185192817;N:2079481,28,90,,,17254566438,13547211711,14188233429,15185192817,2079481,ERX9522049,ERS12503451,ERA16488297,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.00671,0.93031,0.00231,0.11028,0.9932,0.82227,0.30887,0.58272,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-23,Larval,Larval,Whole Organism,All anatomical structures
11135,ERR9981090,ERX9522049,ERS12503451,ERP139797,PRJEB54930,Single cell RNA sequencing of lck GFP transgenic zebrafish,E-MTAB-11991,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,,Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 1 lck control,SAMEA110406305,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406305|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 1 lck control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 1 lck control|strain:Tglck:GFP,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,E MTAB 11991:Sample 1 lck control p,Sample 1 lck control p,Single cell RNA sequencing of lck GFP transgenic zebrafish,The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °,Experimental Factor: stimulus:n1,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139797,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,P25452_2002_S2_L002_R1_001.fastq.gz P25452_2002_S2_L002_R2_001.fastq.gz,fastq fastq,60597886144.0,513541408.0,E MTAB 11991:P25452 2002 S2 L002,0:28 1:90,A:17368154358;C:13649089056;G:14296037620;T:15282869484;N:1735626,28,90,,,17368154358,13649089056,14296037620,15282869484,1735626,ERX9522049,ERS12503451,ERA16488297,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.00656,0.92899,0.00211,0.11059,0.99334,0.82335,0.32311,0.57644,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-23,Larval,Larval,Whole Organism,All anatomical structures
11136,ERR9981087,ERX9522048,ERS12503450,ERP139797,PRJEB54930,Single cell RNA sequencing of lck GFP transgenic zebrafish,E-MTAB-11991,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,,Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 2 lck GO+BA,SAMEA110406304,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406304|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 2 lck GO+BA|strain:Tglck:GFP,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,E MTAB 11991:Sample 2 lck GO+BA p,Sample 2 lck GO+BA p,Single cell RNA sequencing of lck GFP transgenic zebrafish,The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:graphene oxide  30 microgram per milliliter|Experimental Factor: compound:butyrate|Experimental Factor: dose:2.5,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139797,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,P25452_2001_S1_L001_R1_001.fastq.gz P25452_2001_S1_L001_R2_001.fastq.gz,fastq fastq,20866120186.0,176831527.0,E MTAB 11991:P25452 2001 S1 L001,0:28 1:90,A:5933525376;C:4737179804;G:5025711080;T:5168983880;N:720046,28,90,,,5933525376,4737179804,5025711080,5168983880,720046,ERX9522048,ERS12503450,ERA16488297,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.00805,0.92622,0.00259,0.11842,0.99302,0.83027,0.2729,0.57699,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-23,Larval,Larval,Whole Organism,All anatomical structures
11137,ERR9981088,ERX9522048,ERS12503450,ERP139797,PRJEB54930,Single cell RNA sequencing of lck GFP transgenic zebrafish,E-MTAB-11991,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,,Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 2 lck GO+BA,SAMEA110406304,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406304|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 2 lck GO+BA|strain:Tglck:GFP,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,E MTAB 11991:Sample 2 lck GO+BA p,Sample 2 lck GO+BA p,Single cell RNA sequencing of lck GFP transgenic zebrafish,The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:graphene oxide  30 microgram per milliliter|Experimental Factor: compound:butyrate|Experimental Factor: dose:2.5,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139797,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,P25452_2001_S1_L002_R1_001.fastq.gz P25452_2001_S1_L002_R2_001.fastq.gz,fastq fastq,21068682172.0,178548154.0,E MTAB 11991:P25452 2001 S1 L002,0:28 1:90,A:5987758267;C:4786100132;G:5078292970;T:5215926275;N:604528,28,90,,,5987758267,4786100132,5078292970,5215926275,604528,ERX9522048,ERS12503450,ERA16488297,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.00813,0.92702,0.00264,0.11874,0.99283,0.82737,0.30228,0.56929,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-23,Larval,Larval,Whole Organism,All anatomical structures
15009,ERR12306826,ERX11683773,ERS17043893,ERP155237,PRJEB70303,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E-MTAB-13554,Transcriptome Analysis,To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,,Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,Coated,SAMEA114641726,KIS,ENA first public:2024 09 30|External Id:SAMEA114641726|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Coated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Coated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1,,,,,,,,,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E MTAB 13554:Coated p,Coated p,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP155237,NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,230324-Coated_S1_L003_I1_001.fastq.gz 230324-Coated_S1_L003_I2_001.fastq.gz 230324-Coated_S1_L003_R1_001.fastq.gz 230324-Coated_S1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,10050750400.0,62817190.0,E MTAB 13554:230324 Coated S1 L003,0:10 1:10 2:30 3:110,A:1894211982;C:1556769050;G:1595134885;T:1863244619;N:530364,10,10,30,110,1894211982,1556769050,1595134885,1863244619,530364,ERX11683773,ERS17043893,ERA27417303,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-11-20,Hatching,Embryo,Whole Organism,All anatomical structures
15010,ERR12306829,ERX11683773,ERS17043893,ERP155237,PRJEB70303,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E-MTAB-13554,Transcriptome Analysis,To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,,Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,Coated,SAMEA114641726,KIS,ENA first public:2024 09 30|External Id:SAMEA114641726|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Coated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Coated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1,,,,,,,,,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E MTAB 13554:Coated p,Coated p,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP155237,NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,230324-Coated_S1_L004_I1_001.fastq.gz 230324-Coated_S1_L004_I2_001.fastq.gz 230324-Coated_S1_L004_R1_001.fastq.gz 230324-Coated_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,9780757760.0,61129736.0,E MTAB 13554:230324 Coated S1 L004,0:10 1:10 2:30 3:110,A:1844808667;C:1516149264;G:1549838165;T:1813091860;N:383004,10,10,30,110,1844808667,1516149264,1549838165,1813091860,383004,ERX11683773,ERS17043893,ERA27417303,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-11-20,Hatching,Embryo,Whole Organism,All anatomical structures
15011,ERR12306828,ERX11683773,ERS17043893,ERP155237,PRJEB70303,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E-MTAB-13554,Transcriptome Analysis,To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,,Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,Coated,SAMEA114641726,KIS,ENA first public:2024 09 30|External Id:SAMEA114641726|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Coated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Coated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1,,,,,,,,,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E MTAB 13554:Coated p,Coated p,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP155237,NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,230324-Coated_S1_L002_I1_001.fastq.gz 230324-Coated_S1_L002_I2_001.fastq.gz 230324-Coated_S1_L002_R1_001.fastq.gz 230324-Coated_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9639368480.0,60246053.0,E MTAB 13554:230324 Coated S1 L002,0:10 1:10 2:30 3:110,A:1817388578;C:1494319441;G:1527564319;T:1787447672;N:345820,10,10,30,110,1817388578,1494319441,1527564319,1787447672,345820,ERX11683773,ERS17043893,ERA27417303,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-11-20,Hatching,Embryo,Whole Organism,All anatomical structures
15012,ERR12306832,ERX11683773,ERS17043893,ERP155237,PRJEB70303,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E-MTAB-13554,Transcriptome Analysis,To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,,Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,Coated,SAMEA114641726,KIS,ENA first public:2024 09 30|External Id:SAMEA114641726|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Coated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Coated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1,,,,,,,,,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E MTAB 13554:Coated p,Coated p,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP155237,NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,230324-Coated_S1_L001_I1_001.fastq.gz 230324-Coated_S1_L001_I2_001.fastq.gz 230324-Coated_S1_L001_R1_001.fastq.gz 230324-Coated_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,9823147840.0,61394674.0,E MTAB 13554:230324 Coated S1 L001,0:10 1:10 2:30 3:110,A:1851113558;C:1521671335;G:1558230628;T:1822067428;N:331191,10,10,30,110,1851113558,1521671335,1558230628,1822067428,331191,ERX11683773,ERS17043893,ERA27417303,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-11-20,Hatching,Embryo,Whole Organism,All anatomical structures
15013,ERR12306833,ERX11683774,ERS17043894,ERP155237,PRJEB70303,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E-MTAB-13554,Transcriptome Analysis,To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,,Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,Uncoated,SAMEA114641727,KIS,ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Uncoated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1,,,,,,,,,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E MTAB 13554:Uncoated p,Uncoated p,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP155237,NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,230324-Uncoated_S2_L001_I1_001.fastq.gz 230324-Uncoated_S2_L001_I2_001.fastq.gz 230324-Uncoated_S2_L001_R1_001.fastq.gz 230324-Uncoated_S2_L001_R2_001.fastq.gz,fastq fastq fastq fastq,8871716800.0,55448230.0,E MTAB 13554:230324 Uncoated S2 L001,0:10 1:10 2:30 3:110,A:1718985845;C:1319560520;G:1372197713;T:1688254655;N:306567,10,10,30,110,1718985845,1319560520,1372197713,1688254655,306567,ERX11683774,ERS17043894,ERA27417303,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-11-20,Hatching,Embryo,Whole Organism,All anatomical structures
