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
9166,ERR2788341,ERX2797590,ERS2709706,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7292228,SAMEA4890710,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890710|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7292228|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:pool 4|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7292228|scientific name:Danio rerio|sex:2 female  1 male|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7292228 p,5149STDY7292228 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP|Experimental Factor: infect:n1,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7292228.bam 5149STDY7292228.bam.bai,bam bam,37970494940.0,387454030.0,E MTAB 7159:5149STDY7292228,0:98,A:11476520187;C:7571635167;G:8189594199;T:10701044279;N:31701108,98,,,,11476520187,7571635167,8189594199,10701044279,31701108,ERX2797590,ERS2709706,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.87568,,0.2122,,0.82582,,0.5259,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9167,ERR2788340,ERX2797589,ERS2709705,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7274848,SAMEA4890709,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890709|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274848|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 3|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274848|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274848 p,5149STDY7274848 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Vibrio Anguillarum,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7274848.bam 5149STDY7274848.bam.bai,bam bam,34517322840.0,352217580.0,E MTAB 7159:5149STDY7274848,0:98,A:10635243399;C:6658515314;G:7525079510;T:9695995344;N:2489273,98,,,,10635243399,6658515314,7525079510,9695995344,2489273,ERX2797589,ERS2709705,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.86206,,0.18065,,0.83514,,0.53609,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9168,ERR2788339,ERX2797588,ERS2709704,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7274847,SAMEA4890708,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890708|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274847|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 2|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274847|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274847 p,5149STDY7274847 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Anisakis simplex,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7274847.bam 5149STDY7274847.bam.bai,bam bam,34467649678.0,351710711.0,E MTAB 7159:5149STDY7274847,0:98,A:10609988948;C:6722093635;G:7464497879;T:9667814950;N:3254266,98,,,,10609988948,6722093635,7464497879,9667814950,3254266,ERX2797588,ERS2709704,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.88751,,0.21835,,0.83771,,0.53927,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9169,ERR2788338,ERX2797587,ERS2709703,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7274846,SAMEA4890707,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890707|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274846|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 1|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274846|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274846 p,5149STDY7274846 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:n1,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7274846.bam 5149STDY7274846.bam.bai,bam bam,35052538472.0,357678964.0,E MTAB 7159:5149STDY7274846,0:98,A:10698116265;C:6858102477;G:7626019661;T:9866905792;N:3394277,98,,,,10698116265,6858102477,7626019661,9866905792,3394277,ERX2797587,ERS2709703,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.88916,,0.21537,,0.83802,,0.5336,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9898,ERR4194114,ERX4155254,ERS4601292,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 2,SAMEA6873729,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873729|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 2|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 2|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 2 s,Sample 2 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:8|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA8h_1_S2_L001.bam,bam,10087287534.0,99874134.0,E MTAB 9193:cDNA8h 1 S2 L001,0:101,A:2892833391;C:2022466595;G:2198646699;T:2962268446;N:11072403,101,,,,2892833391,2022466595,2198646699,2962268446,11072403,ERX4155254,ERS4601292,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93609,,0.12902,,0.82158,,0.5062,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9899,ERR4194115,ERX4155254,ERS4601292,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 2,SAMEA6873729,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873729|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 2|age:8|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 2|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 2 s,Sample 2 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:8|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA8h_1_S2_L002.bam,bam,10191911414.0,100910014.0,E MTAB 9193:cDNA8h 1 S2 L002,0:101,A:2923216190;C:2043975715;G:2221734566;T:2992798366;N:10186577,101,,,,2923216190,2043975715,2221734566,2992798366,10186577,ERX4155254,ERS4601292,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93445,,0.13038,,0.824,,0.49774,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9900,ERR4194112,ERX4155253,ERS4601291,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 1,SAMEA6873728,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873728|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 1|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 1 s,Sample 1 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:6|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA6h_1_S1_L001.bam,bam,7181772357.0,71106657.0,E MTAB 9193:cDNA6h 1 S1 L001,0:101,A:2074032710;C:1415439071;G:1544274166;T:2140112533;N:7913877,101,,,,2074032710,1415439071,1544274166,2140112533,7913877,ERX4155253,ERS4601291,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.9297,,0.12156,,0.8117,,0.51457,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9901,ERR4194113,ERX4155253,ERS4601291,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 1,SAMEA6873728,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873728|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 1|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 1|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 1 s,Sample 1 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:6|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA6h_1_S1_L002.bam,bam,7256542253.0,71846953.0,E MTAB 9193:cDNA6h 1 S1 L002,0:101,A:2096163385;C:1430325700;G:1560530043;T:2162265616;N:7257509,101,,,,2096163385,1430325700,1560530043,2162265616,7257509,ERX4155253,ERS4601291,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.92882,,0.12127,,0.81162,,0.51457,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9902,ERR4194128,ERX4155256,ERS4601294,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 4,SAMEA6873731,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873731|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 4|age:13|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 4|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 4 s,Sample 4 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:13|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA13h_1_control_S1_L001.bam,bam,10785974123.0,106791823.0,E MTAB 9193:cDNA13h 1 control S1 L001,0:101,A:3007305661;C:2241057062;G:2505494392;T:2986021199;N:46095809,101,,,,3007305661,2241057062,2505494392,2986021199,46095809,ERX4155256,ERS4601294,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.67094,,0.07571,,0.92951,,0.5272,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9903,ERR4194129,ERX4155256,ERS4601294,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 4,SAMEA6873731,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873731|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 4|age:13|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 4|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 4 s,Sample 4 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:13|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA13h_1_control_S1_L002.bam,bam,10595192294.0,104902894.0,E MTAB 9193:cDNA13h 1 control S1 L002,0:101,A:2971916419;C:2204229263;G:2390854035;T:2949877754;N:78314823,101,,,,2971916419,2204229263,2390854035,2949877754,78314823,ERX4155256,ERS4601294,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.67255,,0.08054,,0.91583,,0.52661,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9904,ERR4194116,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_1_S3_L001.bam,bam,1622536412.0,16556494.0,E MTAB 9193:cDNA10h 1 S3 L001,0:98,A:491141175;C:317161060;G:354179755;T:459976409;N:78013,98,,,,491141175,317161060,354179755,459976409,78013,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93238,,0.13033,,0.89132,,0.47076,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9905,ERR4194117,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_1_S3_L002.bam,bam,1484328776.0,15146212.0,E MTAB 9193:cDNA10h 1 S3 L002,0:98,A:450782055;C:290088574;G:322801188;T:420570801;N:86158,98,,,,450782055,290088574,322801188,420570801,86158,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.92846,,0.13128,,0.89923,,0.46879,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9906,ERR4194118,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_1_S3_L003.bam,bam,1578833116.0,16110542.0,E MTAB 9193:cDNA10h 1 S3 L003,0:98,A:477600666;C:308260969;G:347303289;T:445467384;N:200808,98,,,,477600666,308260969,347303289,445467384,200808,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93107,,0.12965,,0.91265,,0.47375,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9907,ERR4194119,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_1_S3_L004.bam,bam,1859564994.0,18975153.0,E MTAB 9193:cDNA10h 1 S3 L004,0:98,A:562936790;C:364057256;G:406607636;T:525811595;N:151717,98,,,,562936790,364057256,406607636,525811595,151717,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93453,,0.1266,,0.87714,,0.46957,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9908,ERR4194120,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_2_S3_L001.bam,bam,1156341102.0,11799399.0,E MTAB 9193:cDNA10h 2 S3 