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
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
28725,SRR26623262,SRX22323921,SRS19374450,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep1  cirbpb scars,GSM7875190,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep1  cirbpb scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875190,GSM7875190: Lineage tracing rep1  cirbpb scars; Danio rerio; OTHER,GSM7875190 r1,GSM7875190,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP469552,,loader:fastq load.py,lin1_cirbpb_scar_R1.fastq.gz lin1_cirbpb_scar_R2.fastq.gz,fastq fastq,157576336.0,949552.0,GSM7875190 r1,,,,,,,,,,,,SRX22323921,SRS19374450,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00141,0.78069,0.00053,0.00877,0.99857,0.97822,0.33536,0.05199,28,120,T,B,sc-like readlen,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28726,SRR26623263,SRX22323920,SRS19374449,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep1  cfl1 scars,GSM7875189,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep1  cfl1 scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875189,GSM7875189: Lineage tracing rep1  cfl1 scars; Danio rerio; OTHER,GSM7875189 r1,GSM7875189,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP469552,,loader:fastq load.py,lin1_cfl1_scar_R2.fastq.gz lin1_cfl1_scar_R1.fastq.gz,fastq fastq,381453696.0,2184402.0,GSM7875189 r1,,,,,,,,,,,,SRX22323920,SRS19374449,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.0002,0.91626,0.00014,0.00132,0.99987,0.99726,0.16666,0.56363,28,120,T,B,sc-like readlen,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28727,SRR26623264,SRX22323919,SRS19374448,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep1  actb2 scars,GSM7875188,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep1  actb2 scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875188,GSM7875188: Lineage tracing rep1  actb2 scars; Danio rerio; OTHER,GSM7875188 r1,GSM7875188,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP469552,,loader:fastq load.py,lin1_actb2_scar_R1.fastq.gz lin1_actb2_scar_R2.fastq.gz,fastq fastq,491682118.0,2851156.0,GSM7875188 r1,,,,,,,,,,,,SRX22323919,SRS19374448,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00051,0.41901,0.00032,0.0029,0.99945,0.99182,0.57575,0.007,28,120,T,B,sc-like readlen,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28728,SRR26623265,SRX22323918,SRS19374446,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep1  actb1 scars,GSM7875187,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep1  actb1 scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875187,GSM7875187: Lineage tracing rep1  actb1 scars; Danio rerio; OTHER,GSM7875187 r1,GSM7875187,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP469552,,loader:fastq load.py,lin1_actb1_scar_R1.fastq.gz lin1_actb1_scar_R2.fastq.gz,fastq fastq,390405832.0,2283319.0,GSM7875187 r1,,,,,,,,,,,,SRX22323918,SRS19374446,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00038,0.73548,0.00017,0.00057,0.99963,0.99571,0.29729,0.00243,28,120,T,B,sc-like readlen,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28729,SRR26623266,SRX22323917,SRS19374447,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Brain 23   telencephalon  Notch inhibition  scSLAMseq,GSM7875186,,source name:adult brain|tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|treatment:Notch inhibition DAPT|geo loc name:missing|collection date:missing,Brain 23   telencephalon  Notch inhibition  scSLAMseq,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. Library strategy: scSLAM seq,adult brain,Notch inhibiton: zebrafish were incubated in a water bath containing system water with 50 µM DAPT Gamma Secretase Inhibitor  Sigma Aldrich for 48 hours.,The samples were prepared according to a scSLAM seq protocol  adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts  200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected  and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day  the reaction was quanched with a quenching buffer containing 100 mM DTT  post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|treatment:Notch inhibition DAPT,GSM7875186,GSM7875186: Brain 23   telencephalon  Notch inhibition  scSLAMseq; Danio rerio; OTHER,GSM7875186 r1,GSM7875186,1,The samples were prepared according to a scSLAM seq protocol  adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts  200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected  and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day  the reaction was quanched with a quenching buffer containing 100 mM DTT  post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469552,,loader:fastq load.py,b23_ni_tre_R1.fastq.gz b23_ni_tre_R2.fastq.gz,fastq fastq,62392458570.0,271271559.0,GSM7875186 r1,0:28 1:202,A:18682905645;C:13783082970;G:14751373116;T:15161083446;N:14013393,28,202,,,18682905645,13783082970,14751373116,15161083446,14013393,SRX22323917,SRS19374447,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.01404,0.82351,0.00466,0.1026,0.99129,0.86774,0.36033,0.67345,28,202,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28730,SRR26623267,SRX22323916,SRS19374445,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Brain 22   telencephalon  control  scSLAMseq,GSM7875185,,source name:adult brain|tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|treatment:Control DMSO|geo loc name:missing|collection date:missing,Brain 22   telencephalon  control  scSLAMseq,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. Library strategy: scSLAM seq,adult brain,Control for Notch inhibition: zebrafish were incubated in a water bath containing system water with 1:200 diluted DMSO for 48 hours.,The samples were prepared according to a scSLAM seq protocol  adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts  200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected  and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day  the reaction was quanched with a quenching buffer containing 100 mM DTT  post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|treatment:Control DMSO,GSM7875185,GSM7875185: Brain 22   telencephalon  control  scSLAMseq; Danio rerio; OTHER,GSM7875185 r1,GSM7875185,1,The samples were prepared according to a scSLAM seq protocol  adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts  200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected  and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day  the reaction was quanched with a quenching buffer containing 100 mM DTT  post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469552,,loader:fastq load.py,b22_ni_con_R1.fastq.gz b22_ni_con_R2.fastq.gz,fastq fastq,59793114490.0,259970063.0,GSM7875185 r1,0:28 1:202,A:18600519530;C:12714987967;G:14147370465;T:14316863915;N:13372613,28,202,,,18600519530,12714987967,14147370465,14316863915,13372613,SRX22323916,SRS19374445,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.01402,0.79448,0.00498,0.11405,0.99074,0.8518,0.39874,0.67082,28,202,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28754,SRR26623291,SRX22323897,SRS19374426,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep2  ube2e1 scars,GSM7875196,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep2  ube2e1 scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875196,GSM7875196: Lineage tracing rep2  ube2e1 scars; Danio rerio; OTHER,GSM7875196 r1,GSM7875196,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469552,,loader:fastq load.py,lin2_ube2e1_scar_R1.fastq.gz lin2_ube2e1_scar_R2.fastq.gz,fastq fastq,213092161.0,1190459.0,GSM7875196 r1,,,,,,,,,,,,SRX22323897,SRS19374426,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00752,0.90776,0.00286,0.01739,0.99346,0.95444,0.46002,0.96817,28,151,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28755,SRR26623292,SRX22323896,SRS19374425,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep2  rpl39 scars,GSM7875195,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep2  rpl39 scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875195,GSM7875195: Lineage tracing rep2  rpl39 scars; Danio rerio; OTHER,GSM7875195 r1,GSM7875195,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469552,,loader:fastq load.py,lin2_rpl39_scar_R2.fastq.gz lin2_rpl39_scar_R1.fastq.gz,fastq fastq,1023403502.0,5717338.0,GSM7875195 r1,,,,,,,,,,,,SRX22323896,SRS19374425,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00086,0.83744,0.0003,0.00337,0.99845,0.97057,0.26605,0.40241,28,151,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28756,SRR26623293,SRX22323895,SRS19374424,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep2  cirbpb scars,GSM7875194,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep2  cirbpb scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875194,GSM7875194: Lineage tracing rep2  cirbpb scars; Danio rerio; OTHER,GSM7875194 r1,GSM7875194,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469552,,loader:fastq load.py,lin2_cirbpb_scar_R1.fastq.gz lin2_cirbpb_scar_R2.fastq.gz,fastq fastq,276120388.0,1542572.0,GSM7875194 r1,,,,,,,,,,,,SRX22323895,SRS19374424,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00206,0.80328,0.00078,0.00662,0.9975,0.98039,0.55421,0.0258,28,151,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28757,SRR26623294,SRX22323894,SRS19374423,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep2  cfl1 scars,GSM7875193,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep2  cfl1 scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875193,GSM7875193: Lineage tracing rep2  cfl1 scars; Danio rerio; OTHER,GSM7875193 r1,GSM7875193,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP469552,,loader:fastq load.py,lin2_cfl1_scar_R1.fastq.gz lin2_cfl1_scar_R2.fastq.gz,fastq fastq,791318009.0,4420771.0,GSM7875193 r1,,,,,,,,,,,,SRX22323894,SRS19374423,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00067,0.46079,0.00055,0.16353,0.99965,0.99332,0.52631,0.44939,28,151,T,B,sc-like readlen,illumina,novaseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28758,SRR26623295,SRX22323893,SRS19374421,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep1  ube2e1 scars,GSM7875192,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep1  ube2e1 scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875192,GSM7875192: Lineage tracing rep1  ube2e1 scars; Danio rerio; OTHER,GSM7875192 r1,GSM7875192,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP469552,,loader:fastq load.py,lin1_ube2e1_scar_R1.fastq.gz lin1_ube2e1_scar_R2.fastq.gz,fastq fastq,99407618.0,601781.0,GSM7875192 r1,,,,,,,,,,,,SRX22323893,SRS19374421,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00657,0.84532,0.00205,0.03049,0.99537,0.95286,0.43306,0.19203,28,150,T,B,sc-like readlen,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