15014,ERR12306830,ERX11683774,ERS17043894,ERP155237,PRJEB70303,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E-MTAB-13554,Transcriptome Analysis,To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,,Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,Uncoated,SAMEA114641727,KIS,ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Uncoated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1,,,,,,,,,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E MTAB 13554:Uncoated p,Uncoated p,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP155237,NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,230324-Uncoated_S2_L003_I1_001.fastq.gz 230324-Uncoated_S2_L003_I2_001.fastq.gz 230324-Uncoated_S2_L003_R1_001.fastq.gz 230324-Uncoated_S2_L003_R2_001.fastq.gz,fastq fastq fastq fastq,9075478720.0,56721742.0,E MTAB 13554:230324 Uncoated S2 L003,0:10 1:10 2:30 3:110,A:1758677834;C:1349774831;G:1404463433;T:1725994897;N:480625,10,10,30,110,1758677834,1349774831,1404463433,1725994897,480625,ERX11683774,ERS17043894,ERA27417303,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-11-20,Hatching,Embryo,Whole Organism,All anatomical structures
15015,ERR12306831,ERX11683774,ERS17043894,ERP155237,PRJEB70303,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E-MTAB-13554,Transcriptome Analysis,To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,,Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,Uncoated,SAMEA114641727,KIS,ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Uncoated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1,,,,,,,,,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E MTAB 13554:Uncoated p,Uncoated p,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP155237,NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,230324-Uncoated_S2_L002_I1_001.fastq.gz 230324-Uncoated_S2_L002_I2_001.fastq.gz 230324-Uncoated_S2_L002_R1_001.fastq.gz 230324-Uncoated_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,8705210880.0,54407568.0,E MTAB 13554:230324 Uncoated S2 L002,0:10 1:10 2:30 3:110,A:1687330583;C:1295837902;G:1345522657;T:1655826422;N:314916,10,10,30,110,1687330583,1295837902,1345522657,1655826422,314916,ERX11683774,ERS17043894,ERA27417303,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-11-20,Hatching,Embryo,Whole Organism,All anatomical structures
15016,ERR12306827,ERX11683774,ERS17043894,ERP155237,PRJEB70303,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E-MTAB-13554,Transcriptome Analysis,To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,,Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,Uncoated,SAMEA114641727,KIS,ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Uncoated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1,,,,,,,,,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,E MTAB 13554:Uncoated p,Uncoated p,10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 μm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurförsöksetiska nämnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100 nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3ʹ Reagent Kits v3.1 with 14 PCR cycles.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,NextSeq 550,,ERP155237,NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets,ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30,230324-Uncoated_S2_L004_I1_001.fastq.gz 230324-Uncoated_S2_L004_I2_001.fastq.gz 230324-Uncoated_S2_L004_R1_001.fastq.gz 230324-Uncoated_S2_L004_R2_001.fastq.gz,fastq fastq fastq fastq,8846203360.0,55288771.0,E MTAB 13554:230324 Uncoated S2 L004,0:10 1:10 2:30 3:110,A:1715100047;C:1316853239;G:1367208350;T:1682248092;N:355082,10,10,30,110,1715100047,1316853239,1367208350,1682248092,355082,ERX11683774,ERS17043894,ERA27417303,European Bioinformatics Institute|European Nucleotide Archive,European Bioinformatics Institute|European Nucleotide Archive,,,,,,,,,,,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-11-20,Hatching,Embryo,Whole Organism,All anatomical structures
24656,SRR25491963,SRX21223193,SRS18479996,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S12,GSM7676118,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S12,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676118,GSM7676118: KBTRE  cut  replicate S12; Danio rerio; RNA Seq,GSM7676118 r1,GSM7676118,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTREcut_S12_L001_R2_001.fastq.gz H27K5BCX2_KBTREcut_S12_L001_R1_001.fastq.gz H27K5BCX2_KBTREcut_S12_L001_I1_001.fastq.gz,fastq fastq fastq,664936140.0,5037395.0,GSM7676118 r1,0:8 1:26 2:98,A:143407233;C:100996340;G:110567290;T:138539687;N:154160,8,26,98,,143407233,100996340,110567290,138539687,154160,SRX21223193,SRS18479996,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91249,,0.11469,,0.85372,,0.50388,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24657,SRR25491964,SRX21223193,SRS18479996,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S12,GSM7676118,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S12,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676118,GSM7676118: KBTRE  cut  replicate S12; Danio rerio; RNA Seq,GSM7676118 r1,GSM7676118,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTREcut_S12_L001_R2_001.fastq.gz HFJ5GBCX2_KBTREcut_S12_L001_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S12_L001_I1_001.fastq.gz,fastq fastq fastq,645128748.0,4887339.0,GSM7676118 r2,0:8 1:26 2:98,A:139238913;C:98013961;G:107274566;T:134050699;N:381083,8,26,98,,139238913,98013961,107274566,134050699,381083,SRX21223193,SRS18479996,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91125,,0.11373,,0.85226,,0.50246,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24658,SRR25491965,SRX21223193,SRS18479996,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S12,GSM7676118,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S12,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676118,GSM7676118: KBTRE  cut  replicate S12; Danio rerio; RNA Seq,GSM7676118 r1,GSM7676118,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTREcut_S12_L001_I1_001.fastq.gz HYLGMBCXY_KBTREcut_S12_L001_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S12_L001_R2_001.fastq.gz,fastq fastq fastq,701173044.0,5311917.0,GSM7676118 r3,0:8 1:26 2:98,A:151296425;C:106327416;G:116370981;T:144230427;N:2342617,8,26,98,,151296425,106327416,116370981,144230427,2342617,SRX21223193,SRS18479996,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91082,,0.11168,,0.85245,,0.5097,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24659,SRR25491966,SRX21223193,SRS18479996,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S12,GSM7676118,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S12,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676118,GSM7676118: KBTRE  cut  replicate S12; Danio rerio; RNA Seq,GSM7676118 r1,GSM7676118,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTREcut_S12_L001_I1_001.fastq.gz HYWGVBCXY_KBTREcut_S12_L001_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S12_L001_R2_001.fastq.gz,fastq fastq fastq,656204604.0,4971247.0,GSM7676118 r4,0:8 1:26 2:98,A:141756368;C:99522317;G:109015686;T:136785011;N:102824,8,26,98,,141756368,99522317,109015686,136785011,102824,SRX21223193,SRS18479996,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.90953,,0.11383,,0.85212,,0.49917,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24660,SRR25492087,SRX21223193,SRS18479996,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S12,GSM7676118,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S12,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676118,GSM7676118: KBTRE  cut  replicate S12; Danio rerio; RNA Seq,GSM7676118 r1,GSM7676118,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTREcut_S12_L002_I1_001.fastq.gz H27K5BCX2_KBTREcut_S12_L002_R1_001.fastq.gz H27K5BCX2_KBTREcut_S12_L002_R2_001.fastq.gz,fastq fastq fastq,658691616.0,4990088.0,GSM7676118 r5,0:8 1:26 2:98,A:142071317;C:100089239;G:109564812;T:137176685;N:126571,8,26,98,,142071317,100089239,109564812,137176685,126571,SRX21223193,SRS18479996,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9118,,0.11359,,0.85307,,0.49119,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24661,SRR25492088,SRX21223193,SRS18479996,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S12,GSM7676118,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S12,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676118,GSM7676118: KBTRE  cut  replicate S12; Danio rerio; RNA Seq,GSM7676118 r1,GSM7676118,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTREcut_S12_L002_I1_001.fastq.gz HFJ5GBCX2_KBTREcut_S12_L002_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S12_L002_R2_001.fastq.gz,fastq fastq fastq,626035872.0,4742696.0,GSM7676118 r6,0:8 1:26 2:98,A:135079818;C:95138940;G:104158101;T:130050700;N:356649,8,26,98,,135079818,95138940,104158101,130050700,356649,SRX21223193,SRS18479996,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9103,,0.11494,,0.85378,,0.48986,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24662,SRR25492089,SRX21223193,SRS18479996,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S12,GSM7676118,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S12,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676118,GSM7676118: KBTRE  cut  replicate S12; Danio rerio; RNA Seq,GSM7676118 r1,GSM7676118,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTREcut_S12_L002_I1_001.fastq.gz HYLGMBCXY_KBTREcut_S12_L002_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S12_L002_R2_001.fastq.gz,fastq fastq fastq,693479028.0,5253629.0,GSM7676118 r7,0:8 1:26 2:98,A:149676332;C:105134718;G:115079858;T:142696573;N:2268161,8,26,98,,149676332,105134718,115079858,142696573,2268161,SRX21223193,SRS18479996,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91107,,0.11027,,0.85354,,0.50421,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24663,SRR25492090,SRX21223193,SRS18479996,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S12,GSM7676118,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S12,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676118,GSM7676118: KBTRE  cut  replicate S12; Danio rerio; RNA Seq,GSM7676118 r1,GSM7676118,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTREcut_S12_L002_R2_001.fastq.gz HYWGVBCXY_KBTREcut_S12_L002_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S12_L002_I1_001.fastq.gz,fastq fastq fastq,656957664.0,4976952.0,GSM7676118 r8,0:8 1:26 2:98,A:141922523;C:99627529;G:109167065;T:136992486;N:31693,8,26,98,,141922523,99627529,109167065,136992486,31693,SRX21223193,SRS18479996,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91107,,0.11379,,0.85346,,0.50695,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24664,SRR25491967,SRX21223192,SRS18479995,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S10,GSM7676116,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S10,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676116,GSM7676116: KBTRE  cut  replicate S10; Danio rerio; RNA Seq,GSM7676116 r1,GSM7676116,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTREcut_S10_L001_R2_001.fastq.gz H27K5BCX2_KBTREcut_S10_L001_R1_001.fastq.gz H27K5BCX2_KBTREcut_S10_L001_I1_001.fastq.gz,fastq fastq fastq,1062185256.0,8046858.0,GSM7676116 r1,0:8 1:26 2:98,A:230014489;C:161623855;G:176773666;T:219935294;N:244780,8,26,98,,230014489,161623855,176773666,219935294,244780,SRX21223192,SRS18479995,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91294,,0.11493,,0.85719,,0.50794,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24665,SRR25491968,SRX21223192,SRS18479995,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S10,GSM7676116,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S10,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676116,GSM7676116: KBTRE  cut  replicate S10; Danio rerio; RNA Seq,GSM7676116 r1,GSM7676116,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTREcut_S10_L001_R2_001.fastq.gz HFJ5GBCX2_KBTREcut_S10_L001_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S10_L001_I1_001.fastq.gz,fastq fastq fastq,1034539308.0,7837419.0,GSM7676116 r2,0:8 1:26 2:98,A:224616171;C:157304961;G:172084243;T:213455656;N:606031,8,26,98,,224616171,157304961,172084243,213455656,606031,SRX21223192,SRS18479995,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91287,,0.11588,,0.85415,,0.50804,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24666,SRR25491969,SRX21223192,SRS18479995,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S10,GSM7676116,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S10,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676116,GSM7676116: KBTRE  cut  replicate S10; Danio rerio; RNA Seq,GSM7676116 r1,GSM7676116,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTREcut_S10_L001_R2_001.fastq.gz HYLGMBCXY_KBTREcut_S10_L001_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S10_L001_I1_001.fastq.gz,fastq fastq fastq,1122858660.0,8506505.0,GSM7676116 r3,0:8 1:26 2:98,A:243355100;C:170483208;G:186449194;T:229601473;N:3748515,8,26,98,,243355100,170483208,186449194,229601473,3748515,SRX21223192,SRS18479995,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91213,,0.11262,,0.8561,,0.49742,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24667,SRR25491970,SRX21223192,SRS18479995,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S10,GSM7676116,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S10,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676116,GSM7676116: KBTRE  cut  replicate S10; Danio rerio; RNA Seq,GSM7676116 r1,GSM7676116,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTREcut_S10_L001_I1_001.fastq.gz HYWGVBCXY_KBTREcut_S10_L001_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S10_L001_R2_001.fastq.gz,fastq fastq fastq,1044506496.0,7912928.0,GSM7676116 r4,0:8 1:26 2:98,A:226413586;C:158757664;G:173768785;T:216364905;N:162004,8,26,98,,226413586,158757664,173768785,216364905,162004,SRX21223192,SRS18479995,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9121,,0.11332,,0.85401,,0.51062,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24668,SRR25491971,SRX21223192,SRS18479995,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S10,GSM7676116,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S10,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676116,GSM7676116: KBTRE  cut  replicate S10; Danio rerio; RNA Seq,GSM7676116 r1,GSM7676116,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTREcut_S10_L002_I1_001.fastq.gz HYLGMBCXY_KBTREcut_S10_L002_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S10_L002_R2_001.fastq.gz,fastq fastq fastq,1110246720.0,8410960.0,GSM7676116 r7,0:8 1:26 2:98,A:240787456;C:168521971;G:184254856;T:227029149;N:3680648,8,26,98,,240787456,168521971,184254856,227029149,3680648,SRX21223192,SRS18479995,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91246,,0.11301,,0.85449,,0.50422,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24669,SRR25491972,SRX21223192,SRS18479995,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S10,GSM7676116,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S10,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676116,GSM7676116: KBTRE  cut  replicate S10; Danio rerio; RNA Seq,GSM7676116 r1,GSM7676116,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTREcut_S10_L002_I1_001.fastq.gz HYWGVBCXY_KBTREcut_S10_L002_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S10_L002_R2_001.fastq.gz,fastq fastq fastq,1046026740.0,7924445.0,GSM7676116 r8,0:8 1:26 2:98,A:226911006;C:158976256;G:173939936;T:216718492;N:49920,8,26,98,,226911006,158976256,173939936,216718492,49920,SRX21223192,SRS18479995,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91267,,0.11377,,0.8548,,0.50065,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24670,SRR25491989,SRX21223192,SRS18479995,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S10,GSM7676116,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S10,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676116,GSM7676116: KBTRE  cut  replicate S10; Danio rerio; RNA Seq,GSM7676116 r1,GSM7676116,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTREcut_S10_L002_I1_001.fastq.gz H27K5BCX2_KBTREcut_S10_L002_R1_001.fastq.gz H27K5BCX2_KBTREcut_S10_L002_R2_001.fastq.gz,fastq fastq fastq,1052457252.0,7973161.0,GSM7676116 r5,0:8 1:26 2:98,A:227727118;C:160159228;G:175278732;T:218004542;N:200158,8,26,98,,227727118,160159228,175278732,218004542,200158,SRX21223192,SRS18479995,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91307,,0.11551,,0.85634,,0.50392,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24671,SRR25491990,SRX21223192,SRS18479995,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S10,GSM7676116,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S10,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676116,GSM7676116: KBTRE  cut  replicate S10; Danio rerio; RNA Seq,GSM7676116 r1,GSM7676116,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTREcut_S10_L002_I1_001.fastq.gz HFJ5GBCX2_KBTREcut_S10_L002_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S10_L002_R2_001.fastq.gz,fastq fastq fastq,1003744500.0,7604125.0,GSM7676116 r6,0:8 1:26 2:98,A:217741909;C:152712224;G:167110758;T:207073522;N:565837,8,26,98,,217741909,152712224,167110758,207073522,565837,SRX21223192,SRS18479995,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91357,,0.11506,,0.85504,,0.49763,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24672,SRR25491973,SRX21223191,SRS18479994,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S11,GSM7676117,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S11,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676117,GSM7676117: KBTRE  cut  replicate S11; Danio rerio; RNA Seq,GSM7676117 r1,GSM7676117,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTREcut_S11_L001_I1_001.fastq.gz H27K5BCX2_KBTREcut_S11_L001_R1_001.fastq.gz H27K5BCX2_KBTREcut_S11_L001_R2_001.fastq.gz,fastq fastq fastq,927688740.0,7027945.0,GSM7676117 r1,0:8 1:26 2:98,A:200105466;C:141029173;G:154321296;T:193068023;N:214652,8,26,98,,200105466,141029173,154321296,193068023,214652,SRX21223191,SRS18479994,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91282,,0.1155,,0.85283,,0.5061,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24673,SRR25491974,SRX21223191,SRS18479994,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S11,GSM7676117,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S11,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676117,GSM7676117: KBTRE  cut  replicate S11; Danio rerio; RNA Seq,GSM7676117 r1,GSM7676117,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTREcut_S11_L001_R2_001.fastq.gz HFJ5GBCX2_KBTREcut_S11_L001_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S11_L001_I1_001.fastq.gz,fastq fastq fastq,897789420.0,6801435.0,GSM7676117 r2,0:8 1:26 2:98,A:193853631;C:136435624;G:149320255;T:186400739;N:530381,8,26,98,,193853631,136435624,149320255,186400739,530381,SRX21223191,SRS18479994,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91186,,0.11485,,0.85429,,0.49592,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24674,SRR25491975,SRX21223191,SRS18479994,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S11,GSM7676117,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S11,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676117,GSM7676117: KBTRE  cut  replicate S11; Danio rerio; RNA Seq,GSM7676117 r1,GSM7676117,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTREcut_S11_L001_R2_001.fastq.gz HYLGMBCXY_KBTREcut_S11_L001_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S11_L001_I1_001.fastq.gz,fastq fastq fastq,978294372.0,7411321.0,GSM7676117 r3,0:8 1:26 2:98,A:211132117;C:148425540;G:162317813;T:201164320;N:3269668,8,26,98,,211132117,148425540,162317813,201164320,3269668,SRX21223191,SRS18479994,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91073,,0.1132,,0.8537,,0.50609,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24675,SRR25491976,SRX21223191,SRS18479994,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S11,GSM7676117,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S11,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676117,GSM7676117: KBTRE  cut  replicate S11; Danio rerio; RNA Seq,GSM7676117 r1,GSM7676117,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTREcut_S11_L001_I1_001.fastq.gz HYWGVBCXY_KBTREcut_S11_L001_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S11_L001_R2_001.fastq.gz,fastq fastq fastq,918264996.0,6956553.0,GSM7676117 r4,0:8 1:26 2:98,A:198352554;C:139394187;G:152576773;T:191275437;N:143243,8,26,98,,198352554,139394187,152576773,191275437,143243,SRX21223191,SRS18479994,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91014,,0.1139,,0.85307,,0.50536,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24676,SRR25491977,SRX21223191,SRS18479994,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S11,GSM7676117,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S11,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676117,GSM7676117: KBTRE  cut  replicate S11; Danio rerio; RNA Seq,GSM7676117 r1,GSM7676117,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTREcut_S11_L002_I1_001.fastq.gz H27K5BCX2_KBTREcut_S11_L002_R1_001.fastq.gz H27K5BCX2_KBTREcut_S11_L002_R2_001.fastq.gz,fastq fastq fastq,918134580.0,6955565.0,GSM7676117 r5,0:8 1:26 2:98,A:198094257;C:139568875;G:152735838;T:191072590;N:173810,8,26,98,,198094257,139568875,152735838,191072590,173810,SRX21223191,SRS18479994,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91196,,0.11403,,0.85267,,0.50361,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24677,SRR25491978,SRX21223191,SRS18479994,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S11,GSM7676117,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S11,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676117,GSM7676117: KBTRE  cut  replicate S11; Danio rerio; RNA Seq,GSM7676117 r1,GSM7676117,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTREcut_S11_L002_I1_001.fastq.gz HFJ5GBCX2_KBTREcut_S11_L002_R1_001.fastq.gz HFJ5GBCX2_KBTREcut_S11_L002_R2_001.fastq.gz,fastq fastq fastq,868525152.0,6579736.0,GSM7676117 r6,0:8 1:26 2:98,A:187572958;C:132014722;G:144495273;T:180237409;N:493766,8,26,98,,187572958,132014722,144495273,180237409,493766,SRX21223191,SRS18479994,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91049,,0.11265,,0.85273,,0.49392,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24678,SRR25491979,SRX21223191,SRS18479994,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S11,GSM7676117,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S11,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676117,GSM7676117: KBTRE  cut  replicate S11; Danio rerio; RNA Seq,GSM7676117 r1,GSM7676117,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTREcut_S11_L002_I1_001.fastq.gz