L001,0:98,A:345857612;C:224453195;G:257551986;T:327969064;N:509245,98,,,,345857612,224453195,257551986,327969064,509245,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93863,,0.10744,,0.81984,,0.501,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9909,ERR4194121,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_2_S3_L002.bam,bam,1105219696.0,11277752.0,E MTAB 9193:cDNA10h 2 S3 L002,0:98,A:331051973;C:214369903;G:246546338;T:312897773;N:353709,98,,,,331051973,214369903,246546338,312897773,353709,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93941,,0.10818,,0.82211,,0.50079,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9910,ERR4194122,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_2_S3_L003.bam,bam,1105199606.0,11277547.0,E MTAB 9193:cDNA10h 2 S3 L003,0:98,A:331158619;C:214305131;G:246465559;T:312930408;N:339889,98,,,,331158619,214305131,246465559,312930408,339889,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93767,,0.10645,,0.82329,,0.50057,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9911,ERR4194123,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_2_S3_L004.bam,bam,1108707712.0,11313344.0,E MTAB 9193:cDNA10h 2 S3 L004,0:98,A:331374433;C:215925150;G:247131942;T:313865174;N:411013,98,,,,331374433,215925150,247131942,313865174,411013,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93827,,0.10842,,0.82031,,0.49241,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9912,ERR4194124,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_2_S3_L005.bam,bam,1110084612.0,11327394.0,E MTAB 9193:cDNA10h 2 S3 L005,0:98,A:332881960;C:215360330;G:247563319;T:313842331;N:436672,98,,,,332881960,215360330,247563319,313842331,436672,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93827,,0.10719,,0.8238,,0.50406,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9913,ERR4194125,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_2_S3_L006.bam,bam,1113812728.0,11365436.0,E MTAB 9193:cDNA10h 2 S3 L006,0:98,A:333112288;C:216649152;G:248341020;T:315338848;N:371420,98,,,,333112288,216649152,248341020,315338848,371420,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93843,,0.10675,,0.82079,,0.49284,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9914,ERR4194126,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_2_S3_L007.bam,bam,1119495748.0,11423426.0,E MTAB 9193:cDNA10h 2 S3 L007,0:98,A:335288339;C:217283719;G:249624836;T:316900388;N:398466,98,,,,335288339,217283719,249624836,316900388,398466,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93711,,0.10749,,0.82266,,0.49382,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9915,ERR4194127,ERX4155255,ERS4601293,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 3,SAMEA6873730,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873730|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 3|age:10|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 3|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 3 s,Sample 3 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:10|Experimental Factor: RNA interference:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA10h_2_S3_L008.bam,bam,1175946688.0,11999456.0,E MTAB 9193:cDNA10h 2 S3 L008,0:98,A:351364169;C:228318193;G:261971072;T:333863943;N:429311,98,,,,351364169,228318193,261971072,333863943,429311,ERX4155255,ERS4601293,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.93851,,0.10755,,0.82158,,0.49895,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9916,ERR4194130,ERX4155257,ERS4601295,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 5,SAMEA6873732,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873732|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 5|age:13|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 5|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 5 s,Sample 5 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:13|Experimental Factor: RNA interference:morpholino mediated Gata5/6 knockdown,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA13h_2_gata56KD_S2_L001.bam,bam,7791309377.0,77141677.0,E MTAB 9193:cDNA13h 2 gata56KD S2 L001,0:101,A:2198242220;C:1593746618;G:1784167452;T:2181979820;N:33173267,101,,,,2198242220,1593746618,1784167452,2181979820,33173267,ERX4155257,ERS4601295,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.66736,,0.08039,,0.93026,,0.50796,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
9917,ERR4194131,ERX4155257,ERS4601295,ERP122151,PRJEB38705,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E-MTAB-9193,Transcriptome Analysis,TgBACgata5:EGFP transgenic line was used to isolate mesendoderm cells enriched for cardiac lineage. Wild type embryos at 6  8  10  13 hpf and morpholinos injected Gata5/6 know down KD embryos at 13 hpf were pre screened for GFP signal and dissociated into single cell suspension in separate wells. GFP+ cells at each condition were isolated through fluorescent activated cell sorting FACS. Single cell cDNA libraries were constructed through the 10x Chromium Single Cell Gene Expression platform. Final sequencing was performed on an Illumina HiSeq 2500 platform Rapid Run Model. Note that the 10h single cell library was sequenced twice Named as cDNA10h 1* and cDNA10h 2* separately.,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,,Protocols: WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Sample 5,SAMEA6873732,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada",ENA FIRST PUBLIC:2020 12 31T11:11:47Z|ENA LAST UPDATE:2020 06 04T16:16:46Z|External Id:SAMEA6873732|INSDC center name:Developmental and Stem Cell Biology  Sickkids  Toronto  Canada; Genetics and Genome Biology  Sickkids  Toronto  Canada; Molecular Genetics  University of Toronto  Toronto  Canada|INSDC first public:2020 12 31T11:11:47Z|INSDC last update:2020 06 04T16:16:46Z|INSDC status:public|Submitter Id:E MTAB 9193:Sample 5|age:13|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo stage|genotype:TgBACgata5: EGFPpd25|immunophenotype:GFP+|individual:embryo pool 100 200|organism part:mesendoderm|sample name:E MTAB 9193:Sample 5|scientific name:Danio rerio|sex:mixed,,,,,,,,,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,E MTAB 9193:Sample 5 s,Sample 5 s,Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,WT and Gata5/6KD TgBAC gata5: EGFP embryos were synchronized and dechorionated with pronase Sigma  Cat# 11459643001 at desired stages. For embryos at gastrulation stages 6 hpf  8 hpf  10 hpf  the dissociation was performed by incubating embryos in 200 μl calcium free Ringer solution 116 mM NaCl  2.6 mM KCl  5 mM HEPE  pH 7.0 for 5 min followed by 500ul TrpLE GIBCO  TrypLE Express Enzyme  cat #: 12604 013 at room temperature. Dissociation was monitored under a dissecting scope and embryos were homogenized every 5min until single cell suspensions were generated. Embryos at the early segmentation stage 13 hpf were treated similarly but incubated with 500 ul of 0.25 Trypsin GIBCO  Trypsin2.5%  no phenol red  cat#: 15090046/ EDTA instead of TrpLE for dissociation. post dissociation  Cells were washed twice with DMEM 1% FBS. DAPI was added at a concentration of 5ug/ml to exclude dead cells right before the Fluorescence activated cell sorting FACS. FACS was performed on Sony SH800S Cell Sorter  MoFlo XDP or MoFlo Astrios with a 100 μm nozzle by the SickKids UHN Flow and Mass Cytometry Facility. Around 20 000 to 50 000 gata5GFP+ cells were obtained in one FACS experiment. Single cell suspensions post FACS were loaded into the 10x machine and RNA was extracted based on Chromium Single Cell three prime Reagent Kits v2 protocol. Libraries were constructed using the 10x v2 chemistry.,Experimental Factor: age:13|Experimental Factor: RNA interference:morpholino mediated Gata5/6 knockdown,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,ERP122151,Illumina HiSeq 2500 sequencing; Single cell transcriptome analysis of gata5GFP labelled WT and Gata5/6 deficient cells from early gastrulation to early somitogenesis in zebrafish,ENA FIRST PUBLIC:2021 06 02|ENA LAST UPDATE:2021 12 01,cDNA13h_2_gata56KD_S2_L002.bam,bam,7658149967.0,75823267.0,E MTAB 9193:cDNA13h 2 gata56KD S2 L002,0:101,A:2172230233;C:1568805100;G:1703587704;T:2157181071;N:56345859,101,,,,2172230233,1568805100,1703587704,2157181071,56345859,ERX4155257,ERS4601295,ERA2667966,"Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive","Developmental and Stem Cell Biology, Sickkids, Toronto, Canada; Genetics and Genome Biology, Sickkids, Toronto, Canada; Molecular Genetics, University of Toronto, Toronto, Canada|European Nucleotide Archive",1,0.66565,,0.08597,,0.91804,,0.51772,,101,,B,,usable mapping rate,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Canada,2020-06-04,Multi-stage,Embryo,Embryo Imprecise,All anatomical structures
10163,ERR5714657,ERX5430029,ERS6251768,ERP128324,PRJEB44291,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E-MTAB-10360,Transcriptome Analysis,Macrophage colony stimulating factor receptor M CSFR/CSF1R signaling is crucial for the differentiation  proliferation  and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases  including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore  it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human related diseases. Here  we investigate the roles of zebrafish csf1ra and csf1rb in adult myelopoiesis using single cell RNA sequencing. Our analysis of adult whole kidney marrow WKM hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease  mostly in cancerogenesis.,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,,Protocols: Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,WT,SAMEA8567093,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 04 24|ENA last update:2021 04 14|External Id:SAMEA8567093|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 04 24T00:22:33Z|INSDC last update:2021 04 14T14:09:18Z|INSDC status:public|Submitter Id:E MTAB 10360:WT|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:head kidney|sample name:E MTAB 10360:WT|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E MTAB 10360:WT p,WT p,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP128324,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,WT.bam,bam,1041394032.0,18596322.0,E MTAB 10360:WT,0:56,A:284652376;C:244349479;G:255850754;T:255536179;N:1005244,56,,,,284652376,244349479,255850754,255536179,1005244,ERX5430029,ERS6251768,ERA3959104,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.9192,,0.10547,,0.84782,,0.53778,,56,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2021-04-14,Adult,Adult,Multi-tissue,Multi-system