28759,SRR26623296,SRX22323892,SRS19374422,SRP469552,PRJNA1034159,Dissecting the spatiotemporal diversity of adult neural stem cells,GSE246714,Other,Adult stem cells are important for tissue turnover and regeneration. However  in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here  we dissected the diversity of neural stem cells in the adult zebrafish brain  an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells  with some subtypes being restricted to a single brain region  while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation  with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain  FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region  as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation.,,pubmed:38365956,,Lineage tracing rep1  rpl39 scars,GSM7875191,,source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing,Lineage tracing rep1  rpl39 scars,The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect  the gene expression matrices were processed with the SoupX tool Young & Behjati  2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al  2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1  actb2  cfl1  cirbpb  rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis  see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping  further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline.,adult brain,,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M],GSM7875191,GSM7875191: Lineage tracing rep1  rpl39 scars; Danio rerio; OTHER,GSM7875191 r1,GSM7875191,1,Adult zebrafish brain tissue was extracted  optionally dissected to select a specific region of interest telencephalon  diencephalon  mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly  the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter  washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA  then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples  a papain dissociation protocol Worthington kit  according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing  the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target  specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit  so they could be sequenced on the same platform.,,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP469552,,loader:fastq load.py,lin1_rpl39_scar_R1.fastq.gz lin1_rpl39_scar_R2.fastq.gz,fastq fastq,401898718.0,2276836.0,GSM7875191 r1,,,,,,,,,,,,SRX22323892,SRS19374422,SRA1743007,"Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine","Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine",2,0.00037,0.2642,0.00015,0.00086,0.99922,0.99026,0.23076,0.42455,28,120,T,B,sc-like readlen,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2023-10-31,Adult,Adult,Brain,Nervous System
29187,SRR8176747,SRX4996876,SRS4031879,SRP480945,PRJNA1055160,Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain,PRJNA1055160,Other,We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf,,pubmed:38529407,,Nadia 19dpf ZZ Gonad Single Cell RNA Seq,Nadia 19dpf ZZ Gonad Single Cell RNA Seq,,strain:Nadia|age:19 dpf provider:John H. Postlethwait  University of Oregon|genotype:ZZ|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: Nadia 19dpf ZZ gonad,Nadia 19dpf ZZ gonad,Nadia 19dpf ZZ gonad,A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP480945,,loader:fastq load.py,,,15090036999.0,107021539.0,zz 19NAmale I1 001.fastq.gz,0:8 1:133,A:4154103253;C:3402890354;G:3765557416;T:3755723849;N:11762127,8,133,,,4154103253,3402890354,3765557416,3755723849,11762127,SRX4996876,SRS4031879,SRA807619,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2018-11-08,Larval,Larval,Gonad,Reproductive System
29188,SRR8176753,SRX4996870,SRS4031878,SRP480945,PRJNA1055160,Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain,PRJNA1055160,Other,We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf,,pubmed:38529407,,Nadia 30dpf ZZ Gonad Single Cell RNA Seq,Nadia 30dpf ZZ Gonad Single Cell RNA Seq,,strain:Nadia|age:30 dpf provider:John H. Postlethwait  University of Oregon|genotype:ZZ|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: Nadia 30dpf ZZ gonad,Nadia 30dpf ZZ gonad,Nadia 30dpf ZZ gonad,A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP480945,,loader:fastq load.py,,,23587173438.0,167284918.0,1 I1 001.fastq.gz,0:8 1:133,A:6732844252;C:4934497997;G:5685086026;T:6219863789;N:14881374,8,133,,,6732844252,4934497997,5685086026,6219863789,14881374,SRX4996870,SRS4031878,SRA807619,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2018-11-08,Juvenile,Juvenile,Gonad,Reproductive System
29189,SRR8176754,SRX4996869,SRS4031877,SRP480945,PRJNA1055160,Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain,PRJNA1055160,Other,We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf,,pubmed:38529407,,Nadia 30dpf ZW Gonad Single Cell RNA Seq,Nadia 30dpf ZW Gonad Single Cell RNA Seq,,strain:Nadia|age:30 dpf provider:John H. Postlethwait  University of Oregon|genotype:ZW|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: Nadia 30dpf ZW gonad,Nadia 30dpf ZW gonad,Nadia 30dpf ZW gonad,A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP480945,,loader:fastq load.py,,,43358808480.0,307509280.0,2 I1 001.fastq.gz,0:8 1:133,A:12290612367;C:8880655083;G:10261318751;T:11898771792;N:27450487,8,133,,,12290612367,8880655083,10261318751,11898771792,27450487,SRX4996869,SRS4031877,SRA807619,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2018-11-08,Juvenile,Juvenile,Gonad,Reproductive System
29190,SRR8176756,SRX4996867,SRS4031876,SRP480945,PRJNA1055160,Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain,PRJNA1055160,Other,We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf,,pubmed:38529407,,Nadia 19dpf ZW Gonad Single Cell RNA Seq,Nadia 19dpf ZW Gonad Single Cell RNA Seq,,strain:Nadia|age:19 dpf provider:John H. Postlethwait  University of Oregon|genotype:ZW|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: Nadia 19dpf ZW gonad,Nadia 19dpf ZW gonad,Nadia 19dpf ZW gonad,A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP480945,,loader:fastq load.py,,,17141425554.0,121570394.0,zw 19NAfem I1 001.fastq.gz,0:8 1:133,A:4656207219;C:3824531650;G:4322736498;T:4324676442;N:13273745,8,133,,,4656207219,3824531650,4322736498,4324676442,13273745,SRX4996867,SRS4031876,SRA807619,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2018-11-08,Larval,Larval,Gonad,Reproductive System
29808,SRR27450807,SRX23122487,SRS20076037,SRP482328,PRJNA1061565,Akt is the main kinase mediating the embryonic specification of artery cells,GSE252648,Transcriptome Analysis,This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.,,pubmed:39101673,,Zebrafish  EC  24hpf  Aktmutant,GSM8004755,,source name:FAC sorted cells|tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:Aktmutant|geo loc name:missing|collection date:missing,Zebrafish  EC  24hpf  Aktmutant,The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes  features and matrix,FAC sorted cells,No treatments,Wild type  aktmutant  Tgkdrl:mCherry tissue  were dissected at 24 hpf. Dissected  tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell  10x genomics,Normal zebrafish growth condition,tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:Aktmutant,GSM8004755,GSM8004755: Zebrafish  EC  24hpf  Aktmutant; Danio rerio; RNA Seq,GSM8004755 r1,GSM8004755,1,Wild type  aktmutant  Tgkdrl:mCherry tissue  were dissected at 24 hpf. Dissected  tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell  10x genomics,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP482328,,loader:fastq load.py,mu1-23-19_DRT_S2_L001_I1_001.fastq.gz mu1-23-19_DRT_S2_L001_R1_001.fastq.gz mu1-23-19_DRT_S2_L001_R2_001.fastq.gz,fastq fastq fastq,23281472741.0,183318683.0,GSM8004755 r1,0:8 1:28 2:91,A:4703583066;C:3702175361;G:3998796644;T:4271932211;N:5512871,8,28,91,,4703583066,3702175361,3998796644,4271932211,5512871,SRX23122487,SRS20076037,SRA1780571,"Nicoli lab, School of Medicine, Yale University","Nicoli lab, School of Medicine, Yale University",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-01-05,Pharyngula,Embryo,Multi-tissue,Multi-system
29809,SRR27450808,SRX23122487,SRS20076037,SRP482328,PRJNA1061565,Akt is the main kinase mediating the embryonic specification of artery cells,GSE252648,Transcriptome Analysis,This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.,,pubmed:39101673,,Zebrafish  EC  24hpf  Aktmutant,GSM8004755,,source name:FAC sorted cells|tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:Aktmutant|geo loc name:missing|collection date:missing,Zebrafish  EC  24hpf  Aktmutant,The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes  features and matrix,FAC sorted cells,No treatments,Wild type  aktmutant  Tgkdrl:mCherry tissue  were dissected at 24 hpf. Dissected  tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell  10x genomics,Normal zebrafish growth condition,tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:Aktmutant,GSM8004755,GSM8004755: Zebrafish  EC  24hpf  Aktmutant; Danio rerio; RNA Seq,GSM8004755 r1,GSM8004755,1,Wild type  aktmutant  Tgkdrl:mCherry tissue  were dissected at 24 hpf. Dissected  tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell  10x genomics,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP482328,,loader:fastq load.py,mu1-23-19_DRT_S2_L002_I1_001.fastq.gz mu1-23-19_DRT_S2_L002_R1_001.fastq.gz mu1-23-19_DRT_S2_L002_R2_001.fastq.gz,fastq fastq fastq,21009317138.0,165427694.0,GSM8004755 r2,0:8 1:28 2:91,A:4231955850;C:3363548064;G:3603913589;T:3849411287;N:5091364,8,28,91,,4231955850,3363548064,3603913589,3849411287,5091364,SRX23122487,SRS20076037,SRA1780571,"Nicoli lab, School of Medicine, Yale University","Nicoli lab, School of Medicine, Yale University",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-01-05,Pharyngula,Embryo,Multi-tissue,Multi-system
29810,SRR27450809,SRX23122486,SRS20076036,SRP482328,PRJNA1061565,Akt is the main kinase mediating the embryonic specification of artery cells,GSE252648,Transcriptome Analysis,This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.,,pubmed:39101673,,Zebrafish  EC  24hpf  WT,GSM8004754,,source name:FAC sorted cells|tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT|geo loc name:missing|collection date:missing,Zebrafish  EC  24hpf  WT,The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes  features and matrix,FAC sorted cells,No treatments,Wild type  aktmutant  Tgkdrl:mCherry tissue  were dissected at 24 hpf. Dissected  tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell  10x genomics,Normal zebrafish growth condition,tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT,GSM8004754,GSM8004754: Zebrafish  EC  24hpf  WT; Danio rerio; RNA Seq,GSM8004754 r1,GSM8004754,1,Wild type  aktmutant  Tgkdrl:mCherry tissue  were dissected at 24 hpf. Dissected  tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell  10x genomics,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP482328,,loader:fastq load.py,wt1-23-19_DRT_S1_L001_I1_001.fastq.gz wt1-23-19_DRT_S1_L001_R1_001.fastq.gz wt1-23-19_DRT_S1_L001_R2_001.fastq.gz,fastq fastq fastq,22261273232.0,175285616.0,GSM8004754 r1,0:8 1:28 2:91,A:4475749188;C:3578353646;G:3836029871;T:4055646794;N:5211557,8,28,91,,4475749188,3578353646,3836029871,4055646794,5211557,SRX23122486,SRS20076036,SRA1780571,"Nicoli lab, School of Medicine, Yale University","Nicoli lab, School of Medicine, Yale University",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-01-05,Pharyngula,Embryo,Multi-tissue,Multi-system
29811,SRR27450810,SRX23122486,SRS20076036,SRP482328,PRJNA1061565,Akt is the main kinase mediating the embryonic specification of artery cells,GSE252648,Transcriptome Analysis,This study aimed at understanding the function of Akt signaling in vascular development in Zebrafish. Overall design: This study used Zebrafish endothelial cells sorted from WT and akt full mutant embryos at 24hpf. Endothelial cells were sorted via the use of transgenic line kdrl:mCherry+. Only mCherry+ were sequenced. So here you can find sample WT and sample akt mutant.,,pubmed:39101673,,Zebrafish  EC  24hpf  WT,GSM8004754,,source name:FAC sorted cells|tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT|geo loc name:missing|collection date:missing,Zebrafish  EC  24hpf  WT,The barcoded processing  gene counting and aggregation were made using the Cell Ranger software Version 5.0.0 Downstream analysis were performed on R studio using Seurat Supplementary files format and content: Tab separated values files and matrix files Assembly: Assembly: Lawson Annotation V4.3.2 Supplementary files format and content: 3 files of barcodes  features and matrix,FAC sorted cells,No treatments,Wild type  aktmutant  Tgkdrl:mCherry tissue  were dissected at 24 hpf. Dissected  tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3’ Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell  10x genomics,Normal zebrafish growth condition,tissue:FAC sorted cells|cell line:kdrl:mCherry+|cell type:Endothelial Cells|genotype:WT,GSM8004754,GSM8004754: Zebrafish  EC  24hpf  WT; Danio rerio; RNA Seq,GSM8004754 r1,GSM8004754,1,Wild type  aktmutant  Tgkdrl:mCherry tissue  were dissected at 24 hpf. Dissected  tissues were dissociated into single cell suspensions and subjected to FACS.mCherry+ cells  which had 85% cell viability  were loaded onto the 10X Genomics Chromium instrument for a targeted recovery of 10 000 cells per sample. 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell three prime Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions Transcriptomic single cell  10x genomics,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP482328,,loader:fastq load.py,wt1-23-19_DRT_S1_L002_I1_001.fastq.gz wt1-23-19_DRT_S1_L002_R1_001.fastq.gz wt1-23-19_DRT_S1_L002_R2_001.fastq.gz,fastq fastq fastq,20084395188.0,158144844.0,GSM8004754 r2,0:8 1:28 2:91,A:4028678970;C:3250176957;G:3455600305;T:3651884457;N:4840115,8,28,91,,4028678970,3250176957,3455600305,3651884457,4840115,SRX23122486,SRS20076036,SRA1780571,"Nicoli lab, School of Medicine, Yale University","Nicoli lab, School of Medicine, Yale University",,,,,,,,,,,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-01-05,Pharyngula,Embryo,Multi-tissue,Multi-system