HYLGMBCXY_KBTREcut_S11_L002_R1_001.fastq.gz HYLGMBCXY_KBTREcut_S11_L002_R2_001.fastq.gz,fastq fastq fastq,967222872.0,7327446.0,GSM7676117 r7,0:8 1:26 2:98,A:208757589;C:146699883;G:160504752;T:198933585;N:3193899,8,26,98,,208757589,146699883,160504752,198933585,3193899,SRX21223191,SRS18479994,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91068,,0.11108,,0.85449,,0.48271,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24679,SRR25491980,SRX21223191,SRS18479994,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  cut  replicate S11,GSM7676117,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  cut  replicate S11,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676117,GSM7676117: KBTRE  cut  replicate S11; Danio rerio; RNA Seq,GSM7676117 r1,GSM7676117,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTREcut_S11_L002_I1_001.fastq.gz HYWGVBCXY_KBTREcut_S11_L002_R1_001.fastq.gz HYWGVBCXY_KBTREcut_S11_L002_R2_001.fastq.gz,fastq fastq fastq,918366636.0,6957323.0,GSM7676117 r8,0:8 1:26 2:98,A:198420992;C:139446089;G:152636322;T:191270874;N:43377,8,26,98,,198420992,139446089,152636322,191270874,43377,SRX21223191,SRS18479994,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.91125,,0.11279,,0.85212,,0.49708,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24680,SRR25491981,SRX21223190,SRS18479993,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S8,GSM7676115,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S8,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676115,GSM7676115: KBTGR  normal  replicate S8; Danio rerio; RNA Seq,GSM7676115 r1,GSM7676115,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRnormal_S8_L001_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S8_L001_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S8_L001_R2_001.fastq.gz,fastq fastq fastq,1367764332.0,10361851.0,GSM7676115 r1,0:8 1:26 2:98,A:291792120;C:211871917;G:233940380;T:277543215;N:313766,8,26,98,,291792120,211871917,233940380,277543215,313766,SRX21223190,SRS18479993,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92841,,0.09159,,0.82191,,0.48306,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24681,SRR25491982,SRX21223190,SRS18479993,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S8,GSM7676115,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S8,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676115,GSM7676115: KBTGR  normal  replicate S8; Danio rerio; RNA Seq,GSM7676115 r1,GSM7676115,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRnormal_S8_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S8_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S8_L001_R2_001.fastq.gz,fastq fastq fastq,1324750284.0,10035987.0,GSM7676115 r2,0:8 1:26 2:98,A:282670428;C:205193043;G:226649784;T:268220709;N:792762,8,26,98,,282670428,205193043,226649784,268220709,792762,SRX21223190,SRS18479993,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92859,,0.09205,,0.82039,,0.48039,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24682,SRR25491983,SRX21223190,SRS18479993,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S8,GSM7676115,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S8,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676115,GSM7676115: KBTGR  normal  replicate S8; Danio rerio; RNA Seq,GSM7676115 r1,GSM7676115,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRnormal_S8_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S8_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S8_L001_R2_001.fastq.gz,fastq fastq fastq,1442154120.0,10925410.0,GSM7676115 r3,0:8 1:26 2:98,A:307172615;C:223150292;G:246311885;T:289234193;N:4821195,8,26,98,,307172615,223150292,246311885,289234193,4821195,SRX21223190,SRS18479993,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92841,,0.08941,,0.82331,,0.49215,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24683,SRR25491984,SRX21223190,SRS18479993,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S8,GSM7676115,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S8,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676115,GSM7676115: KBTGR  normal  replicate S8; Danio rerio; RNA Seq,GSM7676115 r1,GSM7676115,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRnormal_S8_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S8_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S8_L001_R2_001.fastq.gz,fastq fastq fastq,1358634684.0,10292687.0,GSM7676115 r4,0:8 1:26 2:98,A:290016958;C:210290529;G:232317191;T:275847772;N:210876,8,26,98,,290016958,210290529,232317191,275847772,210876,SRX21223190,SRS18479993,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92745,,0.09192,,0.82229,,0.49666,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24684,SRR25491985,SRX21223190,SRS18479993,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S8,GSM7676115,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S8,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676115,GSM7676115: KBTGR  normal  replicate S8; Danio rerio; RNA Seq,GSM7676115 r1,GSM7676115,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRnormal_S8_L002_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S8_L002_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S8_L002_R2_001.fastq.gz,fastq fastq fastq,1353664092.0,10255031.0,GSM7676115 r5,0:8 1:26 2:98,A:288847376;C:209739068;G:231593033;T:274552362;N:261199,8,26,98,,288847376,209739068,231593033,274552362,261199,SRX21223190,SRS18479993,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92838,,0.09211,,0.82207,,0.48301,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24685,SRR25491986,SRX21223190,SRS18479993,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S8,GSM7676115,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S8,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676115,GSM7676115: KBTGR  normal  replicate S8; Danio rerio; RNA Seq,GSM7676115 r1,GSM7676115,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRnormal_S8_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S8_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S8_L002_R2_001.fastq.gz,fastq fastq fastq,1282964496.0,9719428.0,GSM7676115 r6,0:8 1:26 2:98,A:273803342;C:198769671;G:219587842;T:259615174;N:727915,8,26,98,,273803342,198769671,219587842,259615174,727915,SRX21223190,SRS18479993,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92815,,0.09094,,0.82189,,0.47933,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24686,SRR25491987,SRX21223190,SRS18479993,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S8,GSM7676115,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S8,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676115,GSM7676115: KBTGR  normal  replicate S8; Danio rerio; RNA Seq,GSM7676115 r1,GSM7676115,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRnormal_S8_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S8_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S8_L002_R2_001.fastq.gz,fastq fastq fastq,1425314880.0,10797840.0,GSM7676115 r7,0:8 1:26 2:98,A:303654013;C:220453444;G:243409971;T:285937241;N:4733651,8,26,98,,303654013,220453444,243409971,285937241,4733651,SRX21223190,SRS18479993,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92724,,0.09059,,0.82345,,0.49626,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24687,SRR25491988,SRX21223190,SRS18479993,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S8,GSM7676115,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S8,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676115,GSM7676115: KBTGR  normal  replicate S8; Danio rerio; RNA Seq,GSM7676115 r1,GSM7676115,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRnormal_S8_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S8_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S8_L002_R2_001.fastq.gz,fastq fastq fastq,1358584788.0,10292309.0,GSM7676115 r8,0:8 1:26 2:98,A:290131069;C:210271668;G:232237599;T:275940105;N:65841,8,26,98,,290131069,210271668,232237599,275940105,65841,SRX21223190,SRS18479993,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92858,,0.09144,,0.82089,,0.49057,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24688,SRR25491991,SRX21223189,SRS18479992,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S7,GSM7676114,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S7,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676114,GSM7676114: KBTGR  normal  replicate S7; Danio rerio; RNA Seq,GSM7676114 r1,GSM7676114,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRnormal_S7_L001_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S7_L001_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S7_L001_R2_001.fastq.gz,fastq fastq fastq,1045774224.0,7922532.0,GSM7676114 r1,0:8 1:26 2:98,A:224743708;C:161896286;G:178467180;T:211061243;N:239719,8,26,98,,224743708,161896286,178467180,211061243,239719,SRX21223189,SRS18479992,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92898,,0.0948,,0.82576,,0.48767,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24689,SRR25491992,SRX21223189,SRS18479992,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S7,GSM7676114,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S7,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676114,GSM7676114: KBTGR  normal  replicate S7; Danio rerio; RNA Seq,GSM7676114 r1,GSM7676114,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRnormal_S7_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S7_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S7_L001_R2_001.fastq.gz,fastq fastq fastq,1023737880.0,7755590.0,GSM7676114 r2,0:8 1:26 2:98,A:220339751;C:158506697;G:174717320;T:205879340;N:604712,8,26,98,,220339751,158506697,174717320,205879340,604712,SRX21223189,SRS18479992,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.93138,,0.09445,,0.82319,,0.49095,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24690,SRR25491993,SRX21223189,SRS18479992,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S7,GSM7676114,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S7,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676114,GSM7676114: KBTGR  normal  replicate S7; Danio rerio; RNA Seq,GSM7676114 r1,GSM7676114,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRnormal_S7_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S7_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S7_L001_R2_001.fastq.gz,fastq fastq fastq,1107722484.0,8391837.0,GSM7676114 r3,0:8 1:26 2:98,A:237628383;C:171310823;G:188847113;T:220892571;N:3721136,8,26,98,,237628383,171310823,188847113,220892571,3721136,SRX21223189,SRS18479992,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92932,,0.09165,,0.82432,,0.48843,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24691,SRR25491994,SRX21223189,SRS18479992,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S7,GSM7676114,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S7,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676114,GSM7676114: KBTGR  normal  replicate S7; Danio rerio; RNA Seq,GSM7676114 r1,GSM7676114,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRnormal_S7_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S7_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S7_L001_R2_001.fastq.gz,fastq