10164,ERR5714656,ERX5430028,ERS6251767,ERP128324,PRJEB44291,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E-MTAB-10360,Transcriptome Analysis,Macrophage colony stimulating factor receptor M CSFR/CSF1R signaling is crucial for the differentiation  proliferation  and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases  including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore  it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human related diseases. Here  we investigate the roles of zebrafish csf1ra and csf1rb in adult myelopoiesis using single cell RNA sequencing. Our analysis of adult whole kidney marrow WKM hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease  mostly in cancerogenesis.,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,,Protocols: Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,Rb,SAMEA8567092,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 04 24|ENA last update:2021 04 14|External Id:SAMEA8567092|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 04 24T00:22:33Z|INSDC last update:2021 04 14T14:09:18Z|INSDC status:public|Submitter Id:E MTAB 10360:Rb|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:csf1rb4bp|organism part:head kidney|sample name:E MTAB 10360:Rb|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E MTAB 10360:Rb p,Rb p,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,Experimental Factor: genotype:csf1rb4bp,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP128324,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,Rb.bam,bam,1069920824.0,19105729.0,E MTAB 10360:Rb,0:56,A:299856824;C:238947539;G:256649537;T:273433744;N:1033180,56,,,,299856824,238947539,256649537,273433744,1033180,ERX5430028,ERS6251767,ERA3959104,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.94145,,0.11133,,0.83191,,0.52892,,56,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2021-04-14,Adult,Adult,Multi-tissue,Multi-system
10165,ERR5714655,ERX5430027,ERS6251766,ERP128324,PRJEB44291,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E-MTAB-10360,Transcriptome Analysis,Macrophage colony stimulating factor receptor M CSFR/CSF1R signaling is crucial for the differentiation  proliferation  and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases  including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore  it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human related diseases. Here  we investigate the roles of zebrafish csf1ra and csf1rb in adult myelopoiesis using single cell RNA sequencing. Our analysis of adult whole kidney marrow WKM hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease  mostly in cancerogenesis.,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,,Protocols: Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,Ra,SAMEA8567091,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA first public:2021 04 24|ENA last update:2021 04 14|External Id:SAMEA8567091|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 04 24T00:22:33Z|INSDC last update:2021 04 14T14:09:18Z|INSDC status:public|Submitter Id:E MTAB 10360:Ra|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:csf1ra5bp|organism part:head kidney|sample name:E MTAB 10360:Ra|strain:AB,,,,,,,,,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,E MTAB 10360:Ra p,Ra p,Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,Whole kidney marrow was collected from 6 mpf zebrafish wt  csf1raΔ5bp  or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting  washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further  total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v3.1  16 rxns PN 1000121 was used for library preparation.,Experimental Factor: genotype:csf1ra5bp,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,NextSeq 500,,ERP128324,NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows,ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14,Ra.bam,bam,1009240400.0,18022150.0,E MTAB 10360:Ra,0:56,A:279849736;C:230130588;G:247312130;T:250994600;N:953346,56,,,,279849736,230130588,247312130,250994600,953346,ERX5430027,ERS6251766,ERA3959104,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,1,0.95705,,0.10915,,0.84788,,0.47011,,56,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2021-04-14,Adult,Adult,Multi-tissue,Multi-system
10166,ERR5762357,ERX5471113,ERS6291553,ERP128548,PRJEB44492,scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,E-MTAB-10370,Transcriptome Analysis,GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice  its role during adult hematopoiesis is incompletely understood. In zebrafish  mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs  whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation  but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells  we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population  we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09,,Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.,wt2 gata2b,SAMEA8606934,Erasmus Medical Center,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606934|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:wt2 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:wt2 gata2b|sampling site:kidney marrow|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,E MTAB 10370:wt2 gata2b p,wt2 gata2b p,scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using  FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells.  cDNA was prepared using the manufacturers  protocol 10x Chromium V2. Library was prepared using the manufacturers  protocol 10x Chromium V2.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP128548,Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09,wt2_gata2b.bam,bam,25266437196.0,277653156.0,E MTAB 10370:wt2 gata2b,0:91,A:7555470312;C:5144518052;G:5682746714;T:6882396490;N:1305628,91,,,,7555470312,5144518052,5682746714,6882396490,1305628,ERX5471113,ERS6291553,ERA4089475,Erasmus Medical Center|European Nucleotide Archive,Erasmus Medical Center|European Nucleotide Archive,1,0.90876,,0.18424,,0.84017,,0.55508,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Netherlands,2022-04-09,Adult,Adult,Kidney,Renal System
10167,ERR5762356,ERX5471112,ERS6291552,ERP128548,PRJEB44492,scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,E-MTAB-10370,Transcriptome Analysis,GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice  its role during adult hematopoiesis is incompletely understood. In zebrafish  mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs  whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation  but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells  we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population  we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09,,Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.,wt1 gata2b,SAMEA8606933,Erasmus Medical Center,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606933|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:wt1 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:wt1 gata2b|sampling site:kidney marrow|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,E MTAB 10370:wt1 gata2b p,wt1 gata2b p,scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using  FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells.  cDNA was prepared using the manufacturers  protocol 10x Chromium V2. Library was prepared using the manufacturers  protocol 10x Chromium V2.,Experimental Factor: genotype:wild type genotype,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP128548,Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09,wt1_gata2b.bam,bam,36376708095.0,399744045.0,E MTAB 10370:wt1 gata2b,0:91,A:10397161431;C:8128518427;G:8799445454;T:9049686061;N:1896722,91,,,,10397161431,8128518427,8799445454,9049686061,1896722,ERX5471112,ERS6291552,ERA4089475,Erasmus Medical Center|European Nucleotide Archive,Erasmus Medical Center|European Nucleotide Archive,1,0.94708,,0.08938,,0.85449,,0.52917,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Netherlands,2022-04-09,Adult,Adult,Kidney,Renal System
10168,ERR5762355,ERX5471111,ERS6291551,ERP128548,PRJEB44492,scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,E-MTAB-10370,Transcriptome Analysis,GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice  its role during adult hematopoiesis is incompletely understood. In zebrafish  mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs  whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation  but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells  we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population  we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09,,Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.,hom2 gata2b,SAMEA8606932,Erasmus Medical Center,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606932|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:hom2 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:gata2b / |isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:hom2 gata2b|sampling site:kidney marrow|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,E MTAB 10370:hom2 gata2b p,hom2 gata2b p,scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using  FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells.  cDNA was prepared using the manufacturers  protocol 10x Chromium V2. Library was prepared using the manufacturers  protocol 10x Chromium V2.,Experimental Factor: genotype:gata2b / ,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP128548,Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09,hom2_gata2b.bam,bam,22416887402.0,246339422.0,E MTAB 10370:hom2 gata2b,0:91,A:6732382430;C:4540586585;G:4933684272;T:6209137814;N:1096301,91,,,,6732382430,4540586585,4933684272,6209137814,1096301,ERX5471111,ERS6291551,ERA4089475,Erasmus Medical Center|European Nucleotide Archive,Erasmus Medical Center|European Nucleotide Archive,1,0.91306,,0.21566,,0.83469,,0.53782,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Netherlands,2022-04-09,Adult,Adult,Kidney,Renal System