30012,SRR28164886,SRX23795142,SRS20618185,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,10x Genomics multiplexing  CMO,scRNA seq  wild type and hamp /   36 hpf  CMO,Zebrafish embryo scRNA seq  wild type and hamp /   36 hpf  CMO,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf  CMO|dev stage:36 hpf  CMO|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:WT/hamp knockdown|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq  wild type and hamp /   36 hpf  CMO,C 3,C 3,10x Genomics multiplexing  CMO,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,36h_Multiplexing_Capture_S1_L001_R2_001.fastq.gz 36h_Multiplexing_Capture_S1_L001_R1_001.fastq.gz,fastq fastq,42856660500.0,142855535.0,36h Multiplexing Capture S1 L001 R1 001.fastq.gz,0:150 1:150,A:8992350191;C:10354632010;G:13923089582;T:9585439035;N:1149682,150,150,,,8992350191,10354632010,13923089582,9585439035,1149682,SRX23795142,SRS20618185,SRA1813495,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.0,0.0,0.0,0.0,1.0,1.0,,,150,150,T,T,mates < 9% mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-02-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
30013,SRR28164887,SRX23795141,SRS20618186,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,10x Genomics multiplexing  CMO,scRNA seq  wild type and hamp /   24 hpf  CMO,Zebrafish embryo scRNA seq  wild type and hamp /   24 hpf  CMO,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:24 hpf  CMO|dev stage:24 hpf  CMO|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:WT/hamp knockdown|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq  wild type and hamp /   24 hpf  CMO,C 2,C 2,10x Genomics multiplexing  CMO,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,24h_Multiplexing_Capture_S1_L001_R2_001.fastq.gz 24h_Multiplexing_Capture_S1_L001_R1_001.fastq.gz,fastq fastq,45212181900.0,150707273.0,24h Multiplexing Capture S1 L001 R1 001.fastq.gz,0:150 1:150,A:9741878752;C:11183590476;G:14447932886;T:9837582173;N:1197613,150,150,,,9741878752,11183590476,14447932886,9837582173,1197613,SRX23795141,SRS20618186,SRA1813495,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.0,0.0,0.0,0.0,1.0,1.0,,,150,150,T,T,mates < 9% mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-02-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
30014,SRR28164888,SRX23795140,SRS20618184,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,10x Genomics multiplexing  CMO,scRNA seq  wild type and hamp /   12 hpf  CMO,Zebrafish embryo scRNA seq  wild type and hamp /   12 hpf  CMO,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:12 hpf  CMO|dev stage:12 hpf  CMO|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:WT/hamp knockdown|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq  wild type and hamp /   12 hpf  CMO,C 1,C 1,10x Genomics multiplexing  CMO,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,12h_Multiplexing_Capture_S1_L001_R2_001.fastq.gz 12h_Multiplexing_Capture_S1_L001_R1_001.fastq.gz,fastq fastq,23801259900.0,79337533.0,12h Multiplexing Capture S1 L001 R1 001.fastq.gz,0:150 1:150,A:5110000752;C:5818733743;G:7758205963;T:5113684708;N:634734,150,150,,,5110000752,5818733743,7758205963,5113684708,634734,SRX23795140,SRS20618184,SRA1813495,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.0,0.0,0.0,0.0,1.0,1.0,,,150,150,T,T,mates < 9% mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-02-29,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
30015,SRR28164889,SRX23795139,SRS20618183,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,10x Genomics multiplexing  GEX,scRNA seq  wild type and hamp /   36 hpf  GEX,Zebrafish embryo scRNA seq  wild type and hamp /   36 hpf  GEX,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:36 hpf  GEX|dev stage:36 hpf  GEX|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:WT/hamp knockdown|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq  wild type and hamp /   36 hpf  GEX,G 3,G 3,10x Genomics multiplexing  GEX,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,36h_Gene_Expression_S1_L001_R2_001.fastq.gz 36h_Gene_Expression_S1_L001_R1_001.fastq.gz,fastq fastq,140285088600.0,467616962.0,36h Gene Expression S1 L001 R1 001.fastq.gz,0:150 1:150,A:41651884464;C:24916307056;G:25991077208;T:47722140024;N:3679848,150,150,,,41651884464,24916307056,25991077208,47722140024,3679848,SRX23795139,SRS20618183,SRA1813495,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.00148,0.91873,0.0,0.15509,0.99985,0.78086,0.57142,0.52919,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-02-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
30016,SRR28164890,SRX23795138,SRS20618182,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,10x Genomics multiplexing  GEX,scRNA seq  wild type and hamp /   24 hpf  GEX,Zebrafish embryo scRNA seq  wild type and hamp /   24 hpf  GEX,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:24 hpf  GEX|dev stage:24 hpf  GEX|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:WT/hamp knockdown|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq  wild type and hamp /   24 hpf  GEX,G 2,G 2,10x Genomics multiplexing  GEX,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,24h_Gene_Expression_S1_L001_R1_001.fastq.gz 24h_Gene_Expression_S1_L001_R2_001.fastq.gz,fastq fastq,147407645100.0,491358817.0,24h Gene Expression S1 L001 R1 001.fastq.gz,0:150 1:150,A:43802123106;C:26617386219;G:27720887375;T:49263400239;N:3848161,150,150,,,43802123106,26617386219,27720887375,49263400239,3848161,SRX23795138,SRS20618182,SRA1813495,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.00129,0.92038,0.00042,0.15021,0.99993,0.77581,0.33333,0.51584,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-02-29,Pharyngula,Embryo,Embryo Imprecise,All anatomical structures
30017,SRR28164891,SRX23795137,SRS20618181,SRP485064,PRJNA1067370,zebrafish embryo for scRNA seq and bulk RNA seq,PRJNA1067370,Other,Hepcidin hamp is a key regulator for the maintenance of iron metabolism. How hamp affects the mechanism of zebrafish hematopoiesis is still largely unknown. Here  we have generated a stable hamp mutant zebrafish model by using the CRISPR/Cas9 system.We found that iron overload occurred in several tissues of zebrafish  and the hemoglobin content decreased significantly during embryonic development.Single cell profiling demonstrated that hematopoietic actors were aberrantly expressed  and hematopoietic progenitor cells appeared a group of cell clusters with relatively delayed development  accompanied by ferroptosis.,,,10x Genomics multiplexing  GEX,scRNA seq  wild type and hamp /   12 hpf  GEX,Zebrafish embryo scRNA seq  wild type and hamp /   12 hpf  GEX,,strain:not applicable|isolate:not collected|breed:Danio|cultivar:not applicable|ecotype:not applicable|age:12 hpf  GEX|dev stage:12 hpf  GEX|collection date:2022 10|geo loc name:not applicable|sex:not applicable|tissue:embryo|genotype:WT/hamp knockdown|sample type:whole organism|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq  wild type and hamp /   12 hpf  GEX,G 1,G 1,10x Genomics multiplexing  GEX,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP485064,,,12h_Gene_Expression_S1_L001_R2_001.fastq.gz 12h_Gene_Expression_S1_L001_R1_001.fastq.gz,fastq fastq,204426398700.0,681421329.0,12h Gene Expression S1 L001 R1 001.fastq.gz,0:150 1:150,A:61302872939;C:35072603645;G:37153666376;T:70891933893;N:5321847,150,150,,,61302872939,35072603645,37153666376,70891933893,5321847,SRX23795137,SRS20618181,SRA1813495,Shanghai Ocean University|College of Fisheries and Life,Shanghai Ocean University,2,0.00085,0.9058,0.0,0.12081,0.99991,0.80231,0.5,0.52456,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-02-29,Segmentation,Embryo,Embryo Imprecise,All anatomical structures
32783,SRR29438460,SRX24951082,SRS21654793,SRP514388,PRJNA1124950,Deciphering the Toxic Effects of Polystyrene Nanoparticle on Erythropoiesis at Single Cell Resolution,GSE270075,Transcriptome Analysis,The toxic effects of polystyrene nanoparticles on aquatic ecosystems have been predominantly studied  with a focus on oxidative stress and inflammatory responses. However  this study comprehensively examined the effects of polystyrene nanoparticles on the development of zebrafish embryos using single cell RNA sequencing analysis  explicitly investigating their effects on erythropoiesis. In vivo experiments were conducted using zebrafish embryos to validate the single cell RNA sequencing analysis. Exposure to polystyrene nanoparticles resulted in a decrease in the proportion of mature erythrocytes due to an increase in immature erythrocytes during the erythrocyte differentiation process. Additionally  heme synthesis was impaired  leading to a decrease in the proportion of erythrocytes. These findings indicated the toxic effects of polystyrene nanoparticles on hematopoiesis. Overall design: 120 hpf zebrafish embryos were pooled as a control groupwild type and 20 nm polystyrene nanoparticles PS20nm exposed group for single cell RNA sequencing.,,pubmed:39846194,,Zebra PS,GSM8334032,,source name:embryos|tissue:embryos|Stage:120 hpf|treatment:PS20nm exposure|geo loc name:missing|collection date:missing,Zebra PS,First  the quality and basic statistics of raw sequencing data were checked through FastQC. post the quality control process  sequencing data were processed through a Cell Ranger v6.0.0 10X Genomics count pipeline using zebrafish genome GRCz11. The zebrafish genome and transcriptome information were downloaded from the Ensembl FTP server release 104  and the index was constructed by processing with the Cell Ranger mkref pipeline. The cellranger count pipeline produces gene expression matrices containing the unique molecular identifier UMI counts per gene  per barcode. Also  clusters with expression profiles and information on differential gene expression were generated from the pipeline. Downstream analysis was performed using Seurat version 4.3.0 in R version 4.2.2 to process data produced through 10x genomics. Assembly: GRCz11 Supplementary files format and content: Three types of processed data files are provided: barcode.tsv  features.tsv  matrix.mtx,embryos,,The samples were carefully resuspended in a cold  calcium  and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7™ Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems  catalog number F23001. Following this  the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech  catalog number 130 090 101 and MS columns Miltenyi Biotech  catalog number 130 042 201 in accordance with the