fastq fastq,1018155600.0,7713300.0,GSM7676114 r4,0:8 1:26 2:98,A:218785960;C:157467573;G:173782025;T:205710180;N:157662,8,26,98,,218785960,157467573,173782025,205710180,157662,SRX21223189,SRS18479992,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92735,,0.09294,,0.82304,,0.48936,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24692,SRR25491995,SRX21223189,SRS18479992,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S7,GSM7676114,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S7,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676114,GSM7676114: KBTGR  normal  replicate S7; Danio rerio; RNA Seq,GSM7676114 r1,GSM7676114,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRnormal_S7_L002_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S7_L002_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S7_L002_R2_001.fastq.gz,fastq fastq fastq,1037896992.0,7862856.0,GSM7676114 r5,0:8 1:26 2:98,A:222624793;C:160770752;G:177337819;T:209629234;N:197290,8,26,98,,222624793,160770752,177337819,209629234,197290,SRX21223189,SRS18479992,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.93038,,0.09291,,0.82513,,0.48834,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24693,SRR25491996,SRX21223189,SRS18479992,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S7,GSM7676114,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S7,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676114,GSM7676114: KBTGR  normal  replicate S7; Danio rerio; RNA Seq,GSM7676114 r1,GSM7676114,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRnormal_S7_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S7_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S7_L002_R2_001.fastq.gz,fastq fastq fastq,994648116.0,7535213.0,GSM7676114 r6,0:8 1:26 2:98,A:213918528;C:154046950;G:169913173;T:200006956;N:565267,8,26,98,,213918528,154046950,169913173,200006956,565267,SRX21223189,SRS18479992,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92863,,0.09237,,0.8244,,0.48574,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24694,SRR25491997,SRX21223189,SRS18479992,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S7,GSM7676114,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S7,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676114,GSM7676114: KBTGR  normal  replicate S7; Danio rerio; RNA Seq,GSM7676114 r1,GSM7676114,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRnormal_S7_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S7_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S7_L002_R2_001.fastq.gz,fastq fastq fastq,1095910068.0,8302349.0,GSM7676114 r7,0:8 1:26 2:98,A:235361030;C:169424678;G:186752468;T:218466797;N:3625229,8,26,98,,235361030,169424678,186752468,218466797,3625229,SRX21223189,SRS18479992,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92887,,0.09019,,0.82696,,0.4934,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24695,SRR25491998,SRX21223189,SRS18479992,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S7,GSM7676114,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S7,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676114,GSM7676114: KBTGR  normal  replicate S7; Danio rerio; RNA Seq,GSM7676114 r1,GSM7676114,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRnormal_S7_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S7_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S7_L002_R2_001.fastq.gz,fastq fastq fastq,1020164640.0,7728520.0,GSM7676114 r8,0:8 1:26 2:98,A:219455597;C:157669416;G:174033845;T:206187545;N:48557,8,26,98,,219455597,157669416,174033845,206187545,48557,SRX21223189,SRS18479992,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.93,,0.0929,,0.82507,,0.48822,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24696,SRR25491999,SRX21223188,SRS18479991,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S6,GSM7676113,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S6,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676113,GSM7676113: KBTGR  normal  replicate S6; Danio rerio; RNA Seq,GSM7676113 r1,GSM7676113,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRnormal_S6_L001_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S6_L001_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S6_L001_R2_001.fastq.gz,fastq fastq fastq,1289409660.0,9768255.0,GSM7676113 r1,0:8 1:26 2:98,A:275297633;C:199461255;G:220403674;T:261830960;N:295468,8,26,98,,275297633,199461255,220403674,261830960,295468,SRX21223188,SRS18479991,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92761,,0.09178,,0.82089,,0.49952,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24697,SRR25492000,SRX21223188,SRS18479991,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S6,GSM7676113,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S6,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676113,GSM7676113: KBTGR  normal  replicate S6; Danio rerio; RNA Seq,GSM7676113 r1,GSM7676113,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRnormal_S6_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S6_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S6_L001_R2_001.fastq.gz,fastq fastq fastq,1254104148.0,9500789.0,GSM7676113 r2,0:8 1:26 2:98,A:267759276;C:194047461;G:214469796;T:254057804;N:742985,8,26,98,,267759276,194047461,214469796,254057804,742985,SRX21223188,SRS18479991,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92863,,0.09263,,0.82016,,0.49849,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24698,SRR25492001,SRX21223188,SRS18479991,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S6,GSM7676113,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S6,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676113,GSM7676113: KBTGR  normal  replicate S6; Danio rerio; RNA Seq,GSM7676113 r1,GSM7676113,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRnormal_S6_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S6_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S6_L001_R2_001.fastq.gz,fastq fastq fastq,1364037444.0,10333617.0,GSM7676113 r3,0:8 1:26 2:98,A:290782963;C:210764004;G:232828321;T:273741440;N:4577738,8,26,98,,290782963,210764004,232828321,273741440,4577738,SRX21223188,SRS18479991,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92727,,0.09037,,0.82339,,0.49743,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24699,SRR25492002,SRX21223188,SRS18479991,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S6,GSM7676113,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S6,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676113,GSM7676113: KBTGR  normal  replicate S6; Danio rerio; RNA Seq,GSM7676113 r1,GSM7676113,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRnormal_S6_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S6_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S6_L001_R2_001.fastq.gz,fastq fastq fastq,1274535900.0,9655575.0,GSM7676113 r4,0:8 1:26 2:98,A:272331035;C:196919570;G:217674747;T:259126322;N:194676,8,26,98,,272331035,196919570,217674747,259126322,194676,SRX21223188,SRS18479991,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9267,,0.09131,,0.82193,,0.49736,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24700,SRR25492003,SRX21223188,SRS18479991,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S6,GSM7676113,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S6,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676113,GSM7676113: KBTGR  normal  replicate S6; Danio rerio; RNA Seq,GSM7676113 r1,GSM7676113,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRnormal_S6_L002_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S6_L002_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S6_L002_R2_001.fastq.gz,fastq fastq fastq,1278788544.0,9687792.0,GSM7676113 r5,0:8 1:26 2:98,A:273089526;C:197794682;G:218629305;T:259640660;N:249443,8,26,98,,273089526,197794682,218629305,259640660,249443,SRX21223188,SRS18479991,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92837,,0.09211,,0.82069,,0.49043,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24701,SRR25492004,SRX21223188,SRS18479991,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S6,GSM7676113,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S6,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676113,GSM7676113: KBTGR  normal  replicate S6; Danio rerio; RNA Seq,GSM7676113 r1,GSM7676113,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRnormal_S6_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S6_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S6_L002_R2_001.fastq.gz,fastq fastq fastq,1218538200.0,9231350.0,GSM7676113 r6,0:8 1:26 2:98,A:260174350;C:188588952;G:208442781;T:246771528;N:694689,8,26,98,,260174350,188588952,208442781,246771528,694689,SRX21223188,SRS18479991,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92755,,0.09174,,0.82152,,0.48524,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24702,SRR25492005,SRX21223188,SRS18479991,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S6,GSM7676113,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S6,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676113,GSM7676113: KBTGR  normal  replicate S6; Danio rerio; RNA Seq,GSM7676113 r1,GSM7676113,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRnormal_S6_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S6_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S6_L002_R2_001.fastq.gz,fastq fastq fastq,1348885428.0,10218829.0,GSM7676113 r7,0:8 1:26 2:98,A:287599265;C:208361077;G:230218011;T:270815023;N:4451866,8,26,98,,287599265,208361077,230218011,270815023,4451866,SRX21223188,SRS18479991,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92616,,0.08938,,0.82189,,0.49517,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24703,SRR25492006,SRX21223188,SRS18479991,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S6,GSM7676113,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S6,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676113,GSM7676113: KBTGR  normal  replicate S6; Danio rerio; RNA Seq,GSM7676113 r1,GSM7676113,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRnormal_S6_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S6_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S6_L002_R2_001.fastq.gz,fastq fastq fastq,1274044596.0,9651853.0,GSM7676113 r8,0:8 1:26 2:98,A:272274110;C:196868273;G:217614843;T:259062639;N:61729,8,26,98,,272274110,196868273,217614843,259062639,61729,SRX21223188,SRS18479991,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92673,,0.09105,,0.82142,,0.48867,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24704,SRR25492007,SRX21223187,SRS18479990,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S5,GSM7676112,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S5,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676112,GSM7676112: KBTGR  normal  replicate S5; Danio rerio; RNA Seq,GSM7676112 r1,GSM7676112,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRnormal_S5_L001_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S5_L001_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S5_L001_R2_001.fastq.gz,fastq fastq fastq,1258754244.0,9536017.0,GSM7676112 r1,0:8 1:26 