10169,ERR5762354,ERX5471110,ERS6291550,ERP128548,PRJEB44492,scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,E-MTAB-10370,Transcriptome Analysis,GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice  its role during adult hematopoiesis is incompletely understood. In zebrafish  mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs  whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation  but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells  we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population  we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09,,Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.,hom1 gata2b,SAMEA8606931,Erasmus Medical Center,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606931|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:hom1 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:gata2b / |isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:hom1 gata2b|sampling site:kidney marrow|sex:female|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,E MTAB 10370:hom1 gata2b p,hom1 gata2b p,scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using  FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells.  cDNA was prepared using the manufacturers  protocol 10x Chromium V2. Library was prepared using the manufacturers  protocol 10x Chromium V2.,Experimental Factor: genotype:gata2b / ,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP128548,Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish,ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09,hom1_gata2b.bam,bam,18004290759.0,197849349.0,E MTAB 10370:hom1 gata2b,0:91,A:5232521408;C:3876317502;G:4287902596;T:4606191653;N:1357600,91,,,,5232521408,3876317502,4287902596,4606191653,1357600,ERX5471110,ERS6291550,ERA4089475,Erasmus Medical Center|European Nucleotide Archive,Erasmus Medical Center|European Nucleotide Archive,1,0.94131,,0.08871,,0.83465,,0.52792,,91,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Netherlands,2022-04-09,Adult,Adult,Kidney,Renal System
10176,ERR5858457,ERX5504346,ERS6343450,ERP128749,PRJEB44676,scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10390,Transcriptome Analysis,To analyse lesion induced gene regulation in progenitor cells at single cell resolution  we performed single cell RNAseq on FACS isolated her4.3:GFP progenitor cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.,Naive,SAMEA8658904,University Of Edinburgh,ENA first public:2021 05 24|ENA last update:2021 05 24|External Id:SAMEA8658904|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 05 24T00:14:32Z|INSDC last update:2021 05 24T00:14:32Z|INSDC status:public|Submitter Id:E MTAB 10390:Naive|age:4|broker name:ArrayExpress|cell type:ependymo radial glial cell|common name:zebrafish|developmental stage:larval day 4|immunophenotype:Her4.3+ positive|organism part:spinal cord|sample name:E MTAB 10390:Naive|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10390:Naive p,Naive p,scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP128749,Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24,Naive.bam,bam,44972162730.0,499690697.0,E MTAB 10390:Naive,0:90,A:13658826375;C:8733304343;G:9348137569;T:13228064343;N:3830100,90,,,,13658826375,8733304343,9348137569,13228064343,3830100,ERX5504346,ERS6343450,ERA4142789,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.89428,,0.32693,,0.75276,,0.5314,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-05-24,Larval,Larval,Spinal Cord,Nervous System
10177,ERR5858456,ERX5504345,ERS6343449,ERP128749,PRJEB44676,scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10390,Transcriptome Analysis,To analyse lesion induced gene regulation in progenitor cells at single cell resolution  we performed single cell RNAseq on FACS isolated her4.3:GFP progenitor cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.,Lesi1d,SAMEA8658903,University Of Edinburgh,ENA first public:2021 05 24|ENA last update:2021 05 24|External Id:SAMEA8658903|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 05 24T00:14:32Z|INSDC last update:2021 05 24T00:14:32Z|INSDC status:public|Submitter Id:E MTAB 10390:Lesi1d|age:4|broker name:ArrayExpress|cell type:ependymo radial glial cell|common name:zebrafish|developmental stage:larval day 4|immunophenotype:Her4.3+ positive|injury:spinal injury lesion|organism part:spinal cord|sample name:E MTAB 10390:Lesi1d|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10390:Lesioned p,Lesioned p,scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines.,Experimental Factor: injury:spinal injury lesion,RNA-Seq,TRANSCRIPTOMIC,Oligo-dT,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP128749,Illumina NovaSeq 6000 paired end sequencing; scRNAseq of her4.3+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 05 24|ENA LAST UPDATE:2021 05 24,Lesioned.bam,bam,49902588630.0,554473207.0,E MTAB 10390:Lesioned,0:90,A:14713351178;C:10191139050;G:10897887675;T:14095967201;N:4243526,90,,,,14713351178,10191139050,10897887675,14095967201,4243526,ERX5504345,ERS6343449,ERA4142789,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.91197,,0.29137,,0.7568,,0.56523,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-05-24,Larval,Larval,Spinal Cord,Nervous System
10186,ERR6212423,ERX5847531,ERS7094943,ERP130388,PRJEB46176,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10379_3,Transcriptome Analysis,To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution  we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Naive,SAMEA9361876,University Of Edinburgh,ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361876|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Naive|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|organism part:spinal cord|sample name:E MTAB 10379 3:Naive|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10379 3:Naive p,Naive p,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP130388,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,Mpeg_Naive_I1.fastq.gz Mpeg_Naive_R1.fastq.gz Mpeg_Naive_R2.fastq.gz,fastq fastq fastq,60168324125.0,481346593.0,E MTAB 10379 3:Naive,0:8 1:27 2:90,A:12424400694;C:9366563781;G:10029312355;T:11497237299;N:3679241,8,27,90,,12424400694,9366563781,10029312355,11497237299,3679241,ERX5847531,ERS7094943,ERA5186263,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.94834,,0.09482,,0.802,,0.5277,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-07-08,Larval,Larval,Multi-tissue,Multi-system
10187,ERR6212422,ERX5847530,ERS7094942,ERP130388,PRJEB46176,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10379_3,Transcriptome Analysis,To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution  we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Lesi1d,SAMEA9361875,University Of Edinburgh,ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361875|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Lesi1d|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|injury:spinal cord lesion|organism part:spinal cord|sample name:E MTAB 10379 3:Lesi1d|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10379 3:Lesioned p,Lesioned p,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Experimental Factor: injury:spinal cord lesion,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP130388,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,Mpeg_Lesioned_I1.fastq.gz Mpeg_Lesioned_R1.fastq.gz Mpeg_Lesioned_R2.fastq.gz,fastq fastq fastq,61701873000.0,493614984.0,E MTAB 10379 3:Lesioned,0:8 1:27 2:90,A:12952533019;C:9222397450;G:9920185920;T:12326470894;N:3761277,8,27,90,,12952533019,9222397450,9920185920,12326470894,3761277,ERX5847530,ERS7094942,ERA5186263,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.93082,,0.10862,,0.80302,,0.54924,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-07-08,Larval,Larval,Multi-tissue,Multi-system
10403,ERR8527374,ERX8137561,ERS10539829,ERP135430,PRJEB50826,scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,E-MTAB-11079_2,Transcriptome Analysis,Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted  from pooled kidneys of ren+/+ or ren /  zebrafish  which carried ren:RFP and acta2:EGFP reporter genes  allowing the isolation of renin expressing cells and smooth muscle cells.,ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10,,Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA  specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.,ZF2,SAMEA12941033,University Of Edinburgh,ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941033|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF2|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP; ren / |individual:9 12 kidneys pooled|inferred cell type:recruited RLC|organism part:kidney|phenotype:ren knockout|sample name:E MTAB 11079 2:ZF2|sex:mixed|strain:WIK,,,,,,,,,NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,E MTAB 11079 2:ZF2 p,ZF2 p,scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively.  Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA   specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.,Experimental Factor: phenotype:ren knockout,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,NextSeq 500,,ERP135430,NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10,ZF2_S2_L002_I1_001.fastq.gz ZF2_S2_L002_R1_001.fastq.gz ZF2_S2_L002_R2_001.fastq.gz,fastq fastq fastq,38557081640.0,125185330.0,E MTAB 11079 2:ZF2 S2 L002,0:8 1:150 2:150,A:13781315856;C:6436030786;G:6578059630;T:10759631611;N:561117,8,150,150,,13781315856,6436030786,6578059630,10759631611,561117,ERX8137561,ERS10539829,ERA9016154,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.0,0.84449,0.0,0.09657,1.0,0.8242,,0.52635,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,size_fractionation,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-06-10,Adult,Adult,Multi-tissue,Multi-system
10404,ERR8527377,ERX8137561,ERS10539829,ERP135430,PRJEB50826,scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,E-MTAB-11079_2,Transcriptome Analysis,Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted  from pooled kidneys of ren+/+ or ren /  zebrafish  which carried ren:RFP and acta2:EGFP reporter genes  allowing the isolation of renin expressing cells and smooth muscle cells.,ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10,,Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA  specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.,ZF2,SAMEA12941033,University Of Edinburgh,ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941033|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF2|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP; ren / |individual:9 12 kidneys pooled|inferred cell type:recruited RLC|organism part:kidney|phenotype:ren knockout|sample name:E MTAB 11079 2:ZF2|sex:mixed|strain:WIK,,,,,,,,,NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,E MTAB 11079 2:ZF2 p,ZF2 p,scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively.  Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA   specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.,Experimental Factor: phenotype:ren knockout,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,NextSeq 500,,ERP135430,NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10,ZF2_S2_L001_I1_001.fastq.gz ZF2_S2_L001_R1_001.fastq.gz ZF2_S2_L001_R2_001.fastq.gz,fastq fastq fastq,38872269128.0,126208666.0,E MTAB 11079 2:ZF2 S2 L001,0:8 1:150 2:150,A:15151865400;C:6355030057;G:6591732598;T:9763441371;N:530374,8,150,150,,15151865400,6355030057,6591732598,9763441371,530374,ERX8137561,ERS10539829,ERA9016154,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.0,0.84526,0.0,0.09779,1.0,0.82609,,0.54388,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,size_fractionation,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-06-10,Adult,Adult,Multi-tissue,Multi-system