manufacturer’s guidelines. Following the guidelines of the 10x Chromium Single Cell 5’ v2 protocol 10x Genomics  document number CG000331  Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell 5’ Reagent v2 kits 10x Genomics  PN 1000244. In brief  the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5′ Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics  PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs  RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction  where barcoded full length cDNA was synthesized from mRNA  the barcoded cDNA molecules were enriched with PCR. For the preparation of the 5’ Gene Expression Library  the amplified cDNA underwent a series of steps  including enzymatic fragmentation  end repair  A tailing  adapter ligation  and index PCR.,,tissue:embryos|Stage:120 hpf|treatment:PS20nm exposure,GSM8334032,GSM8334032: Zebra PS; Danio rerio; RNA Seq,GSM8334032 r1,GSM8334032,1,The samples were carefully resuspended in a cold  calcium  and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7™ Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems  catalog number F23001. Following this  the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech  catalog number 130 090 101 and MS columns Miltenyi Biotech  catalog number 130 042 201 in accordance with the manufacturer's guidelines. Following the guidelines of the 10x Chromium Single Cell five prime v2 protocol 10x Genomics  document number CG000331  Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell five prime Reagent v2 kits 10x Genomics  PN 1000244. In brief  the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5′ Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics  PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs  RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction  where barcoded full length cDNA was synthesized from mRNA  the barcoded cDNA molecules were enriched with PCR. For the preparation of the five prime Gene Expression Library  the amplified cDNA underwent a series of steps  including enzymatic fragmentation  end repair  A tailing  adapter ligation  and index PCR.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP514388,,,Zebra_PS_S1_L003_R2_001.fastq.gz Zebra_PS_S1_L003_R1_001.fastq.gz,fastq fastq,46515993156.0,400999941.0,GSM8334032 r1,0:26 1:90,A:10540890310;C:12256097063;G:11432529211;T:12270960287;N:15516285,26,90,,,10540890310,12256097063,11432529211,12270960287,15516285,SRX24951082,SRS21654793,SRA1904713,Pusan National University,Pusan National University,2,0.07013,0.96133,0.0269,0.15067,0.98135,0.78849,0.31441,0.54509,26,90,T,B,sc-like readlen,illumina,hiseq_era,5prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,South Korea,2024-06-17,Larval,Larval,Embryo Imprecise,All anatomical structures
32784,SRR29438461,SRX24951081,SRS21654792,SRP514388,PRJNA1124950,Deciphering the Toxic Effects of Polystyrene Nanoparticle on Erythropoiesis at Single Cell Resolution,GSE270075,Transcriptome Analysis,The toxic effects of polystyrene nanoparticles on aquatic ecosystems have been predominantly studied  with a focus on oxidative stress and inflammatory responses. However  this study comprehensively examined the effects of polystyrene nanoparticles on the development of zebrafish embryos using single cell RNA sequencing analysis  explicitly investigating their effects on erythropoiesis. In vivo experiments were conducted using zebrafish embryos to validate the single cell RNA sequencing analysis. Exposure to polystyrene nanoparticles resulted in a decrease in the proportion of mature erythrocytes due to an increase in immature erythrocytes during the erythrocyte differentiation process. Additionally  heme synthesis was impaired  leading to a decrease in the proportion of erythrocytes. These findings indicated the toxic effects of polystyrene nanoparticles on hematopoiesis. Overall design: 120 hpf zebrafish embryos were pooled as a control groupwild type and 20 nm polystyrene nanoparticles PS20nm exposed group for single cell RNA sequencing.,,pubmed:39846194,,Zebra Control,GSM8334031,,source name:embryos|tissue:embryos|Stage:120 hpf|treatment:Wild type|geo loc name:missing|collection date:missing,Zebra Control,First  the quality and basic statistics of raw sequencing data were checked through FastQC. post the quality control process  sequencing data were processed through a Cell Ranger v6.0.0 10X Genomics count pipeline using zebrafish genome GRCz11. The zebrafish genome and transcriptome information were downloaded from the Ensembl FTP server release 104  and the index was constructed by processing with the Cell Ranger mkref pipeline. The cellranger count pipeline produces gene expression matrices containing the unique molecular identifier UMI counts per gene  per barcode. Also  clusters with expression profiles and information on differential gene expression were generated from the pipeline. Downstream analysis was performed using Seurat version 4.3.0 in R version 4.2.2 to process data produced through 10x genomics. Assembly: GRCz11 Supplementary files format and content: Three types of processed data files are provided: barcode.tsv  features.tsv  matrix.mtx,embryos,,The samples were carefully resuspended in a cold  calcium  and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7™ Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems  catalog number F23001. Following this  the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech  catalog number 130 090 101 and MS columns Miltenyi Biotech  catalog number 130 042 201 in accordance with the manufacturer’s guidelines. Following the guidelines of the 10x Chromium Single Cell 5’ v2 protocol 10x Genomics  document number CG000331  Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell 5’ Reagent v2 kits 10x Genomics  PN 1000244. In brief  the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5′ Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics  PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs  RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction  where barcoded full length cDNA was synthesized from mRNA  the barcoded cDNA molecules were enriched with PCR. For the preparation of the 5’ Gene Expression Library  the amplified cDNA underwent a series of steps  including enzymatic fragmentation  end repair  A tailing  adapter ligation  and index PCR.,,tissue:embryos|Stage:120 hpf|treatment:Wild type,GSM8334031,GSM8334031: Zebra Control; Danio rerio; RNA Seq,GSM8334031 r1,GSM8334031,1,The samples were carefully resuspended in a cold  calcium  and magnesium free solution containing 0.04% BSA/PBS. Cell counting was performed using the LUNA FX7™ Automated Fluorescence Cell Counter Logos Biosystems with acridine orange AO and propidium iodide PI staining Logos Biosystems  catalog number F23001. Following this  the cells were processed using the Dead Cells Removal Kit Miltenyi Biotech  catalog number 130 090 101 and MS columns Miltenyi Biotech  catalog number 130 042 201 in accordance with the manufacturer's guidelines. Following the guidelines of the 10x Chromium Single Cell five prime v2 protocol 10x Genomics  document number CG000331  Single Cell RNA seq libraries were generated using the 10x Chromium Controller and the Next Gem Single Cell five prime Reagent v2 kits 10x Genomics  PN 1000244. In brief  the cell suspension aiming for a recovery of 10 000 cells was combined with the reverse transcription master mix and loaded along with Single Cell 5′ Gel Beads and Partitioning Oil into a Single Cell K Chip 10x Genomics  PN 1000286 to create single cell Gel Bead in emulsion GEM droplets. Within these GEMs  RNA transcripts from single cells were uniquely barcoded and reverse transcribed. post the GEM RT reaction  where barcoded full length cDNA was synthesized from mRNA  the barcoded cDNA molecules were enriched with PCR. For the preparation of the five prime Gene Expression Library  the amplified cDNA underwent a series of steps  including enzymatic fragmentation  end repair  A tailing  adapter ligation  and index PCR.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP514388,,,Zebra_Control_S1_L002_R1_001.fastq.gz Zebra_Control_S1_L002_R2_001.fastq.gz,fastq fastq,44451768632.0,383204902.0,GSM8334031 r1,0:26 1:90,A:10119968829;C:11732695259;G:10981098564;T:11603155786;N:14850194,26,90,,,10119968829,11732695259,10981098564,11603155786,14850194,SRX24951081,SRS21654792,SRA1904713,Pusan National University,Pusan National University,2,0.07283,0.96543,0.02838,0.15165,0.98052,0.78464,0.32149,0.56384,26,90,T,B,sc-like readlen,illumina,hiseq_era,5prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,South Korea,2024-06-17,Larval,Larval,Embryo Imprecise,All anatomical structures
34465,SRR31769117,SRX27130830,SRS23587817,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #3,GSM8691398,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #3,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7,GSM8691398,GSM8691398: adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #3; Danio rerio; RNA Seq,GSM8691398 r1,GSM8691398,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Uninjured-7DPI-3_GRO2357A6_S5_L001_R1_001.fastq.gz Uninjured-7DPI-3_GRO2357A6_S5_L001_R2_001.fastq.gz,fastq fastq,63524967830.0,538347185.0,GSM8691398 r1,0:28 1:90,A:18434935191;C:13740021920;G:14509703351;T:16838781338;N:1526030,28,90,,,18434935191,13740021920,14509703351,16838781338,1526030,SRX27130830,SRS23587817,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34466,SRR31769118,SRX27130829,SRS23587816,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #2,GSM8691397,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #2,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7,GSM8691397,GSM8691397: adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #2; Danio rerio; RNA Seq,GSM8691397 r1,GSM8691397,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Uninjured-7DPI-2_GRO2559A7_S11_L001_R1_001.fastq.gz Uninjured-7DPI-2_GRO2559A7_S11_L001_R2_001.fastq.gz,fastq fastq,117155938094.0,992846933.0,GSM8691397 r1,0:28 1:90,A:33056566549;C:26122865037;G:28068647978;T:29904980565;N:2877965,28,90,,,33056566549,26122865037,28068647978,29904980565,2877965,SRX27130829,SRS23587816,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34467,SRR31769119,SRX27130828,SRS23587815,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #1,GSM8691396,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #1,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 7,GSM8691396,GSM8691396: adult zebrafish retinal ganglion cells  day 7 uninjured  fish set #1; Danio rerio; RNA Seq,GSM8691396 r1,GSM8691396,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Uninjured-7DPI-1_GRO2559A5_S3_L001_R1_001.fastq.gz Uninjured-7DPI-1_GRO2559A5_S3_L001_R2_001.fastq.gz,fastq fastq,88479846662.0,749829209.0,GSM8691396 r1,0:28 1:90,A:24973204142;C:19680603454;G:21127682533;T:22696187157;N:2169376,28,90,,,24973204142,19680603454,21127682533,22696187157,2169376,SRX27130828,SRS23587815,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34468,SRR31769120,SRX27130827,SRS23587814,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #3,GSM8691395,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #3,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691395,GSM8691395: adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #3; Danio rerio; RNA Seq,GSM8691395 r1,GSM8691395,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Injured-7DPI-3_GRO2357A5_S9_L001_R1_001.fastq.gz Injured-7DPI-3_GRO2357A5_S9_L001_R2_001.fastq.gz,fastq fastq,52866571338.0,448021791.0,GSM8691395 r1,0:28 1:90,A:15008347140;C:11559305260;G:12319521011;T:13978097023;N:1300904,28,90,,,15008347140,11559305260,12319521011,13978097023,1300904,SRX27130827,SRS23587814,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34469,SRR31769121,SRX27130826,SRS23587813,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #2,GSM8691394,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #2,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691394,GSM8691394: adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #2; Danio rerio; RNA Seq,GSM8691394 r1,GSM8691394,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Injured-7DPI-2_GRO2559A8_S13_L001_R1_001.fastq.gz Injured-7DPI-2_GRO2559A8_S13_L001_R2_001.fastq.gz,fastq fastq,122844941704.0,1041058828.0,GSM8691394 r1,0:28 1:90,A:34628566594;C:27526793155;G:30025691872;T:30660901278;N:2988805,28,90,,,34628566594,27526793155,30025691872,30660901278,2988805,SRX27130826,SRS23587813,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34470,SRR31769122,SRX27130825,SRS23587812,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #1,GSM8691393,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #1,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691393,GSM8691393: adult zebrafish retinal ganglion cells  7 xxx post injury  fish set #1; Danio rerio; RNA Seq,GSM8691393 r1,GSM8691393,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Injured-7DPI-1_GRO2559A6_S7_L001_R1_001.fastq.gz Injured-7DPI-1_GRO2559A6_S7_L001_R2_001.fastq.gz,fastq fastq,120896581754.0,1024547303.0,GSM8691393 r1,0:28 1:90,A:33711894389;C:26892614943;G:28832438626;T:31456652089;N:2981707,28,90,,,33711894389,26892614943,28832438626,31456652089,2981707,SRX27130825,SRS23587812,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34471,SRR31769123,SRX27130824,SRS23587811,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #3,GSM8691392,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #3,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1,GSM8691392,GSM8691392: adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #3; Danio rerio; RNA Seq,GSM8691392 r1,GSM8691392,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Uninjured-1DPI-3_GRO2657A19_S4_L001_R1_001.fastq.gz Uninjured-1DPI-3_GRO2657A19_S4_L001_R2_001.fastq.gz,fastq fastq,59387016872.0,503279804.0,GSM8691392 r1,0:28 1:90,A:17711412598;C:12536566614;G:13563786736;T:15573793585;N:1457339,28,90,,,17711412598,12536566614,13563786736,15573793585,1457339,SRX27130824,SRS23587811,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34472,SRR31769124,SRX27130823,SRS23587810,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #2,GSM8691391,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #2,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1,GSM8691391,GSM8691391: adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #2; Danio rerio; RNA Seq,GSM8691391 r1,GSM8691391,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Uninjured-1DPI-2_GRO2553A7_S10_L001_R1_001.fastq.gz Uninjured-1DPI-2_GRO2553A7_S10_L001_R2_001.fastq.gz,fastq fastq,106157704906.0,899641567.0,GSM8691391 r1,0:28 1:90,A:29822848120;C:23694191955;G:25190535492;T:27447524885;N:2604454,28,90,,,29822848120,23694191955,25190535492,27447524885,2604454,SRX27130823,SRS23587810,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34473,SRR31769125,SRX27130822,SRS23587809,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #1,GSM8691390,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #1,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:uninjured|time:day 1,GSM8691390,GSM8691390: adult zebrafish retinal ganglion cells  day 1 uninjured  fish set #1; Danio rerio; RNA Seq,GSM8691390 r1,GSM8691390,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Uninjured-1DPI-1_GRO2553A5_S2_L001_R1_001.fastq.gz Uninjured-1DPI-1_GRO2553A5_S2_L001_R2_001.fastq.gz,fastq fastq,123090850164.0,1043142798.0,GSM8691390 r1,0:28 1:90,A:34510432265;C:27448485343;G:28965763692;T:32163144642;N:3024222,28,90,,,34510432265,27448485343,28965763692,32163144642,3024222,SRX27130822,SRS23587809,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34474,SRR31769126,SRX27130821,SRS23587808,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #4,GSM8691389,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #4,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691389,GSM8691389: adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #4; Danio rerio; RNA Seq,GSM8691389 r1,GSM8691389,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Injured-1DPI-4_GRO2657A20_S8_L001_R1_001.fastq.gz Injured-1DPI-4_GRO2657A20_S8_L001_R2_001.fastq.gz,fastq fastq,72232326244.0,612138358.0,GSM8691389 r1,0:28 1:90,A:20998820884;C:15527703707;G:16387036598;T:19316988726;N:1776329,28,90,,,20998820884,15527703707,16387036598,19316988726,1776329,SRX27130821,SRS23587808,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34475,SRR31769127,SRX27130820,SRS23587807,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #3,GSM8691388,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #3,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691388,GSM8691388: adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #3; Danio rerio; RNA Seq,GSM8691388 r1,GSM8691388,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Injured-1DPI-3_GRO2357A4_S1_L001_R1_001.fastq.gz Injured-1DPI-3_GRO2357A4_S1_L001_R2_001.fastq.gz,fastq fastq,72891590238.0,617725341.0,GSM8691388 r1,0:28 1:90,A:20358858846;C:16164883435;G:16927165785;T:19438889715;N:1792457,28,90,,,20358858846,16164883435,16927165785,19438889715,1792457,SRX27130820,SRS23587807,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34476,SRR31769128,SRX27130819,SRS23587806,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #2,GSM8691387,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #2,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691387,GSM8691387: adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #2; Danio rerio; RNA Seq,GSM8691387 r1,GSM8691387,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Injured-1DPI-2_GRO2553A8_S12_L001_R1_001.fastq.gz Injured-1DPI-2_GRO2553A8_S12_L001_R2_001.fastq.gz,fastq fastq,91792694538.0,777904191.0,GSM8691387 r1,0:28 1:90,A:25675360853;C:20502226198;G:22024452743;T:23588401816;N:2252928,28,90,,,25675360853,20502226198,22024452743,23588401816,2252928,SRX27130819,SRS23587806,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
34477,SRR31769129,SRX27130818,SRS23587805,SRP552478,PRJNA1200128,Single Cell Profiling of Zebrafish Retinal Ganglion Cells Reveal an Injury Response Mediated by Cell Dedifferentiation and Leukocytes [scRNA Seq],GSE284729,Transcriptome Analysis,Retinal ganglion cells RGCs are the sole projection neurons connecting the retina to the brain and therefore play a critical role in vision. Death of RGCs during glaucoma results in irreversible loss of vision as RGCs do not xxx post injury in the human eye. There are no FDA approved drugs to prevent RGC death and/or promote RGC xxx post injury. There is a critical need to better understand the molecular underpinnings of neuroprotection in vivo that can then be leveraged to develop new therapeutic approaches. Unlike mammals  zebrafish RGCs are resilient to injury and this study characterizes zebrafish retinal ganglion cell injury response to optic nerve transection ONT using isl2b:eGFP transgenic fish line  single cell and bulk RNA sequencing and in situ hybridization. We demonstrate that zebrafish RGCs do not show subtype specific resilience to injury but show a distinct temporal injury response which includes an increase in subtype 3  a cell population having progenitor and regenerative identity. Overall design: Seven single cell RNA libraries were prepared from FACS purified retinal ganglion cells RGC from pooled tissue from seven sets of adult zebrafish: four libraries from injured tissue post optic nerve transection at 2 timepoints: 1 and 7 xxx post injury dpi  and three libraries from uninjured tissue on the same days.,,,,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #1,GSM8691386,,source name:retina|tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury|geo loc name:missing|collection date:missing,adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #1,The cellranger count pipeline version 6.1.2 was used for alignment  using default arguments  producing a filtered matrix containing UMI counts. The Seurat package was used to preprocess and integrate the samples  following the preprocessing workflow outlined by Kölsch et al. Briefly  for each sample  filtered matrices were log normalized using the NormalizeData function with default arguments. Next all genes are scaled and centered using the ScaleData function and highly variable genes are identified using FindVariableFeatures with nfeatures=1500. Samples are then integrated using the FindIntegrationAnchors and IntegrateData functions with dims=1:40. Next  integrated data is re scaled and PCA  TSNE  and UMAP embeddings are computed using Seurat’s RunPCA  RunUMAP  and RunTSNE functions. Lastly  an initial clustering was computed of the integrated data using FindNeighbors dims=1:40 and FindClusters. To focus on retinal ganglion cell populations  clusters were filtered out that expressed both marker genes for contaminant cell types and lacked expression of RGC markers. Specifically  clusters were removed that had high expression of at least two of the following genes: opn1lw2  opn1mw2  opn1mw1  opn1sw2  opn1lw1  gngt2b  gngt2a  rho  crx  pde6c  pde6ga  opn6a  vsx1  glula  cabp5a  cabp2a  gng13b  gad1b  cd82a  gad2  pax6b  pax6a  cd74a  fcer1gl  and apoeb. Doublets from each sample were annotated and removed using scDblFinder with default parameters. Assembly: Danio rerio reference genome and annotations from GRCz11 from Ensembl  version 106 Supplementary files format and content: Tab delimited files from cellranger outs/raw feature bc matrix,retina,Optic nerve transection ONT was performed under dissecting microscope. The optic nerve in the left eye was severed while the right eye became the uninjured sham control.,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the 3’ v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3’ v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer’s protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,isl2b:GFP transgenic zebrafish Danio rerio used in this study were 3 6 maintained on a 14:10 hour light:dark cycle at 28C.,tissue:retina|cell line:adult retinal ganglion cells from isl2b:eGFP transgenic fish line|cell type:retinal ganglion cells|genotype:isl2b:eGFP transgenic fish line|treatment:optic nerve transection|time:day xxx post injury,GSM8691386,GSM8691386: adult zebrafish retinal ganglion cells  1 xxx post injury  fish set #1; Danio rerio; RNA Seq,GSM8691386 r1,GSM8691386,1,1 and 7 xxx post injury dpi  the retina were harvested  cells dissociated using papain digestion  and RGCs were FACS isolated into BSA/PBS for downstream processing using the three prime v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression three prime v2 kit on the Chromium platform 10X Genomics  Pleasanton  CA following the manufacturer's protocol. Briefly  single cells were partitioned into Gel beads in EMulsion GEMs in the Chromium instrument followed by cell lysis and barcoded reverse transcription of RNA  amplification  enzymatic fragmentation  50 adaptor attachment and sample indexing. On average  approximately 7 000 single cells were loaded on each channel and approximately 2 000  4 000 cells were recovered. Libraries were sequenced on NovaSeq S2 100 platform Paired end reads: Read 1: 26 bases  Read 2: 98 bases.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP552478,,,Injured-1DPI-1_GRO2553A6_S6_L001_R1_001.fastq.gz Injured-1DPI-1_GRO2553A6_S6_L001_R2_001.fastq.gz,fastq fastq,82801648902.0,701708889.0,GSM8691386 r1,0:28 1:90,A:22655489308;C:18871676339;G:19992651055;T:21279810265;N:2021935,28,90,,,22655489308,18871676339,19992651055,21279810265,2021935,SRX27130818,SRS23587805,SRA2037459,"Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin","Bioinformatics Consulting Group, Center for Biomedical Research Support, The University of Texas at Austin",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2024-12-18,Adult,Adult,Eye,Sensory System