2:98,A:269418553;C:194370105;G:214652075;T:255806804;N:282129,8,26,98,,269418553,194370105,214652075,255806804,282129,SRX21223187,SRS18479990,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9286,,0.09296,,0.82288,,0.48038,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24705,SRR25492008,SRX21223187,SRS18479990,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S5,GSM7676112,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S5,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676112,GSM7676112: KBTGR  normal  replicate S5; Danio rerio; RNA Seq,GSM7676112 r1,GSM7676112,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRnormal_S5_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S5_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S5_L001_R2_001.fastq.gz,fastq fastq fastq,1217159724.0,9220907.0,GSM7676112 r2,0:8 1:26 2:98,A:260789467;C:187945962;G:207550436;T:246642449;N:720572,8,26,98,,260789467,187945962,207550436,246642449,720572,SRX21223187,SRS18479990,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.93045,,0.09356,,0.82386,,0.4736,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24706,SRR25492009,SRX21223187,SRS18479990,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S5,GSM7676112,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S5,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676112,GSM7676112: KBTGR  normal  replicate S5; Danio rerio; RNA Seq,GSM7676112 r1,GSM7676112,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRnormal_S5_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S5_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S5_L001_R2_001.fastq.gz,fastq fastq fastq,1327996824.0,10060582.0,GSM7676112 r3,0:8 1:26 2:98,A:283722392;C:204894097;G:226054109;T:266823827;N:4442611,8,26,98,,283722392,204894097,226054109,266823827,4442611,SRX21223187,SRS18479990,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92793,,0.09118,,0.82513,,0.48007,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24707,SRR25492010,SRX21223187,SRS18479990,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S5,GSM7676112,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S5,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676112,GSM7676112: KBTGR  normal  replicate S5; Danio rerio; RNA Seq,GSM7676112 r1,GSM7676112,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRnormal_S5_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S5_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S5_L001_R2_001.fastq.gz,fastq fastq fastq,1255655808.0,9512544.0,GSM7676112 r4,0:8 1:26 2:98,A:268848025;C:193752306;G:214061624;T:255371933;N:195424,8,26,98,,268848025,193752306,214061624,255371933,195424,SRX21223187,SRS18479990,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92719,,0.09327,,0.82221,,0.47626,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24708,SRR25492011,SRX21223187,SRS18479990,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S5,GSM7676112,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S5,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676112,GSM7676112: KBTGR  normal  replicate S5; Danio rerio; RNA Seq,GSM7676112 r1,GSM7676112,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRnormal_S5_L002_I1_001.fastq.gz H27K5BCX2_KBTGRnormal_S5_L002_R1_001.fastq.gz H27K5BCX2_KBTGRnormal_S5_L002_R2_001.fastq.gz,fastq fastq fastq,1246449072.0,9442796.0,GSM7676112 r5,0:8 1:26 2:98,A:266772235;C:192514744;G:212592908;T:253285733;N:228388,8,26,98,,266772235,192514744,212592908,253285733,228388,SRX21223187,SRS18479990,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92776,,0.09295,,0.82333,,0.48441,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24709,SRR25492012,SRX21223187,SRS18479990,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S5,GSM7676112,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S5,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676112,GSM7676112: KBTGR  normal  replicate S5; Danio rerio; RNA Seq,GSM7676112 r1,GSM7676112,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRnormal_S5_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S5_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRnormal_S5_L002_R2_001.fastq.gz,fastq fastq fastq,1176943812.0,8916241.0,GSM7676112 r6,0:8 1:26 2:98,A:252114687;C:181782204;G:200782194;T:238444957;N:667576,8,26,98,,252114687,181782204,200782194,238444957,667576,SRX21223187,SRS18479990,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92798,,0.09407,,0.82225,,0.47898,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24710,SRR25492013,SRX21223187,SRS18479990,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S5,GSM7676112,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S5,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676112,GSM7676112: KBTGR  normal  replicate S5; Danio rerio; RNA Seq,GSM7676112 r1,GSM7676112,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRnormal_S5_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S5_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRnormal_S5_L002_R2_001.fastq.gz,fastq fastq fastq,1312162368.0,9940624.0,GSM7676112 r7,0:8 1:26 2:98,A:280415120;C:202362829;G:223408996;T:263680714;N:4313493,8,26,98,,280415120,202362829,223408996,263680714,4313493,SRX21223187,SRS18479990,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9269,,0.09153,,0.82386,,0.48775,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24711,SRR25492014,SRX21223187,SRS18479990,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  normal  replicate S5,GSM7676112,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  normal  replicate S5,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676112,GSM7676112: KBTGR  normal  replicate S5; Danio rerio; RNA Seq,GSM7676112 r1,GSM7676112,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRnormal_S5_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S5_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRnormal_S5_L002_R2_001.fastq.gz,fastq fastq fastq,1254798732.0,9506051.0,GSM7676112 r8,0:8 1:26 2:98,A:268758608;C:193670297;G:213835768;T:255268464;N:59861,8,26,98,,268758608,193670297,213835768,255268464,59861,SRX21223187,SRS18479990,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9283,,0.09341,,0.82211,,0.49121,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24712,SRR25492015,SRX21223186,SRS18479989,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S16,GSM7676111,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S16,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676111,GSM7676111: KBTGR  cut  replicate S16; Danio rerio; RNA Seq,GSM7676111 r1,GSM7676111,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRcut_S16_L001_I1_001.fastq.gz H27K5BCX2_KBTGRcut_S16_L001_R1_001.fastq.gz H27K5BCX2_KBTGRcut_S16_L001_R2_001.fastq.gz,fastq fastq fastq,1733777364.0,13134677.0,GSM7676111 r1,0:8 1:26 2:98,A:377310857;C:268033707;G:292815269;T:348639631;N:398882,8,26,98,,377310857,268033707,292815269,348639631,398882,SRX21223186,SRS18479989,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92457,,0.10972,,0.83684,,0.49054,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24713,SRR25492016,SRX21223186,SRS18479989,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S16,GSM7676111,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S16,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676111,GSM7676111: KBTGR  cut  replicate S16; Danio rerio; RNA Seq,GSM7676111 r1,GSM7676111,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRcut_S16_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S16_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S16_L001_R2_001.fastq.gz,fastq fastq fastq,1693931844.0,12832817.0,GSM7676111 r2,0:8 1:26 2:98,A:370335488;C:261641086;G:285793090;T:338853348;N:993054,8,26,98,,370335488,261641086,285793090,338853348,993054,SRX21223186,SRS18479989,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9257,,0.11044,,0.83593,,0.49929,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24714,SRR25492017,SRX21223186,SRS18479989,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S16,GSM7676111,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S16,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676111,GSM7676111: KBTGR  cut  replicate S16; Danio rerio; RNA Seq,GSM7676111 r1,GSM7676111,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRcut_S16_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRcut_S16_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRcut_S16_L001_R2_001.fastq.gz,fastq fastq fastq,1822627488.0,13807784.0,GSM7676111 r3,0:8 1:26 2:98,A:396109320;C:281479505;G:307344748;T:362166256;N:6063003,8,26,98,,396109320,281479505,307344748,362166256,6063003,SRX21223186,SRS18479989,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9237,,0.1075,,0.83733,,0.49995,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24715,SRR25492018,SRX21223186,SRS18479989,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S16,GSM7676111,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S16,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676111,GSM7676111: KBTGR  cut  replicate S16; Danio rerio; RNA Seq,GSM7676111 r1,GSM7676111,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRcut_S16_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRcut_S16_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRcut_S16_L001_R2_001.fastq.gz,fastq fastq fastq,1686941784.0,12779862.0,GSM7676111 r4,0:8 1:26 2:98,A:366995826;C:260455612;G:284984185;T:339737397;N:253456,8,26,98,,366995826,260455612,284984185,339737397,253456,SRX21223186,SRS18479989,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92245,,0.10934,,0.83583,,0.5109,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24716,SRR25492019,SRX21223186,SRS18479989,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S16,GSM7676111,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S16,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676111,GSM7676111: KBTGR  cut  replicate S16; Danio rerio; RNA Seq,GSM7676111 r1,GSM7676111,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRcut_S16_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRcut_S16_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRcut_S16_L002_R2_001.fastq.gz,fastq fastq fastq,1800605268.0,13640949.0,GSM7676111 r7,0:8 1:26 2:98,A:392033512;C:277884536;G:303332072;T:357657308;N:5905574,8,26,98,,392033512,277884536,303332072,357657308,5905574,SRX21223186,SRS18479989,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92264,,0.10865,,0.83771,,0.4962,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24717,SRR25492020,SRX21223186,SRS18479989,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S16,GSM7676111,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S16,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676111,GSM7676111: KBTGR  cut  replicate S16; Danio rerio; RNA Seq,GSM7676111 r1,GSM7676111,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRcut_S16_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRcut_S16_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRcut_S16_L002_R2_001.fastq.gz,fastq fastq fastq,1687212120.0,12781910.0,GSM7676111 r8,0:8 1:26 