10405,ERR8527376,ERX8137560,ERS10539828,ERP135430,PRJEB50826,scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,E-MTAB-11079_2,Transcriptome Analysis,Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted  from pooled kidneys of ren+/+ or ren /  zebrafish  which carried ren:RFP and acta2:EGFP reporter genes  allowing the isolation of renin expressing cells and smooth muscle cells.,ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10,,Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA  specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.,ZF1,SAMEA12941032,University Of Edinburgh,ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941032|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF1|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP|individual:9 12 kidneys pooled|inferred cell type:juxtaglomerular cell|organism part:kidney|phenotype:wild type|sample name:E MTAB 11079 2:ZF1|sex:mixed|strain:WIK,,,,,,,,,NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,E MTAB 11079 2:ZF1 p,ZF1 p,scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively.  Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA   specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.,Experimental Factor: phenotype:wild type,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,NextSeq 500,,ERP135430,NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10,ZF1_S1_L002_I1_001.fastq.gz ZF1_S1_L002_R1_001.fastq.gz ZF1_S1_L002_R2_001.fastq.gz,fastq fastq fastq,39415722500.0,127973125.0,E MTAB 11079 2:ZF1 S1 L002,0:8 1:150 2:150,A:14261012964;C:6339158428;G:6467430919;T:11323758989;N:576200,8,150,150,,14261012964,6339158428,6467430919,11323758989,576200,ERX8137560,ERS10539828,ERA9016154,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.0,0.81065,0.0,0.08289,1.0,0.82434,,0.52903,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,size_fractionation,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-06-10,Adult,Adult,Multi-tissue,Multi-system
10406,ERR8527375,ERX8137560,ERS10539828,ERP135430,PRJEB50826,scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,E-MTAB-11079_2,Transcriptome Analysis,Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted  from pooled kidneys of ren+/+ or ren /  zebrafish  which carried ren:RFP and acta2:EGFP reporter genes  allowing the isolation of renin expressing cells and smooth muscle cells.,ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10,,Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA  specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.,ZF1,SAMEA12941032,University Of Edinburgh,ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941032|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF1|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP|individual:9 12 kidneys pooled|inferred cell type:juxtaglomerular cell|organism part:kidney|phenotype:wild type|sample name:E MTAB 11079 2:ZF1|sex:mixed|strain:WIK,,,,,,,,,NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,E MTAB 11079 2:ZF1 p,ZF1 p,scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml  DNAse 400units/ml  Liberase 0.085mg/ml  collagenase 2mg/ml and CaCl2 5mM  at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence  and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence  in order to sort renin expressing cells and smooth muscle cells respectively.  Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly  an sgRNA   specifically targeting exon 2 of the renin gene  was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren /  knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics  PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics  PN 120236 according to manufacturers instructions.,Experimental Factor: phenotype:wild type,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,NextSeq 500,,ERP135430,NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish,ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10,ZF1_S1_L001_I1_001.fastq.gz ZF1_S1_L001_R1_001.fastq.gz ZF1_S1_L001_R2_001.fastq.gz,fastq fastq fastq,39744721324.0,129041303.0,E MTAB 11079 2:ZF1 S1 L001,0:8 1:150 2:150,A:15670316830;C:6278039908;G:6505806971;T:10257683184;N:544007,8,150,150,,15670316830,6278039908,6505806971,10257683184,544007,ERX8137560,ERS10539828,ERA9016154,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.0,0.81031,0.0,0.08495,1.0,0.82169,,0.51724,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,size_fractionation,unknown,sc,single_cell_droplet,10x,,United Kingdom,2022-06-10,Adult,Adult,Multi-tissue,Multi-system
11017,ERR9750937,ERX9298876,ERS12023662,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 2 Uninjured,SAMEA14418104,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418104|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 2 Uninjured|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:heart|sample name:E MTAB 10643:Expt 2 Uninjured|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 2 Uninjured p,Expt 2 Uninjured p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:n1|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E2_Uninjured_S2_L002_I1_001.fastq.gz E2_Uninjured_S2_L002_I2_001.fastq.gz E2_Uninjured_S2_L002_R1_001.fastq.gz E2_Uninjured_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9325673775.0,69079065.0,E MTAB 10643:Expt 2 Uninjured,0:10 1:10 2:28 3:87,A:1619571910;C:1420805235;G:1471531128;T:1496998088;N:972294,10,10,28,87,1619571910,1420805235,1471531128,1496998088,972294,ERX9298876,ERS12023662,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.93798,,0.11364,,0.84843,,0.53531,,87,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11018,ERR9750936,ERX9298875,ERS12023661,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 2 Sham,SAMEA14418103,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418103|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 2 Sham|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:sham surgery|organism part:heart|sample name:E MTAB 10643:Expt 2 Sham|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 2 Sham p,Expt 2 Sham p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:sham surgery|Experimental Factor: time:3|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E2_Sham_S1_L002_I1_001.fastq.gz E2_Sham_S1_L002_I2_001.fastq.gz E2_Sham_S1_L002_R1_001.fastq.gz E2_Sham_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11328674040.0,83916104.0,E MTAB 10643:Expt 2 Sham,0:10 1:10 2:28 3:87,A:1955327720;C:1746332187;G:1777122701;T:1820705338;N:1213102,10,10,28,87,1955327720,1746332187,1777122701,1820705338,1213102,ERX9298875,ERS12023661,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.92847,,0.09981,,0.85707,,0.46947,,87,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11019,ERR9750935,ERX9298874,ERS12023660,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 2 3d post amputation,SAMEA14418102,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418102|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 2 3d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 2 3d post amputation|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 2 3d post amputation p,Expt 2 3d post amputation p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:3|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E2_3dpa_S3_L002_I1_001.fastq.gz E2_3dpa_S3_L002_I2_001.fastq.gz E2_3dpa_S3_L002_R1_001.fastq.gz E2_3dpa_S3_L002_R2_001.fastq.gz,fastq fastq fastq fastq,16111486440.0,119344344.0,E MTAB 10643:Expt 2 3d post amputation,0:10 1:10 2:28 3:87,A:2610144058;C:2617445332;G:2496763759;T:2656876552;N:1728227,10,10,28,87,2610144058,2617445332,2496763759,2656876552,1728227,ERX9298874,ERS12023660,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.94868,,0.07071,,0.89221,,0.54333,,87,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11020,ERR9750934,ERX9298873,ERS12023659,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 3 3d post amputation + MMP inhibitor,SAMEA14418101,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418101|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor|sex:male|strain:AB|treatment:matrix metalloproteinase inhibitor,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor p,Expt 3 3d post amputation + MMP inhibitor p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:3|Experimental Factor: treatment:matrix metalloproteinase inhibitor,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E2_3dpa_inhibitor_S4_L002_I1_001.fastq.gz E2_3dpa_inhibitor_S4_L002_I2_001.fastq.gz E2_3dpa_inhibitor_S4_L002_R1_001.fastq.gz E2_3dpa_inhibitor_S4_L002_R2_001.fastq.gz,fastq fastq fastq fastq,8621019270.0,63859402.0,E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor,0:10 1:10 2:28 3:87,A:1438763050;C:1365497247;G:1350808021;T:1399773154;N:926502,10,10,28,87,1438763050,1365497247,1350808021,1399773154,926502,ERX9298873,ERS12023659,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.92796,,0.08671,,0.87176,,0.55088,,87,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11021,ERR9750933,ERX9298872,ERS12023658,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 1 Uninjured,SAMEA14418100,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418100|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 Uninjured|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:heart|sample name:E MTAB 10643:Expt 1 Uninjured|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 1 Uninjured p,Expt 1 Uninjured p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:n1|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E1_Uninjured_S1_L002_I1_001.fastq.gz E1_Uninjured_S1_L002_R1_001.fastq.gz E1_Uninjured_S1_L002_R2_001.fastq.gz,fastq fastq fastq,8575585211.0,67524293.0,E MTAB 10643:Expt 1 Uninjured,0:8 1:28 2:91,A:1801503847;C:1312196506;G:1367890726;T:1663053783;N:65801,8,28,91,,1801503847,1312196506,1367890726,1663053783,65801,ERX9298872,ERS12023658,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.9169,,0.11202,,0.81576,,0.54253,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11022,ERR9750932,ERX9298871,ERS12023657,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 1 7d post amputation,SAMEA14418099,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418099|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 7d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 1 7d post amputation|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 1 7d post amputation p,Expt 1 7d post amputation p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:7|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E1_7d_S3_L002_I1_001.fastq.gz E1_7d_S3_L002_R1_001.fastq.gz E1_7d_S3_L002_R2_001.fastq.gz,fastq fastq fastq,17341796660.0,136549580.0,E MTAB 10643:Expt 1 7d post amputation,0:8 1:28 2:91,A:3506600812;C:2774617588;G:2814960106;T:3329701112;N:132162,8,28,91,,3506600812,2774617588,2814960106,3329701112,132162,ERX9298871,ERS12023657,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.90616,,0.09608,,0.82446,,0.46632,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11023,ERR9750931,ERX9298870,ERS12023656,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 1 3d post amputation,SAMEA14418098,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418098|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 3d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 1 3d post amputation|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 1 3d post amputation p,Expt 1 3d post amputation p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:3|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E1_3d_S2_L002_I1_001.fastq.gz E1_3d_S2_L002_R1_001.fastq.gz E1_3d_S2_L002_R2_001.fastq.gz,fastq fastq fastq,8183008018.0,64433134.0,E MTAB 10643:Expt 1 3d post amputation,0:8 1:28 2:91,A:1630460899;C:1330248096;G:1326144211;T:1576499358;N:62630,8,28,91,,1630460899,1330248096,1326144211,1576499358,62630,ERX9298870,ERS12023656,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.88759,,0.08679,,0.82948,,0.47863,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