35830,SRR33092387,SRX28356288,SRS24685480,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Pachymeninges scRNA seq,GSM8902567,,source name:Pachymeninges|tissue:Pachymeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Pachymeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Pachymeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Pachymeninges,GSM8902567,GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq,GSM8902567 r1,GSM8902567,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,DM3_S4_L001_I1_001.fastq.gz DM3_S4_L001_I2_001.fastq.gz DM3_S4_L001_R1_001.fastq.gz DM3_S4_L001_R2_001.fastq.gz,fastq fastq fastq fastq,11107731642.0,80490809.0,GSM8902567 r1,0:10 1:10 2:28 3:90,A:2157723967;C:1504121492;G:1825572140;T:1756490239;N:264972,10,10,28,90,2157723967,1504121492,1825572140,1756490239,264972,SRX28356288,SRS24685480,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35831,SRR33092396,SRX28356288,SRS24685480,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Pachymeninges scRNA seq,GSM8902567,,source name:Pachymeninges|tissue:Pachymeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Pachymeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Pachymeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Pachymeninges,GSM8902567,GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq,GSM8902567 r1,GSM8902567,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,DM1_S8_L001_I1_001.fastq.gz DM1_S8_L001_R1_001.fastq.gz DM1_S8_L001_R2_001.fastq.gz,fastq fastq fastq,8767935982.0,69038866.0,GSM8902567 r9,0:8 1:28 2:91,A:1900494869;C:1290834687;G:1472019387;T:1618958908;N:228955,8,28,91,,1900494869,1290834687,1472019387,1618958908,228955,SRX28356288,SRS24685480,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35832,SRR33092397,SRX28356288,SRS24685480,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Pachymeninges scRNA seq,GSM8902567,,source name:Pachymeninges|tissue:Pachymeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Pachymeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Pachymeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Pachymeninges,GSM8902567,GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq,GSM8902567 r1,GSM8902567,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,DM6_S5_L002_I1_001.fastq.gz DM6_S5_L002_I2_001.fastq.gz DM6_S5_L002_R1_001.fastq.gz DM6_S5_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9191569902.0,66605579.0,GSM8902567 r8,0:10 1:10 2:28 3:90,A:1725225973;C:1333554410;G:1502913160;T:1432625042;N:183525,10,10,28,90,1725225973,1333554410,1502913160,1432625042,183525,SRX28356288,SRS24685480,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35833,SRR33092398,SRX28356288,SRS24685480,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Pachymeninges scRNA seq,GSM8902567,,source name:Pachymeninges|tissue:Pachymeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Pachymeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Pachymeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Pachymeninges,GSM8902567,GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq,GSM8902567 r1,GSM8902567,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,DM6_S5_L001_I1_001.fastq.gz DM6_S5_L001_I2_001.fastq.gz DM6_S5_L001_R1_001.fastq.gz DM6_S5_L001_R2_001.fastq.gz,fastq fastq fastq fastq,9182505648.0,66539896.0,GSM8902567 r7,0:10 1:10 2:28 3:90,A:1723464701;C:1332487233;G:1501026049;T:1431438610;N:174047,10,10,28,90,1723464701,1332487233,1501026049,1431438610,174047,SRX28356288,SRS24685480,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35834,SRR33092399,SRX28356288,SRS24685480,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Pachymeninges scRNA seq,GSM8902567,,source name:Pachymeninges|tissue:Pachymeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Pachymeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Pachymeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Pachymeninges,GSM8902567,GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq,GSM8902567 r1,GSM8902567,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,DM5_S4_L002_I1_001.fastq.gz DM5_S4_L002_I2_001.fastq.gz DM5_S4_L002_R1_001.fastq.gz DM5_S4_L002_R2_001.fastq.gz,fastq fastq fastq fastq,8580819162.0,62179849.0,GSM8902567 r6,0:10 1:10 2:28 3:90,A:1587762735;C:1253245062;G:1408923693;T:1346083547;N:171373,10,10,28,90,1587762735,1253245062,1408923693,1346083547,171373,SRX28356288,SRS24685480,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35835,SRR33092400,SRX28356288,SRS24685480,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Pachymeninges scRNA seq,GSM8902567,,source name:Pachymeninges|tissue:Pachymeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Pachymeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Pachymeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Pachymeninges,GSM8902567,GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq,GSM8902567 r1,GSM8902567,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,DM5_S4_L001_I1_001.fastq.gz DM5_S4_L001_I2_001.fastq.gz DM5_S4_L001_R1_001.fastq.gz DM5_S4_L001_R2_001.fastq.gz,fastq fastq fastq fastq,8573531934.0,62127043.0,GSM8902567 r5,0:10 1:10 2:28 3:90,A:1586630090;C:1252294774;G:1407253665;T:1345091343;N:163998,10,10,28,90,1586630090,1252294774,1407253665,1345091343,163998,SRX28356288,SRS24685480,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35836,SRR33092401,SRX28356288,SRS24685480,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Pachymeninges scRNA seq,GSM8902567,,source name:Pachymeninges|tissue:Pachymeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Pachymeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Pachymeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Pachymeninges,GSM8902567,GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq,GSM8902567 r1,GSM8902567,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,DM4_S5_L002_I1_001.fastq.gz DM4_S5_L002_I2_001.fastq.gz DM4_S5_L002_R1_001.fastq.gz DM4_S5_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11397415308.0,82589966.0,GSM8902567 r4,0:10 1:10 2:28 3:90,A:2216636094;C:1527643231;G:1900622198;T:1787851155;N:344262,10,10,28,90,2216636094,1527643231,1900622198,1787851155,344262,SRX28356288,SRS24685480,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35837,SRR33092402,SRX28356288,SRS24685480,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Pachymeninges scRNA seq,GSM8902567,,source name:Pachymeninges|tissue:Pachymeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Pachymeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Pachymeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Pachymeninges,GSM8902567,GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq,GSM8902567 r1,GSM8902567,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,DM4_S5_L001_I1_001.fastq.gz DM4_S5_L001_I2_001.fastq.gz DM4_S5_L001_R1_001.fastq.gz DM4_S5_L001_R2_001.fastq.gz,fastq fastq fastq fastq,11531255988.0,83559826.0,GSM8902567 r3,0:10 1:10 2:28 3:90,A:2239272402;C:1547657194;G:1925092927;T:1808081258;N:280559,10,10,28,90,2239272402,1547657194,1925092927,1808081258,280559,SRX28356288,SRS24685480,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35838,SRR33092403,SRX28356288,SRS24685480,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Pachymeninges scRNA seq,GSM8902567,,source name:Pachymeninges|tissue:Pachymeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Pachymeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Pachymeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Pachymeninges,GSM8902567,GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq,GSM8902567 r1,GSM8902567,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,DM3_S4_L002_I1_001.fastq.gz DM3_S4_L002_I2_001.fastq.gz DM3_S4_L002_R1_001.fastq.gz DM3_S4_L002_R2_001.fastq.gz,fastq fastq fastq fastq,10988645094.0,79627863.0,GSM8902567 r2,0:10 1:10 2:28 3:90,A:2137568981;C:1486116359;G:1804028894;T:1738462802;N:330634,10,10,28,90,2137568981,1486116359,1804028894,1738462802,330634,SRX28356288,SRS24685480,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35839,SRR33092404,SRX28356288,SRS24685480,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Pachymeninges scRNA seq,GSM8902567,,source name:Pachymeninges|tissue:Pachymeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Pachymeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Pachymeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Pachymeninges,GSM8902567,GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq,GSM8902567 r1,GSM8902567,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,DM2_S9_L002_I1_001.fastq.gz DM2_S9_L002_R1_001.fastq.gz DM2_S9_L002_R2_001.fastq.gz,fastq fastq fastq,8482264214.0,66789482.0,GSM8902567 r12,0:8 1:28 2:91,A:1871553275;C:1241403117;G:1416606054;T:1548058897;N:221519,8,28,91,,1871553275,1241403117,1416606054,1548058897,221519,SRX28356288,SRS24685480,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35840,SRR33092405,SRX28356288,SRS24685480,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Pachymeninges scRNA seq,GSM8902567,,source name:Pachymeninges|tissue:Pachymeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Pachymeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Pachymeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Pachymeninges,GSM8902567,GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq,GSM8902567 r1,GSM8902567,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,DM2_S9_L001_I1_001.fastq.gz DM2_S9_L001_R1_001.fastq.gz DM2_S9_L001_R2_001.fastq.gz,fastq fastq fastq,8526585309.0,67138467.0,GSM8902567 r11,0:8 1:28 2:91,A:1882385546;C:1247436899;G:1424000842;T:1555556923;N:220287,8,28,91,,1882385546,1247436899,1424000842,1555556923,220287,SRX28356288,SRS24685480,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35841,SRR33092406,SRX28356288,SRS24685480,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Pachymeninges scRNA seq,GSM8902567,,source name:Pachymeninges|tissue:Pachymeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Pachymeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Pachymeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Pachymeninges,GSM8902567,GSM8902567: Zebrafish Adult Pachymeninges scRNA seq; Danio rerio; RNA Seq,GSM8902567 r1,GSM8902567,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,DM1_S8_L002_I1_001.fastq.gz DM1_S8_L002_R1_001.fastq.gz DM1_S8_L002_R2_001.fastq.gz,fastq fastq fastq,8727095068.0,68717284.0,GSM8902567 r10,0:8 1:28 2:91,A:1890991056;C:1285158535;G:1465221643;T:1611675024;N:226586,8,28,91,,1890991056,1285158535,1465221643,1611675024,226586,SRX28356288,SRS24685480,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35842,SRR33092388,SRX28356287,SRS24685479,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Leptomeninges scRNA seq,GSM8902566,,source name:Leptomeninges|tissue:Leptomeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Leptomeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Leptomeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Leptomeninges,GSM8902566,GSM8902566: Zebrafish Adult Leptomeninges scRNA seq; Danio rerio; RNA Seq,GSM8902566 r1,GSM8902566,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,LP5_S3_L001_I1_001.fastq.gz LP5_S3_L001_I2_001.fastq.gz LP5_S3_L001_R1_001.fastq.gz LP5_S3_L001_R2_001.fastq.gz,fastq fastq fastq fastq,15568833630.0,112817635.0,GSM8902566 r3,0:10 1:10 2:28 3:90,A:3095918108;C:2067214324;G:2193944375;T:2796211477;N:298866,10,10,28,90,3095918108,2067214324,2193944375,2796211477,298866,SRX28356287,SRS24685479,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35843,SRR33092389,SRX28356287,SRS24685479,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Leptomeninges