2:98,A:367591713;C:260374660;G:284790982;T:339790038;N:79787,8,26,98,,367591713,260374660,284790982,339790038,79787,SRX21223186,SRS18479989,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92439,,0.11008,,0.83252,,0.48566,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24718,SRR25492035,SRX21223186,SRS18479989,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S16,GSM7676111,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S16,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676111,GSM7676111: KBTGR  cut  replicate S16; Danio rerio; RNA Seq,GSM7676111 r1,GSM7676111,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRcut_S16_L002_I1_001.fastq.gz H27K5BCX2_KBTGRcut_S16_L002_R1_001.fastq.gz H27K5BCX2_KBTGRcut_S16_L002_R2_001.fastq.gz,fastq fastq fastq,1715599116.0,12996963.0,GSM7676111 r5,0:8 1:26 2:98,A:372113041;C:265506989;G:290255809;T:345508071;N:318464,8,26,98,,372113041,265506989,290255809,345508071,318464,SRX21223186,SRS18479989,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92368,,0.10681,,0.83727,,0.49306,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24719,SRR25492036,SRX21223186,SRS18479989,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S16,GSM7676111,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S16,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676111,GSM7676111: KBTGR  cut  replicate S16; Danio rerio; RNA Seq,GSM7676111 r1,GSM7676111,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRcut_S16_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S16_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S16_L002_R2_001.fastq.gz,fastq fastq fastq,1643667564.0,12452027.0,GSM7676111 r6,0:8 1:26 2:98,A:358646057;C:254091415;G:277620310;T:329013074;N:927790,8,26,98,,358646057,254091415,277620310,329013074,927790,SRX21223186,SRS18479989,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92527,,0.1079,,0.83465,,0.49184,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24720,SRR25492021,SRX21223185,SRS18479988,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  normal  replicate S2,GSM7676121,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  normal  replicate S2,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676121,GSM7676121: KBTRE  normal  replicate S2; Danio rerio; RNA Seq,GSM7676121 r1,GSM7676121,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTREnormal_S2_L001_I1_001.fastq.gz H27K5BCX2_KBTREnormal_S2_L001_R1_001.fastq.gz H27K5BCX2_KBTREnormal_S2_L001_R2_001.fastq.gz,fastq fastq fastq,807188844.0,6115067.0,GSM7676121 r1,0:8 1:26 2:98,A:172308620;C:125913345;G:139442237;T:161426336;N:186028,8,26,98,,172308620,125913345,139442237,161426336,186028,SRX21223185,SRS18479988,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92298,,0.08811,,0.85433,,0.4736,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24721,SRR25492022,SRX21223185,SRS18479988,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  normal  replicate S2,GSM7676121,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  normal  replicate S2,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676121,GSM7676121: KBTRE  normal  replicate S2; Danio rerio; RNA Seq,GSM7676121 r1,GSM7676121,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTREnormal_S2_L001_I1_001.fastq.gz HFJ5GBCX2_KBTREnormal_S2_L001_R1_001.fastq.gz HFJ5GBCX2_KBTREnormal_S2_L001_R2_001.fastq.gz,fastq fastq fastq,793147344.0,6008692.0,GSM7676121 r2,0:8 1:26 2:98,A:169497439;C:123759266;G:137078289;T:158052236;N:464586,8,26,98,,169497439,123759266,137078289,158052236,464586,SRX21223185,SRS18479988,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92361,,0.08644,,0.85464,,0.47495,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24722,SRR25492023,SRX21223185,SRS18479988,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  normal  replicate S2,GSM7676121,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  normal  replicate S2,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676121,GSM7676121: KBTRE  normal  replicate S2; Danio rerio; RNA Seq,GSM7676121 r1,GSM7676121,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTREnormal_S2_L001_I1_001.fastq.gz HYLGMBCXY_KBTREnormal_S2_L001_R1_001.fastq.gz HYLGMBCXY_KBTREnormal_S2_L001_R2_001.fastq.gz,fastq fastq fastq,852294828.0,6456779.0,GSM7676121 r3,0:8 1:26 2:98,A:181361509;C:132917413;G:147157966;T:168488477;N:2838977,8,26,98,,181361509,132917413,147157966,168488477,2838977,SRX21223185,SRS18479988,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9234,,0.08441,,0.85681,,0.45235,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24723,SRR25492024,SRX21223185,SRS18479988,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  normal  replicate S2,GSM7676121,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  normal  replicate S2,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676121,GSM7676121: KBTRE  normal  replicate S2; Danio rerio; RNA Seq,GSM7676121 r1,GSM7676121,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTREnormal_S2_L001_I1_001.fastq.gz HYWGVBCXY_KBTREnormal_S2_L001_R1_001.fastq.gz HYWGVBCXY_KBTREnormal_S2_L001_R2_001.fastq.gz,fastq fastq fastq,781758516.0,5922413.0,GSM7676121 r4,0:8 1:26 2:98,A:166724753;C:121839518;G:135085811;T:156626231;N:120161,8,26,98,,166724753,121839518,135085811,156626231,120161,SRX21223185,SRS18479988,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92293,,0.08698,,0.85626,,0.47803,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24724,SRR25492025,SRX21223185,SRS18479988,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  normal  replicate S2,GSM7676121,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  normal  replicate S2,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676121,GSM7676121: KBTRE  normal  replicate S2; Danio rerio; RNA Seq,GSM7676121 r1,GSM7676121,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTREnormal_S2_L002_I1_001.fastq.gz HYLGMBCXY_KBTREnormal_S2_L002_R1_001.fastq.gz HYLGMBCXY_KBTREnormal_S2_L002_R2_001.fastq.gz,fastq fastq fastq,843137856.0,6387408.0,GSM7676121 r7,0:8 1:26 2:98,A:179558862;C:131385546;G:145540868;T:166696387;N:2784321,8,26,98,,179558862,131385546,145540868,166696387,2784321,SRX21223185,SRS18479988,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92281,,0.08446,,0.85685,,0.47524,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24725,SRR25492026,SRX21223185,SRS18479988,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  normal  replicate S2,GSM7676121,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  normal  replicate S2,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676121,GSM7676121: KBTRE  normal  replicate S2; Danio rerio; RNA Seq,GSM7676121 r1,GSM7676121,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTREnormal_S2_L002_I1_001.fastq.gz HYWGVBCXY_KBTREnormal_S2_L002_R1_001.fastq.gz HYWGVBCXY_KBTREnormal_S2_L002_R2_001.fastq.gz,fastq fastq fastq,782789964.0,5930227.0,GSM7676121 r8,0:8 1:26 2:98,A:167092677;C:121959994;G:135189997;T:156882004;N:37574,8,26,98,,167092677,121959994,135189997,156882004,37574,SRX21223185,SRS18479988,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92384,,0.08593,,0.85529,,0.47658,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24726,SRR25492073,SRX21223185,SRS18479988,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  normal  replicate S2,GSM7676121,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  normal  replicate S2,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676121,GSM7676121: KBTRE  normal  replicate S2; Danio rerio; RNA Seq,GSM7676121 r1,GSM7676121,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTREnormal_S2_L002_I1_001.fastq.gz H27K5BCX2_KBTREnormal_S2_L002_R1_001.fastq.gz H27K5BCX2_KBTREnormal_S2_L002_R2_001.fastq.gz,fastq fastq fastq,799492452.0,6056761.0,GSM7676121 r5,0:8 1:26 2:98,A:170481537;C:124727025;G:138222223;T:159980825;N:150968,8,26,98,,170481537,124727025,138222223,159980825,150968,SRX21223185,SRS18479988,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92219,,0.08693,,0.85689,,0.45239,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24727,SRR25492074,SRX21223185,SRS18479988,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTRE  normal  replicate S2,GSM7676121,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTRE  normal  replicate S2,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676121,GSM7676121: KBTRE  normal  replicate S2; Danio rerio; RNA Seq,GSM7676121 r1,GSM7676121,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTREnormal_S2_L002_I1_001.fastq.gz HFJ5GBCX2_KBTREnormal_S2_L002_R1_001.fastq.gz HFJ5GBCX2_KBTREnormal_S2_L002_R2_001.fastq.gz,fastq fastq fastq,771619332.0,5845601.0,GSM7676121 r6,0:8 1:26 2:98,A:164827141;C:120458327;G:133444180;T:153706468;N:432782,8,26,98,,164827141,120458327,133444180,153706468,432782,SRX21223185,SRS18479988,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.9244,,0.086,,0.85752,,0.46487,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24728,SRR25492027,SRX21223184,SRS18479986,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S15,GSM7676110,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S15,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676110,GSM7676110: KBTGR  cut  replicate S15; Danio rerio; RNA Seq,GSM7676110 r1,GSM7676110,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRcut_S15_L001_I1_001.fastq.gz H27K5BCX2_KBTGRcut_S15_L001_R1_001.fastq.gz H27K5BCX2_KBTGRcut_S15_L001_R2_001.fastq.gz,fastq fastq fastq,991634028.0,7512379.0,GSM7676110 r1,0:8 1:26 2:98,A:213910719;C:153374311;G:167803904;T:200905324;N:218884,8,26,98,,213910719,153374311,167803904,200905324,218884,SRX21223184,SRS18479986,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92289,,0.10915,,0.83163,,0.51061,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24729,SRR25492028,SRX21223184,SRS18479986,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S15,GSM7676110,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S15,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676110,GSM7676110: KBTGR  cut  replicate S15; Danio rerio; RNA Seq,GSM7676110 r1,GSM7676110,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRcut_S15_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S15_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S15_L001_R2_001.fastq.gz,fastq fastq fastq,973359420.0,7373935.0,GSM7676110 r2,0:8 1:26 2:98,A:210076453;C:150636615;G:164768683;T:196577221;N:586658,8,26,98,,210076453,150636615,164768683,196577221,586658,SRX21223184,SRS18479986,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92307,,0.10829,,0.8309,,0.50664,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24730,SRR25492029,SRX21223184,SRS18479986,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S15,GSM7676110,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S15,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676110,GSM7676110: KBTGR  cut  replicate S15; Danio rerio; RNA Seq,GSM7676110 r1,GSM7676110,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRcut_S15_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRcut_S15_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRcut_S15_L001_R2_001.fastq.gz,fastq fastq fastq,1041506532.0,7890201.0,GSM7676110 r3,0:8 1:26 