11024,ERR9750930,ERX9298869,ERS12023655,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here  we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured  regenerating 3 days  7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured  sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment.  Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single  viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 1 14d post amputation,SAMEA14418097,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418097|INSDC center alias:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC center name:IGF  CNRS  INSERM  Univ. Montpellier  LabEx ICST  F 34094 Montpellier  France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 14d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 1 14d post amputation|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 1 14d post amputation p,Expt 1 14d post amputation p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this  tissue was gently dissociated and passed through a cell strainer 40um  spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation  RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:14|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E1_14d_S4_L002_I1_001.fastq.gz E1_14d_S4_L002_R1_001.fastq.gz E1_14d_S4_L002_R2_001.fastq.gz,fastq fastq fastq,12911908390.0,101668570.0,E MTAB 10643:Expt 1 14d post amputation,0:8 1:28 2:91,A:2700371496;C:1971281481;G:2062280628;T:2517806408;N:99857,8,28,91,,2700371496,1971281481,2062280628,2517806408,99857,ERX9298869,ERS12023655,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.90771,,0.11048,,0.81523,,0.53024,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System
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
11753,ERR11758614,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S25_L001_R1_001.fastq.gz FliTp124hpf_S25_L001_R2_001.fastq.gz,fastq fastq,226833768.0,1800268.0,E MTAB 13196:FliTp124hpf S25 L001,0:28 1:98,A:65319978;C:50920193;G:49999849;T:60474280;N:119468,28,98,,,65319978,50920193,49999849,60474280,119468,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00122,0.88236,0.00056,0.09684,0.9978,0.89309,0.424,0.44186,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11754,ERR11758619,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S27_L001_R1_001.fastq.gz FliTp124hpf_S27_L001_R2_001.fastq.gz,fastq fastq,261098334.0,2072209.0,E MTAB 13196:FliTp124hpf S27 L001,0:28 1:98,A:76098436;C:58031830;G:57099955;T:69729759;N:138354,28,98,,,76098436,58031830,57099955,69729759,138354,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00109,0.87641,0.00062,0.0976,0.99837,0.90065,0.45555,0.48712,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11755,ERR11758589,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S16_L005_R1_001.fastq.gz FliTp124hpf_S16_L005_R2_001.fastq.gz,fastq fastq,1168367130.0,9272755.0,E MTAB 13196:FliTp124hpf S16 L005,0:28 1:98,A:323651598;C:269884286;G:268030176;T:306695030;N:106040,28,98,,,323651598,269884286,268030176,306695030,106040,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00491,0.90853,0.00131,0.07851,0.99019,0.84331,0.41536,0.48076,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11756,ERR11758638,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S22_L001_R1_001.fastq.gz FliTp124hpf_S22_L001_R2_001.fastq.gz,fastq fastq,864786636.0,6863386.0,E MTAB 13196:FliTp124hpf S22 L001,0:28 1:98,A:241767760;C:198370882;G:198049093;T:226508751;N:90150,28,98,,,241767760,198370882,198049093,226508751,90150,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00375,0.89002,0.00114,0.0769,0.99237,0.84563,0.41796,0.48995,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11757,ERR11758599,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S15_L005_R1_001.fastq.gz FliTp124hpf_S15_L005_R2_001.fastq.gz,fastq fastq,1795799502.0,14252377.0,E MTAB 13196:FliTp124hpf S15 L005,0:28 1:98,A:500590460;C:413239086;G:410401125;T:471402890;N:165941,28,98,,,500590460,413239086,410401125,471402890,165941,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00492,0.91242,0.0012,0.08044,0.99007,0.84668,0.42778,0.49291,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11758,ERR11758601,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S26_L001_R1_001.fastq.gz FliTp124hpf_S26_L001_R2_001.fastq.gz,fastq fastq,266141358.0,2112233.0,E MTAB 13196:FliTp124hpf S26 L001,0:28 1:98,A:76996100;C:59592346;G:58963461;T:70457732;N:131719,28,98,,,76996100,59592346,58963461,70457732,131719,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00106,0.88422,0.00046,0.09358,0.99782,0.89449,0.47826,0.48948,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11759,ERR11758630,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S14_L005_R1_001.fastq.gz FliTp124hpf_S14_L005_R2_001.fastq.gz,fastq fastq,1812847428.0,14387678.0,E MTAB 13196:FliTp124hpf S14 L005,0:28 1:98,A:502956890;C:417865079;G:416595454;T:475266679;N:163326,28,98,,,502956890,417865079,416595454,475266679,163326,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00483,0.91317,0.00123,0.07918,0.99036,0.84143,0.40704,0.4819,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11760,ERR11758603,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S13_L005_R1_001.fastq.gz FliTp124hpf_S13_L005_R2_001.fastq.gz,fastq fastq,1544281830.0,12256205.0,E MTAB 13196:FliTp124hpf S13 L005,0:28 1:98,A:428008915;C:356252081;G:354333187;T:405545992;N:141655,28,98,,,428008915,356252081,354333187,405545992,141655,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00507,0.91025,0.00138,0.07858,0.98987,0.84295,0.41793,0.4891,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11761,ERR11758613,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S21_L001_R1_001.fastq.gz FliTp124hpf_S21_L001_R2_001.fastq.gz,fastq fastq,761441436.0,6043186.0,E MTAB 13196:FliTp124hpf S21 L001,0:28 1:98,A:212876877;C:174700212;G:174244892;T:199537401;N:82054,28,98,,,212876877,174700212,174244892,199537401,82054,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00334,0.88899,0.00106,0.07762,0.99322,0.84476,0.42792,0.48783,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11762,ERR11758645,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S23_L001_R1_001.fastq.gz FliTp124hpf_S23_L001_R2_001.fastq.gz,fastq fastq,873938772.0,6936022.0,E MTAB 13196:FliTp124hpf S23 L001,0:28 1:98,A:245075115;C:199879929;G:199312177;T:229576663;N:94888,28,98,,,245075115,199879929,199312177,229576663,94888,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00361,0.88671,0.00104,0.07855,0.99255,0.84723,0.41141,0.4885,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11763,ERR11758598,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S28_L001_R1_001.fastq.gz FliTp124hpf_S28_L001_R2_001.fastq.gz,fastq fastq,164465532.0,1305282.0,E MTAB 13196:FliTp124hpf S28 L001,0:28 1:98,A:47319366;C:37063279;G:36394680;T:43602586;N:85621,28,98,,,47319366,37063279,36394680,43602586,85621,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00117,0.88222,0.00058,0.09358,0.99799,0.89217,0.54867,0.48545,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11764,ERR11758593,ERX11157721,ERS16172939,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,fli1tp1 24hpf,SAMEA114192246,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192246|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:fli1tp1 24hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:fli1:DsRed  tp1:eGFP|geographic location country and/or sea:not collected|immunophenotype:fli1:DsRed+  tp1:eGFP+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:fli1tp1 24hpf|scientific name:Danio rerio|strain:fli1:DsRed  tp1:eGFP,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:fli1tp1 24hpf p,fli1tp1 24hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,FliTp124hpf_S24_L001_R1_001.fastq.gz FliTp124hpf_S24_L001_R2_001.fastq.gz,fastq fastq,558365976.0,4431476.0,E MTAB 13196:FliTp124hpf S24 L001,0:28 1:98,A:156054630;C:128109738;G:127885708;T:146256146;N:59754,28,98,,,156054630,128109738,127885708,146256146,59754,ERX11157721,ERS16172939,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00345,0.8879,0.00104,0.07718,0.99322,0.84364,0.38266,0.49193,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11765,ERR11758635,ERX11157720,ERS16172938,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 wt 22hpf,SAMEA114192245,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 wt 22hpf p,etv2 wt 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2Kaede_WT_S6_L001_R1_001.fastq.gz Etv2Kaede_WT_S6_L001_R2_001.fastq.gz,fastq fastq,1144014102.0,9079477.0,E MTAB 13196:Etv2Kaede WT S6 L001,0:28 1:98,A:316366230;C:260322813;G:259447166;T:307680623;N:197270,28,98,,,316366230,260322813,259447166,307680623,197270,ERX11157720,ERS16172938,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00336,0.89267,0.00137,0.13734,0.99545,0.81957,0.3734,0.53458,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11766,ERR11758622,ERX11157720,ERS16172938,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 wt 22hpf,SAMEA114192245,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 wt 22hpf p,etv2 