scRNA seq,GSM8902566,,source name:Leptomeninges|tissue:Leptomeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Leptomeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Leptomeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Leptomeninges,GSM8902566,GSM8902566: Zebrafish Adult Leptomeninges scRNA seq; Danio rerio; RNA Seq,GSM8902566 r1,GSM8902566,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,LP4_S2_L002_I1_001.fastq.gz LP4_S2_L002_I2_001.fastq.gz LP4_S2_L002_R1_001.fastq.gz LP4_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9285387684.0,67285418.0,GSM8902566 r2,0:10 1:10 2:28 3:90,A:1865276237;C:1235101824;G:1340998802;T:1614123547;N:187210,10,10,28,90,1865276237,1235101824,1340998802,1614123547,187210,SRX28356287,SRS24685479,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35844,SRR33092390,SRX28356287,SRS24685479,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Leptomeninges scRNA seq,GSM8902566,,source name:Leptomeninges|tissue:Leptomeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Leptomeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Leptomeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Leptomeninges,GSM8902566,GSM8902566: Zebrafish Adult Leptomeninges scRNA seq; Danio rerio; RNA Seq,GSM8902566 r1,GSM8902566,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,LP3_S15_L002_I1_001.fastq.gz LP3_S15_L002_R1_001.fastq.gz LP3_S15_L002_R2_001.fastq.gz,fastq fastq fastq,9389706646.0,73934698.0,GSM8902566 r8,0:8 1:28 2:91,A:2272647309;C:1189928271;G:1407239573;T:1858001350;N:241015,8,28,91,,2272647309,1189928271,1407239573,1858001350,241015,SRX28356287,SRS24685479,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35845,SRR33092391,SRX28356287,SRS24685479,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Leptomeninges scRNA seq,GSM8902566,,source name:Leptomeninges|tissue:Leptomeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Leptomeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Leptomeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Leptomeninges,GSM8902566,GSM8902566: Zebrafish Adult Leptomeninges scRNA seq; Danio rerio; RNA Seq,GSM8902566 r1,GSM8902566,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,LP3_S15_L001_I1_001.fastq.gz LP3_S15_L001_R1_001.fastq.gz LP3_S15_L001_R2_001.fastq.gz,fastq fastq fastq,9430875982.0,74258866.0,GSM8902566 r7,0:8 1:28 2:91,A:2283581426;C:1194788838;G:1413526478;T:1865417297;N:242767,8,28,91,,2283581426,1194788838,1413526478,1865417297,242767,SRX28356287,SRS24685479,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35846,SRR33092392,SRX28356287,SRS24685479,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Leptomeninges scRNA seq,GSM8902566,,source name:Leptomeninges|tissue:Leptomeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Leptomeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Leptomeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Leptomeninges,GSM8902566,GSM8902566: Zebrafish Adult Leptomeninges scRNA seq; Danio rerio; RNA Seq,GSM8902566 r1,GSM8902566,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,LP2_S14_L002_I1_001.fastq.gz LP2_S14_L002_R1_001.fastq.gz LP2_S14_L002_R2_001.fastq.gz,fastq fastq fastq,8600113229.0,67717427.0,GSM8902566 r6,0:8 1:28 2:91,A:2031057495;C:1116227631;G:1301307083;T:1713473857;N:219791,8,28,91,,2031057495,1116227631,1301307083,1713473857,219791,SRX28356287,SRS24685479,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35847,SRR33092393,SRX28356287,SRS24685479,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Leptomeninges scRNA seq,GSM8902566,,source name:Leptomeninges|tissue:Leptomeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Leptomeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Leptomeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Leptomeninges,GSM8902566,GSM8902566: Zebrafish Adult Leptomeninges scRNA seq; Danio rerio; RNA Seq,GSM8902566 r1,GSM8902566,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,LP2_S14_L001_I1_001.fastq.gz LP2_S14_L001_R1_001.fastq.gz LP2_S14_L001_R2_001.fastq.gz,fastq fastq fastq,8637039114.0,68008182.0,GSM8902566 r5,0:8 1:28 2:91,A:2040552249;C:1120589408;G:1306950110;T:1720431887;N:220908,8,28,91,,2040552249,1120589408,1306950110,1720431887,220908,SRX28356287,SRS24685479,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35848,SRR33092394,SRX28356287,SRS24685479,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Leptomeninges scRNA seq,GSM8902566,,source name:Leptomeninges|tissue:Leptomeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Leptomeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Leptomeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Leptomeninges,GSM8902566,GSM8902566: Zebrafish Adult Leptomeninges scRNA seq; Danio rerio; RNA Seq,GSM8902566 r1,GSM8902566,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,LP5_S3_L002_I1_001.fastq.gz LP5_S3_L002_I2_001.fastq.gz LP5_S3_L002_R1_001.fastq.gz LP5_S3_L002_R2_001.fastq.gz,fastq fastq fastq fastq,15558164850.0,112740325.0,GSM8902566 r4,0:10 1:10 2:28 3:90,A:3093961545;C:2065582935;G:2192533724;T:2794237154;N:313892,10,10,28,90,3093961545,2065582935,2192533724,2794237154,313892,SRX28356287,SRS24685479,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
35849,SRR33092395,SRX28356287,SRS24685479,SRP578043,PRJNA1249042,Anatomical and Molecular Characterization of the Zebrafish Meninges,GSE294335,Transcriptome Analysis,The meninges are a set of connective tissue layers that surround the central nervous system  protecting the brain from mechanical shock  supporting its buoyancy  guarding it from infection and injury  and maintaining brain homeostasis. Despite their critical role  the molecular identity  developmental origins  and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here  we show that the zebrafish  a genetically and experimentally accessible vertebrate  possesses an easily imaged mammalian like meninges. Anatomical and cellular characterization of its composition via histology  electron microscopy  and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double layered dura mater and intricate leptomeningeal layers.  Using single cell transcriptomics  we define the molecular identities of meningeal cell populations  including a unique ependymin epd expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges  provide a foundational description for future zebrafish meningeal research  and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges. Overall design: Single cell expression profiling by high throughput sequencing,,,,Zebrafish Adult Leptomeninges scRNA seq,GSM8902566,,source name:Leptomeninges|tissue:Leptomeninges|geo loc name:missing|collection date:missing,Zebrafish Adult Leptomeninges scRNA seq,cellranger count v7.0.0 Assembly: Assembly: zv11 Supplementary files format and content: Supplementary files format and content: TSV value and matrix files,Leptomeninges,,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,tissue:Leptomeninges,GSM8902566,GSM8902566: Zebrafish Adult Leptomeninges scRNA seq; Danio rerio; RNA Seq,GSM8902566 r1,GSM8902566,1,Cell suspension prepared from 20 leptomeningeal linings 10 from females  10 from males removed from zebrafish comprising 10 000 cells. Cell suspension prepared from 25 pachymeningeal linings 12 from females  13 from males removed from zebrafish comprising 10 000 cells. 10X 3.1 GEM kits following manufacturer recommendations,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP578043,,loader:fastq load.py,LP4_S2_L001_I1_001.fastq.gz LP4_S2_L001_I2_001.fastq.gz LP4_S2_L001_R1_001.fastq.gz LP4_S2_L001_R2_001.fastq.gz,fastq fastq fastq fastq,9290858970.0,67325065.0,GSM8902566 r1,0:10 1:10 2:28 3:90,A:1866460292;C:1235842442;G:1341443403;T:1615329817;N:179896,10,10,28,90,1866460292,1235842442,1341443403,1615329817,179896,SRX28356287,SRS24685479,SRA2109616,"Weinstein Lab, NICHD, NIH","Weinstein Lab, NICHD, NIH",,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2025-04-10,Adult,Adult,Brain,Nervous System
43983,SRR6811832,SRX3768872,SRS3023386,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva F1 2 scar,GSM3032175,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva F1 2 scar,Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode  a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors  we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step  we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step  we aimed to remove easily recognizable sequencing errors. To this end  we consecutively considered scar sequences that have the same cellular barcode and UMI  UMIs that have the same cellular barcode and scar sequence  and cellular barcodes that have the same UMI and scar sequence. In each step  we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI  or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus  but information about scar expression levels was not required in our downstream analysis. In the third filtering step  we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with CIGAR  cell name  cell barcode and UMI sequence.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM3032175,GSM3032175: Larva F1 2 scar; Danio rerio; OTHER,GSM3032175,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032175,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,F1_2_scar_R1.fastq.gz F1_2_scar_R2.fastq.gz,fastq fastq,9301928572.0,75015553.0,GSM3032175 r1,0:26 1:98,A:2682085389;C:3008788535;G:2093169318;T:1516220703;N:1664627,26,98,,,2682085389,3008788535,2093169318,1516220703,1664627,SRX3768872,SRS3023386,SRA623333,GEO,Max Delbrück Center,2,0.0001,0.00173,4e-05,8e-05,0.99983,0.99667,0.33333,0.531,26,98,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Larval,Larval,Trunk,Surface Structure
43984,SRR6811831,SRX3768871,SRS3023388,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva F1 1 scar,GSM3032174,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva F1 1 scar,Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode  a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors  we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step  we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step  we aimed to remove easily recognizable sequencing errors. To this end  we consecutively considered scar sequences that have the same cellular barcode and UMI  UMIs that have the same cellular barcode and scar sequence  and cellular barcodes that have the same UMI and scar sequence. In each step  we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI  or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus  but information about scar expression levels was not required in our downstream analysis. In the third filtering step  we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with CIGAR  cell name  cell barcode and UMI sequence.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM3032174,GSM3032174: Larva F1 1 scar; Danio rerio; OTHER,GSM3032174,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032174,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,F1_1_scar_R1.fastq.gz F1_1_scar_R2.fastq.gz,fastq fastq,7772713576.0,62683174.0,GSM3032174 r1,0:26 1:98,A:2222016153;C:2555237987;G:1722216404;T:1271855931;N:1387101,26,98,,,2222016153,2555237987,1722216404,1271855931,1387101,SRX3768871,SRS3023388,SRA623333,GEO,Max Delbrück Center,2,0.00014,0.00171,8e-05,0.00012,0.99985,0.99642,0.44444,0.45454,26,98,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Larval,Larval,Trunk,Surface Structure