2:98,A:224331472;C:160956885;G:176036393;T:208465176;N:3449772,8,26,98,,224331472,160956885,176036393,208465176,3449772,SRX21223184,SRS18479986,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92046,,0.10509,,0.83179,,0.5158,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24731,SRR25492030,SRX21223184,SRS18479986,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S15,GSM7676110,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S15,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676110,GSM7676110: KBTGR  cut  replicate S15; Danio rerio; RNA Seq,GSM7676110 r1,GSM7676110,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRcut_S15_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRcut_S15_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRcut_S15_L001_R2_001.fastq.gz,fastq fastq fastq,959532816.0,7269188.0,GSM7676110 r4,0:8 1:26 2:98,A:207101192;C:148189510;G:162346748;T:194597135;N:145839,8,26,98,,207101192,148189510,162346748,194597135,145839,SRX21223184,SRS18479986,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92159,,0.10724,,0.83031,,0.51032,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24732,SRR25492031,SRX21223184,SRS18479986,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S15,GSM7676110,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S15,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676110,GSM7676110: KBTGR  cut  replicate S15; Danio rerio; RNA Seq,GSM7676110 r1,GSM7676110,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRcut_S15_L002_I1_001.fastq.gz H27K5BCX2_KBTGRcut_S15_L002_R1_001.fastq.gz H27K5BCX2_KBTGRcut_S15_L002_R2_001.fastq.gz,fastq fastq fastq,981662748.0,7436839.0,GSM7676110 r5,0:8 1:26 2:98,A:211518289;C:151920644;G:166249815;T:198931555;N:189919,8,26,98,,211518289,151920644,166249815,198931555,189919,SRX21223184,SRS18479986,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92149,,0.10822,,0.83078,,0.51544,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24733,SRR25492032,SRX21223184,SRS18479986,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S15,GSM7676110,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S15,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676110,GSM7676110: KBTGR  cut  replicate S15; Danio rerio; RNA Seq,GSM7676110 r1,GSM7676110,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRcut_S15_L002_I1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S15_L002_R1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S15_L002_R2_001.fastq.gz,fastq fastq fastq,945758088.0,7164834.0,GSM7676110 r6,0:8 1:26 2:98,A:203967307;C:146422295;G:160254376;T:190978208;N:531546,8,26,98,,203967307,146422295,160254376,190978208,531546,SRX21223184,SRS18479986,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92245,,0.10759,,0.83142,,0.51632,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24734,SRR25492033,SRX21223184,SRS18479986,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S15,GSM7676110,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S15,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676110,GSM7676110: KBTGR  cut  replicate S15; Danio rerio; RNA Seq,GSM7676110 r1,GSM7676110,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRcut_S15_L002_I1_001.fastq.gz HYLGMBCXY_KBTGRcut_S15_L002_R1_001.fastq.gz HYLGMBCXY_KBTGRcut_S15_L002_R2_001.fastq.gz,fastq fastq fastq,1029633660.0,7800255.0,GSM7676110 r7,0:8 1:26 2:98,A:221920698;C:159045837;G:173908417;T:206140930;N:3409108,8,26,98,,221920698,159045837,173908417,206140930,3409108,SRX21223184,SRS18479986,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92088,,0.10596,,0.83295,,0.51602,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24735,SRR25492034,SRX21223184,SRS18479986,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S15,GSM7676110,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S15,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676110,GSM7676110: KBTGR  cut  replicate S15; Danio rerio; RNA Seq,GSM7676110 r1,GSM7676110,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRcut_S15_L002_I1_001.fastq.gz HYWGVBCXY_KBTGRcut_S15_L002_R1_001.fastq.gz HYWGVBCXY_KBTGRcut_S15_L002_R2_001.fastq.gz,fastq fastq fastq,960845292.0,7279131.0,GSM7676110 r8,0:8 1:26 2:98,A:207492886;C:148360000;G:162496060;T:194960451;N:45441,8,26,98,,207492886,148360000,162496060,194960451,45441,SRX21223184,SRS18479986,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92106,,0.10819,,0.82946,,0.51364,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24736,SRR25492037,SRX21223183,SRS18479987,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S14,GSM7676109,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S14,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676109,GSM7676109: KBTGR  cut  replicate S14; Danio rerio; RNA Seq,GSM7676109 r1,GSM7676109,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,H27K5BCX2_KBTGRcut_S14_L001_I1_001.fastq.gz H27K5BCX2_KBTGRcut_S14_L001_R1_001.fastq.gz H27K5BCX2_KBTGRcut_S14_L001_R2_001.fastq.gz,fastq fastq fastq,2591037900.0,19629075.0,GSM7676109 r1,0:8 1:26 2:98,A:555580990;C:402990210;G:441965039;T:522520043;N:593068,8,26,98,,555580990,402990210,441965039,522520043,593068,SRX21223183,SRS18479987,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92241,,0.10605,,0.83187,,0.51181,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24737,SRR25492038,SRX21223183,SRS18479987,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S14,GSM7676109,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S14,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676109,GSM7676109: KBTGR  cut  replicate S14; Danio rerio; RNA Seq,GSM7676109 r1,GSM7676109,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HFJ5GBCX2_KBTGRcut_S14_L001_I1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S14_L001_R1_001.fastq.gz HFJ5GBCX2_KBTGRcut_S14_L001_R2_001.fastq.gz,fastq fastq fastq,2497809996.0,18922803.0,GSM7676109 r2,0:8 1:26 2:98,A:535857014;C:388641161;G:426148721;T:502295548;N:1492250,8,26,98,,535857014,388641161,426148721,502295548,1492250,SRX21223183,SRS18479987,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92376,,0.10611,,0.83177,,0.49598,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24738,SRR25492039,SRX21223183,SRS18479987,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S14,GSM7676109,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S14,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676109,GSM7676109: KBTGR  cut  replicate S14; Danio rerio; RNA Seq,GSM7676109 r1,GSM7676109,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYLGMBCXY_KBTGRcut_S14_L001_I1_001.fastq.gz HYLGMBCXY_KBTGRcut_S14_L001_R1_001.fastq.gz HYLGMBCXY_KBTGRcut_S14_L001_R2_001.fastq.gz,fastq fastq fastq,2728654500.0,20671625.0,GSM7676109 r3,0:8 1:26 2:98,A:584168882;C:423983386;G:464567203;T:543992364;N:9107415,8,26,98,,584168882,423983386,464567203,543992364,9107415,SRX21223183,SRS18479987,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92388,,0.10372,,0.83181,,0.50245,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures
24739,SRR25492040,SRX21223183,SRS18479987,SRP452960,PRJNA1001330,Ontogenetically distinct neutrophils differ in function and transcriptional profile in zebrafish,GSE239880,Transcriptome Analysis,The current view of hematopoiesis considers leukocytes on a continuum with distinct developmental origins  and which exert non overlapping functions. However  there is little information about ontogenetically distinct neutrophil populations. In this work  using a photoconvertible transgenic zebrafish line; Tgmpx:Dendra2  we selectively label rostral blood island derived and caudal hematopoietic tissue derived neutrophils in vivo during steady state or upon injury. By comparing the migratory properties and single cell expression profiles of both neutrophil populations at steady state we reveal that rostral neutrophils show higher csf3b expression and migration capacity than caudal neutrophils. Upon injury  both populations share a core transcriptional profile as well as subset specific transcriptional signatures. Accordingly  both rostral and caudal neutrophils are recruited to the wound independently of their distance to the injury. While rostral neutrophils respond uniformly  caudal neutrophils respond heterogeneously. Collectively  our results reveal that co existing neutrophils populations with ontogenically distinct origin display key functional differences. Overall design: We photoconverted RBI derived neutrophils in the head two times  at 34hpf and 44hpf  and performed caudal fin transections at 54hpf on the half of each group. Three hours later  we homogenized non cut and cut embryos from each group and separately sorted red and green fluorescent cells. The resulting four groups were analized by scRNAseq.,,,,KBTGR  cut  replicate S14,GSM7676109,,source name:whole embryo|tissue:whole embryo|cell type:neutrophils|geo loc name:missing|collection date:missing,KBTGR  cut  replicate S14,Reads from the four separate conditions flowcells were preprocessed using Seurat in R https://satijalab.org/seurat/ Assembly: GRCz11 Supplementary files format and content: tab separated values files,whole embryo,,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell 3’ Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,tissue:whole embryo|cell type:neutrophils,GSM7676109,GSM7676109: KBTGR  cut  replicate S14; Danio rerio; RNA Seq,GSM7676109 r1,GSM7676109,1,For tissue disaggregation  whole embryos were incubated with a digestion cocktail 10mg/ml collagenase; 5mg/ml hyaluronidase; and 20mg/ml proteinase K and constant mechanical dissociation was exerted for 10 minutes. Cells suspension were filtered through a 40 µm nylon mesh and L 15 medium was added to stop the digestion process. Isolated cells were pelleted  resuspended in L 15 medium and processed by FACS. Red+ and green+ cells were loaded into the Chromium Controller instrument to generate Gel beads in EMulsion GEMs. GEM RT was performed in a C1000 Touch Thermal cycler. post reverse transcription  GEMs were broken  and the single strand cDNA was cleaned up using DynaBeads MyOne Silane Beads and the SPRIselect Reagent Kit. cDNA was amplified using the C1000 Touch Thermal cycler and cleaned up with the SPRIselect Reagent Kit. Libraries were constructed using the GemCode Single Cell three prime Library Kit following these steps: 1 end repair and A tailing  2 adapter ligation  3 postligation cleanup with SPRIselect  4 sample index PCR and cleanup. The barcode sequencing libraries were quantified by quantitative PCR.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP452960,,loader:fastq load.py,HYWGVBCXY_KBTGRcut_S14_L001_I1_001.fastq.gz HYWGVBCXY_KBTGRcut_S14_L001_R1_001.fastq.gz HYWGVBCXY_KBTGRcut_S14_L001_R2_001.fastq.gz,fastq fastq fastq,2618092488.0,19834034.0,GSM7676109 r4,0:8 1:26 2:98,A:561803683;C:406792207;G:446399294;T:528347486;N:392662,8,26,98,,561803683,406792207,446399294,528347486,392662,SRX21223183,SRS18479987,SRA1685258,"Facultad de Ciencias de la vida, Universidad Andres Bello","Facultad de Ciencias de la vida, Universidad Andres Bello",1,0.92126,,0.10547,,0.83161,,0.49641,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,Chile,2023-08-02,Undetermined,Embryo,Whole Organism,All anatomical structures