wt 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2Kaede_WT_S8_L001_R2_001.fastq.gz Etv2Kaede_WT_S8_L001_R1_001.fastq.gz,fastq fastq,919270926.0,7295801.0,E MTAB 13196:Etv2Kaede WT S8 L001,0:28 1:98,A:259787542;C:207541571;G:206711907;T:245072713;N:157193,28,98,,,259787542,207541571,206711907,245072713,157193,ERX11157720,ERS16172938,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00358,0.88757,0.00137,0.15368,0.99551,0.83378,0.36405,0.53733,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11767,ERR11758644,ERX11157720,ERS16172938,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 wt 22hpf,SAMEA114192245,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 wt 22hpf p,etv2 wt 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2Kaede_WT_S5_L001_R2_001.fastq.gz Etv2Kaede_WT_S5_L001_R1_001.fastq.gz,fastq fastq,877658166.0,6965541.0,E MTAB 13196:Etv2Kaede WT S5 L001,0:28 1:98,A:243057461;C:199464116;G:198654377;T:236322700;N:159512,28,98,,,243057461,199464116,198654377,236322700,159512,ERX11157720,ERS16172938,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00328,0.88916,0.00127,0.13782,0.99559,0.81925,0.38227,0.53623,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11768,ERR11758628,ERX11157720,ERS16172938,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 wt 22hpf,SAMEA114192245,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192245|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 wt 22hpf|age:24|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:24 hpf|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 wt 22hpf|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 wt 22hpf p,etv2 wt 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2Kaede_WT_S7_L001_R1_001.fastq.gz Etv2Kaede_WT_S7_L001_R2_001.fastq.gz,fastq fastq,930443598.0,7384473.0,E MTAB 13196:Etv2Kaede WT S7 L001,0:28 1:98,A:258539610;C:211017108;G:209074684;T:251641766;N:170430,28,98,,,258539610,211017108,209074684,251641766,170430,ERX11157720,ERS16172938,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00355,0.88938,0.00148,0.14297,0.99569,0.83358,0.35626,0.53314,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
11769,ERR11758631,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S10_L001_R2_001.fastq.gz Etv2_Traver_S10_L001_R1_001.fastq.gz,fastq fastq,1947733326.0,15458201.0,E MTAB 13196:Etv2 Traver S10 L001,0:28 1:98,A:532150077;C:434208725;G:472140578;T:508906834;N:327112,28,98,,,532150077,434208725,472140578,508906834,327112,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00677,0.92596,0.00142,0.07895,0.98526,0.85123,0.42802,0.53518,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11770,ERR11758646,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S28_L001_R2_001.fastq.gz Etv2_Traver_S28_L001_R1_001.fastq.gz,fastq fastq,1091426920.0,8801830.0,E MTAB 13196:Etv2 Traver S28 L001,0:26 1:98,A:302665480;C:247712584;G:269795015;T:271081940;N:171901,26,98,,,302665480,247712584,269795015,271081940,171901,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00585,0.90012,0.00149,0.07225,0.98746,0.84916,0.39007,0.54873,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11771,ERR11758602,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S25_L001_R2_001.fastq.gz Etv2_Traver_S25_L001_R1_001.fastq.gz,fastq fastq,983616732.0,7932393.0,E MTAB 13196:Etv2 Traver S25 L001,0:26 1:98,A:272974243;C:222949925;G:242884450;T:244652916;N:155198,26,98,,,272974243,222949925,242884450,244652916,155198,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00571,0.90139,0.00143,0.07484,0.98756,0.85019,0.40119,0.54977,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11772,ERR11758647,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S27_L001_R2_001.fastq.gz Etv2_Traver_S27_L001_R1_001.fastq.gz,fastq fastq,1162223232.0,9372768.0,E MTAB 13196:Etv2 Traver S27 L001,0:26 1:98,A:322910431;C:262934167;G:286614718;T:289578468;N:185448,26,98,,,322910431,262934167,286614718,289578468,185448,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00563,0.89924,0.00128,0.07464,0.98762,0.85064,0.38525,0.53889,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11773,ERR11758634,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S12_L001_R2_001.fastq.gz Etv2_Traver_S12_L001_R1_001.fastq.gz,fastq fastq,1979462268.0,15710018.0,E MTAB 13196:Etv2 Traver S12 L001,0:28 1:98,A:539088187;C:442520328;G:480420115;T:517077908;N:355730,28,98,,,539088187,442520328,480420115,517077908,355730,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00707,0.9236,0.00137,0.07727,0.98451,0.85021,0.41845,0.56136,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11774,ERR11758642,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S9_L001_R2_001.fastq.gz Etv2_Traver_S9_L001_R1_001.fastq.gz,fastq fastq,1809560214.0,14361589.0,E MTAB 13196:Etv2 Traver S9 L001,0:28 1:98,A:493206820;C:403886293;G:438502430;T:473641472;N:323199,28,98,,,493206820,403886293,438502430,473641472,323199,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00668,0.92354,0.00141,0.0785,0.98543,0.84938,0.43326,0.52002,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11775,ERR11758623,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S26_L001_R2_001.fastq.gz Etv2_Traver_S26_L001_R1_001.fastq.gz,fastq fastq,1074533780.0,8665595.0,E MTAB 13196:Etv2 Traver S26 L001,0:26 1:98,A:298569273;C:243430874;G:265536499;T:266825982;N:171152,26,98,,,298569273,243430874,265536499,266825982,171152,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00579,0.90109,0.00136,0.07564,0.98788,0.85017,0.3554,0.54362,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11776,ERR11758596,ERX11157719,ERS16172937,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,etv2 15s,SAMEA114192244,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192244|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:etv2 15s|age:16.5|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:15 somite stage|genotype:etv2:Kaede|geographic location country and/or sea:not collected|immunophenotype:etv2:Kaede+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:etv2 15s|scientific name:Danio rerio|strain:etv2:Kaede,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:etv2 15s p,etv2 15s p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,Etv2_Traver_S11_L001_R2_001.fastq.gz Etv2_Traver_S11_L001_R1_001.fastq.gz,fastq fastq,2167279758.0,17200633.0,E MTAB 13196:Etv2 Traver S11 L001,0:28 1:98,A:591928396;C:482735357;G:524267488;T:567952272;N:396245,28,98,,,591928396,482735357,524267488,567952272,396245,ERX11157719,ERS16172937,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00635,0.92351,0.00136,0.07835,0.9865,0.85204,0.41521,0.53672,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11777,ERR11758595,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S36_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S36_L001_R1_001.fastq.gz,fastq fastq,211593816.0,1679316.0,E MTAB 13196:drl h2b dendra tb S36 L001,0:28 1:98,A:62689430;C:45809168;G:45709128;T:57272091;N:113999,28,98,,,62689430,45809168,45709128,57272091,113999,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00192,0.91331,0.00072,0.14588,0.99675,0.89292,0.51304,0.63144,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11778,ERR11758629,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S37_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S37_L001_R1_001.fastq.gz,fastq fastq,980164836.0,7779086.0,E MTAB 13196:drl h2b dendra tb S37 L001,0:28 1:98,A:281375011;C:216067640;G:222839674;T:259781180;N:101331,28,98,,,281375011,216067640,222839674,259781180,101331,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00817,0.89718,0.00237,0.12153,0.98912,0.82643,0.46403,0.64954,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11779,ERR11758618,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S39_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S39_L001_R1_001.fastq.gz,fastq fastq,12118302.0,96177.0,E MTAB 13196:drl h2b dendra tb S39 L001,0:28 1:98,A:3543790;C:2662872;G:2728134;T:3182383;N:1123,28,98,,,3543790,2662872,2728134,3182383,1123,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00786,0.88963,0.0025,0.12543,0.99403,0.88635,0.50098,0.64694,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11780,ERR11758643,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S5_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S5_L005_R1_001.fastq.gz,fastq fastq,2061022698.0,16357323.0,E MTAB 13196:drl h2b dendra tb S5 L005,0:28 1:98,A:587730953;C:457631700;G:470283474;T:545196979;N:179592,28,98,,,587730953,457631700,470283474,545196979,179592,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.01192,0.91661,0.00336,0.12397,0.98518,0.82568,0.45692,0.65555,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11781,ERR11758610,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S38_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S38_L001_R1_001.fastq.gz,fastq fastq,924603120.0,7338120.0,E MTAB 13196:drl h2b dendra tb S38 L001,0:28 1:98,A:265987815;C:203824483;G:210024160;T:244670646;N:96016,28,98,,,265987815,203824483,210024160,244670646,96016,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00773,0.89881,0.00242,0.12145,0.98944,0.82948,0.50529,0.66568,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11782,ERR11758641,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S6_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S6_L005_R1_001.fastq.gz,fastq fastq,1954661562.0,15513187.0,E MTAB 13196:drl h2b dendra tb S6 L005,0:28 1:98,A:558769608;C:433724557;G:445550100;T:516443984;N:173313,28,98,,,558769608,433724557,445550100,516443984,173313,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.0125,0.91697,0.00373,0.12359,0.98447,0.82558,0.4881,0.6456,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11783,ERR11758591,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S35_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S35_L001_R1_001.fastq.gz,fastq fastq,4717188.0,37438.0,E MTAB 13196:drl h2b dendra tb S35 L001,0:28 1:98,A:1419430;C:1014265;G:1016661;T:1264642;N:2190,28,98,,,1419430,1014265,1016661,1264642,2190,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.0012,0.65482,0.00054,0.10783,0.99953,0.97157,0.625,0.63689,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11784,ERR11758606,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S34_L001_R1_001.fastq.gz drl_h2b-dendra_tb_S34_L001_R2_001.fastq.gz,fastq fastq,303645636.0,2409886.0,E MTAB 13196:drl h2b dendra tb S34 L001,0:28 1:98,A:90748559;C:65369482;G:65969002;T:81405258;N:153335,28,98,,,90748559,65369482,65969002,81405258,153335,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00228,0.91262,0.00099,0.14666,0.99638,0.89006,0.47177,0.63109,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11785,ERR11758640,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S40_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S40_L001_R1_001.fastq.gz,fastq fastq,661361022.0,5248897.0,E MTAB 13196:drl h2b dendra tb S40 L001,0:28 1:98,A:190087869;C:145985661;G:150124621;T:175095762;N:67109,28,98,,,190087869,145985661,150124621,175095762,67109,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00785,0.89784,0.00251,0.12159,0.98948,0.83055,0.46095,0.64951,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11786,ERR11758605,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S7_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S7_L005_R1_001.fastq.gz,fastq fastq,25157790.0,199665.0,E MTAB 13196:drl h2b dendra tb S7 L005,0:28 1:98,A:7330053;C:5600451;G:5635840;T:6589498;N:1948,28,98,,,7330053,5600451,5635840,6589498,1948,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.01201,0.91385,0.00341,0.12826,0.98595,0.85161,0.49226,0.64953,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11787,ERR11758600,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S8_L005_R2_001.fastq.gz drl_h2b-dendra_tb_S8_L005_R1_001.fastq.gz,fastq fastq,1422735804.0,11291554.0,E MTAB 13196:drl h2b dendra tb S8 L005,0:28 1:98,A:405788442;C:317299433;G:322206476;T:377317416;N:124037,28,98,,,405788442,317299433,322206476,377317416,124037,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.01226,0.91547,0.0037,0.12565,0.9849,0.83662,0.48279,0.64531,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11788,ERR11758616,ERX11157718,ERS16172936,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl tb,SAMEA114192243,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192243|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl tb|age:10|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:tail bud prominent stage|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl tb|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl tb p,drl tb p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_tb_S33_L001_R2_001.fastq.gz drl_h2b-dendra_tb_S33_L001_R1_001.fastq.gz,fastq fastq,328918212.0,2610462.0,E MTAB 13196:drl h2b dendra tb S33 L001,0:28 1:98,A:98036464;C:71090137;G:71650807;T:87969481;N:171323,28,98,,,98036464,71090137,71650807,87969481,171323,ERX11157718,ERS16172936,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00197,0.89969,0.00087,0.14269,0.99681,0.89134,0.49763,0.63651,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Undetermined,Embryo,Embryo Imprecise,All anatomical structures
11789,ERR11758588,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S12_L005_R2_001.fastq.gz drl_h2b-dendra_22hpf_S12_L005_R1_001.fastq.gz,fastq fastq,970032168.0,7698668.0,E MTAB 13196:drl h2b dendra 22hpf S12 L005,0:28 1:98,A:268176072;C:223973927;G:223251001;T:254545365;N:85803,28,98,,,268176072,223973927,223251001,254545365,85803,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00525,0.91336,0.00127,0.06812,0.98995,0.85395,0.40891,0.4918,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11790,ERR11758597,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S42_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S42_L001_R1_001.fastq.gz,fastq fastq,716572206.0,5687081.0,E MTAB 13196:drl h2b dendra 22hpf S42 L001,0:28 1:98,A:198614388;C:164584363;G:164633280;T:188663484;N:76691,28,98,,,198614388,164584363,164633280,188663484,76691,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00366,0.8889,0.00092,0.06467,0.99261,0.84946,0.41353,0.49235,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11791,ERR11758637,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S44_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S44_L001_R1_001.fastq.gz,fastq fastq,481216932.0,3819182.0,E MTAB 13196:drl h2b dendra 22hpf S44 L001,0:28 1:98,A:133704525;C:110630722;G:110586099;T:126246571;N:49015,28,98,,,133704525,110630722,110586099,126246571,49015,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00352,0.89199,0.00099,0.06481,0.99308,0.85251,0.50101,0.49137,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11792,ERR11758617,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S41_L001_R1_001.fastq.gz drl_h2b-dendra_22hpf_S41_L001_R2_001.fastq.gz,fastq fastq,690504570.0,5480195.0,E MTAB 13196:drl h2b dendra 22hpf S41 L001,0:28 1:98,A:191676994;C:159013582;G:158945690;T:180795403;N:72901,28,98,,,191676994,159013582,158945690,180795403,72901,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00342,0.89103,0.00091,0.06637,0.99289,0.85196,0.42362,0.49417,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11793,ERR11758627,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S10_L005_R2_001.fastq.gz drl_h2b-dendra_22hpf_S10_L005_R1_001.fastq.gz,fastq fastq,1443584898.0,11457023.0,E MTAB 13196:drl h2b dendra 22hpf S10 L005,0:28 1:98,A:398056083;C:333283767;G:332935857;T:379178009;N:131182,28,98,,,398056083,333283767,332935857,379178009,131182,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00494,0.91295,0.00128,0.06617,0.99101,0.84855,0.40479,0.49207,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11794,ERR11758609,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S40_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S40_L001_R1_001.fastq.gz,fastq fastq,139186908.0,1104658.0,E MTAB 13196:drl h2b dendra 22hpf S40 L001,0:28 1:98,A:39986504;C:31169749;G:30838192;T:37121531;N:70932,28,98,,,39986504,31169749,30838192,37121531,70932,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00113,0.88601,0.00057,0.08145,0.99801,0.89808,0.48148,0.48722,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11795,ERR11758633,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S39_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S39_L001_R1_001.fastq.gz,fastq fastq,226310742.0,1796117.0,E MTAB 13196:drl h2b dendra 22hpf S39 L001,0:28 1:98,A:64619137;C:51094203;G:50285631;T:60191319;N:120452,28,98,,,64619137,51094203,50285631,60191319,120452,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00116,0.89046,0.00054,0.07999,0.99797,0.89739,0.58119,0.48393,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11796,ERR11758604,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S9_L005_R1_001.fastq.gz drl_h2b-dendra_22hpf_S9_L005_R2_001.fastq.gz,fastq fastq,1419705504.0,11267504.0,E MTAB 13196:drl h2b dendra 22hpf S9 L005,0:28 1:98,A:390831393;C:328833478;G:328344998;T:371567158;N:128477,28,98,,,390831393,328833478,328344998,371567158,128477,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.00519,0.91357,0.00132,0.0668,0.99042,0.84883,0.46254,0.47002,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
11797,ERR11758608,ERX11157717,ERS16172935,ERP149744,PRJEB64563,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E-MTAB-13196,Transcriptome Analysis,Development of the dorsal aorta is a key step in the establishment of the adult blood forming system  since hematopoietic stem and progenitor cells HSPCs arise from ventral aortic endothelium in all vertebrate animals studied.  Work in zebrafish has demonstrated that arterial and venous endothelial precursors arise from distinct subsets of lateral plate mesoderm.  Here  we profile the transcriptome of the earliest detectable endothelial cells ECs during zebrafish embryogenesis to demonstrate that tissue specific EC programs initiate much earlier than previously appreciated  by the end of gastrulation.  Classic studies in the chick embryo showed that paraxial mesoderm generates a subset of somite derived endothelial cells SDECs that incorporate into the dorsal aorta to replace HSPCs as they exit the aorta and enter circulation.    We describe a conserved program in the zebrafish  where a rare population of endothelial precursors delaminates from the dermomyotome to incorporate exclusively into the developing dorsal aorta.  Whereas SDECs lack hematopoietic potential  they act as a local niche to support the emergence of HSPCs from neighboring hemogenic endothelium.  Thus  at least three subsets of ECs contribute to the developing dorsal aorta:  vascular ECs  hemogenic ECs  and SDECs.  Taken together  our findings indicate that the distinct spatial origins of endothelial precursors dictate different cellular potentials within the developing dorsal aorta.,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,,Protocols: Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,drl 22hpf,SAMEA114192242,Institute of Molecular Genetics of the Czech Academy of Sciences,ENA FIRST PUBLIC:2023 08 01T00:17:16Z|ENA LAST UPDATE:2023 08 01T00:17:16Z|External Id:SAMEA114192242|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2023 08 01T00:17:16Z|INSDC last update:2023 08 01T00:17:16Z|INSDC status:public|Submitter Id:E MTAB 13196:drl 22hpf|age:22|broker name:ArrayExpress|cell type:endothelial cell|collection date:not collected|common name:zebrafish|developmental stage:22 hpf|genotype:drl:H2B Dendra2|geographic location country and/or sea:not collected|immunophenotype:drl:H2B Dendra2+|isolate:not applicable|organism part:embryo|sample name:E MTAB 13196:drl 22hpf|scientific name:Danio rerio|strain:drl:H2B Dendra2,,,,,,,,,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,E MTAB 13196:drl 22hpf p,drl 22hpf p,Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,Dechorionated embryos were collected at defined stages  dissociated by pipetting  centrifugation at 300g for 5 minutes  washed once with PBS  and sorted by FACS. Total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then re suspended in 1x PBS with 0.05% BSA at 800 3000 cells per ml. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3สน GEM  Library & Gel Bead Kit v2 or v3 was used for library preparation.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,PAIRED,ILLUMINA,Illumina HiSeq 2500,,ERP149744,Illumina HiSeq 2500 paired end sequencing; Single cell RNA seq 10x Chromium of FACS sorted drl:H2B Dendra2  etv2:Kaede  fli1:DsRed  and tp1:eGFP transgenic zebrafish embryos,ENA FIRST PUBLIC:2023 08 01|ENA LAST UPDATE:2023 08 01,drl_h2b-dendra_22hpf_S43_L001_R2_001.fastq.gz drl_h2b-dendra_22hpf_S43_L001_R1_001.fastq.gz,fastq fastq,744179814.0,5906189.0,E MTAB 13196:drl h2b dendra 22hpf S43 L001,0:28 1:98,A:206745595;C:171274047;G:171089532;T:194990120;N:80520,28,98,,,206745595,171274047,171089532,194990120,80520,ERX11157717,ERS16172935,ERA25628220,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive,2,0.0033,0.89238,0.00092,0.06573,0.99348,0.85307,0.42184,0.45487,28,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,Czech Republic,2023-08-01,Segmentation,Embryo,Embryo Imprecise,All anatomical structures