43985,SRR6811830,SRX3768870,SRS3023387,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva F1 2 mRNA,GSM3032173,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva F1 2 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM3032173,GSM3032173: Larva F1 2 mRNA; Danio rerio; RNA Seq,GSM3032173,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032173,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,F1_2_wt_R1.fastq.gz F1_2_wt_R2.fastq.gz,fastq fastq,29997480708.0,241915167.0,GSM3032173 r1,0:26 1:98,A:8264355452;C:6830431714;G:7093261338;T:7804053400;N:5378804,26,98,,,8264355452,6830431714,7093261338,7804053400,5378804,SRX3768870,SRS3023387,SRA623333,GEO,Max Delbrück Center,2,0.00307,0.94486,0.00051,0.08199,0.99431,0.82509,0.36875,0.43599,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Larval,Larval,Trunk,Surface Structure
43986,SRR6811829,SRX3768869,SRS3023385,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva F1 1 mRNA,GSM3032172,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva F1 1 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM3032172,GSM3032172: Larva F1 1 mRNA; Danio rerio; RNA Seq,GSM3032172,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032172,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,F1_1_wt_R1.fastq.gz F1_1_wt_R2.fastq.gz,fastq fastq,26685876072.0,215208678.0,GSM3032172 r1,0:26 1:98,A:7365353958;C:6068313931;G:6251004125;T:6996410946;N:4793112,26,98,,,7365353958,6068313931,6251004125,6996410946,4793112,SRX3768869,SRS3023385,SRA623333,GEO,Max Delbrück Center,2,0.00255,0.93758,0.00046,0.08179,0.99515,0.82637,0.35368,0.46605,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Larval,Larval,Trunk,Surface Structure
43987,SRR6811828,SRX3768868,SRS3023414,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Pancreas 3 exo scar,GSM3032171,,source name:Pancreas except primary islet  liver|strain/background:Zebrabow M|tissue:Pancreas except primary islet  liver|developmental stage:Adult,Pancreas 3 exo scar,Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode  a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors  we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step  we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step  we aimed to remove easily recognizable sequencing errors. To this end  we consecutively considered scar sequences that have the same cellular barcode and UMI  UMIs that have the same cellular barcode and scar sequence  and cellular barcodes that have the same UMI and scar sequence. In each step  we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI  or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus  but information about scar expression levels was not required in our downstream analysis. In the third filtering step  we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.,Pancreas except primary islet  liver,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Pancreas except primary islet  liver|developmental stage:Adult,GSM3032171,GSM3032171: Pancreas 3 exo scar; Danio rerio; OTHER,GSM3032171,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032171,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,P7exo_scar_R1.fastq.gz P7exo_scar_R2.fastq.gz,fastq fastq,4291410352.0,34608148.0,GSM3032171 r1,0:26 1:98,A:1266869162;C:1345773385;G:950601988;T:726078376;N:2087441,26,98,,,1266869162,1345773385,950601988,726078376,2087441,SRX3768868,SRS3023414,SRA623333,GEO,Max Delbrück Center,2,0.00014,0.00241,0.00012,0.00024,0.99995,0.99691,0.0,0.65306,26,98,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Adult,Adult,Multi-tissue,Multi-system
43988,SRR6811827,SRX3768867,SRS3023384,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Pancreas 3 endo scar,GSM3032170,,source name:Primary pancreatic islet|strain/background:Zebrabow M|tissue:Primary pancreatic islet|developmental stage:Adult,Pancreas 3 endo scar,Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode  a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors  we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step  we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step  we aimed to remove easily recognizable sequencing errors. To this end  we consecutively considered scar sequences that have the same cellular barcode and UMI  UMIs that have the same cellular barcode and scar sequence  and cellular barcodes that have the same UMI and scar sequence. In each step  we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI  or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus  but information about scar expression levels was not required in our downstream analysis. In the third filtering step  we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.,Primary pancreatic islet,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Primary pancreatic islet|developmental stage:Adult,GSM3032170,GSM3032170: Pancreas 3 endo scar; Danio rerio; OTHER,GSM3032170,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032170,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,P7endo_scar_R1.fastq.gz P7endo_scar_R2.fastq.gz,fastq fastq,2537781396.0,20465979.0,GSM3032170 r1,0:26 1:98,A:741745261;C:801599713;G:561531527;T:431666561;N:1238334,26,98,,,741745261,801599713,561531527,431666561,1238334,SRX3768867,SRS3023384,SRA623333,GEO,Max Delbrück Center,2,0.00014,0.00289,0.00012,0.00028,0.99995,0.99602,1.0,0.68478,26,98,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Adult,Adult,Pancreas,Endocrine System
43989,SRR6811826,SRX3768866,SRS3023382,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Heart 3 scar,GSM3032169,,source name:Heart and blood|strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult,Heart 3 scar,Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode  a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors  we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step  we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step  we aimed to remove easily recognizable sequencing errors. To this end  we consecutively considered scar sequences that have the same cellular barcode and UMI  UMIs that have the same cellular barcode and scar sequence  and cellular barcodes that have the same UMI and scar sequence. In each step  we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI  or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus  but information about scar expression levels was not required in our downstream analysis. In the third filtering step  we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.,Heart and blood,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult,GSM3032169,GSM3032169: Heart 3 scar; Danio rerio; OTHER,GSM3032169,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032169,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,H7_scar_R1.fastq.gz H7_scar_R2.fastq.gz,fastq fastq,3999397296.0,32253204.0,GSM3032169 r1,0:26 1:98,A:1170970784;C:1255843391;G:881154893;T:689473188;N:1955040,26,98,,,1170970784,1255843391,881154893,689473188,1955040,SRX3768866,SRS3023382,SRA623333,GEO,Max Delbrück Center,2,0.00018,0.00228,0.00015,0.00019,0.99991,0.99659,0.8,0.67235,26,98,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Adult,Adult,Multi-tissue,Multi-system
43990,SRR6811825,SRX3768865,SRS3023383,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Brain 3 scar,GSM3032168,,source name:Brain|strain/background:Zebrabow M|tissue:Brain|developmental stage:Adult,Brain 3 scar,Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode  a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors  we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step  we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step  we aimed to remove easily recognizable sequencing errors. To this end  we consecutively considered scar sequences that have the same cellular barcode and UMI  UMIs that have the same cellular barcode and scar sequence  and cellular barcodes that have the same UMI and scar sequence. In each step  we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI  or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus  but information about scar expression levels was not required in our downstream analysis. In the third filtering step  we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.,Brain,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Brain|developmental stage:Adult,GSM3032168,GSM3032168: Brain 3 scar; Danio rerio; OTHER,GSM3032168,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032168,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,B7_scar_R2.fastq.gz B7_scar_R1.fastq.gz,fastq fastq,1359725968.0,10965532.0,GSM3032168 r1,0:26 1:98,A:397239266;C:429529094;G:288126336;T:244165622;N:665650,26,98,,,397239266,429529094,288126336,244165622,665650,SRX3768865,SRS3023383,SRA623333,GEO,Max Delbrück Center,2,0.00032,0.00295,0.00026,0.0003,0.99991,0.99642,0.3,0.64327,26,98,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Adult,Adult,Brain,Nervous System
43991,SRR6811824,SRX3768864,SRS3023381,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva 5 scar,GSM3032167,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva 5 scar,Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode  a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors  we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step  we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step  we aimed to remove easily recognizable sequencing errors. To this end  we consecutively considered scar sequences that have the same cellular barcode and UMI  UMIs that have the same cellular barcode and scar sequence  and cellular barcodes that have the same UMI and scar sequence. In each step  we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI  or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus  but information about scar expression levels was not required in our downstream analysis. In the third filtering step  we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM3032167,GSM3032167: Larva 5 scar; Danio rerio; OTHER,GSM3032167,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032167,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,Z5_scar_R1.fastq.gz Z5_scar_R2.fastq.gz,fastq fastq,7672645700.0,61876175.0,GSM3032167 r1,0:26 1:98,A:2173948352;C:2439410929;G:1714624642;T:1343296377;N:1365400,26,98,,,2173948352,2439410929,1714624642,1343296377,1365400,SRX3768864,SRS3023381,SRA623333,GEO,Max Delbrück Center,2,0.00013,0.00164,9e-05,8e-05,0.99989,0.99669,0.83333,0.4918,26,98,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Larval,Larval,Trunk,Surface Structure
43992,SRR6811823,SRX3768863,SRS3023380,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva 4 scar,GSM3032166,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva 4 scar,Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode  a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors  we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step  we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step  we aimed to remove easily recognizable sequencing errors. To this end  we consecutively considered scar sequences that have the same cellular barcode and UMI  UMIs that have the same cellular barcode and scar sequence  and cellular barcodes that have the same UMI and scar sequence. In each step  we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI  or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus  but information about scar expression levels was not required in our downstream analysis. In the third filtering step  we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM3032166,GSM3032166: Larva 4 scar; Danio rerio; OTHER,GSM3032166,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032166,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,Z4_scar_R1.fastq.gz Z4_scar_R2.fastq.gz,fastq fastq,7236183804.0,58356321.0,GSM3032166 r1,0:26 1:98,A:2080254513;C:2296727471;G:1625115068;T:1232786300;N:1300452,26,98,,,2080254513,2296727471,1625115068,1232786300,1300452,SRX3768863,SRS3023380,SRA623333,GEO,Max Delbrück Center,2,0.00014,0.0016,0.00011,7e-05,0.99993,0.99634,0.33333,0.46694,26,98,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Larval,Larval,Trunk,Surface Structure
43993,SRR6811822,SRX3768862,SRS3023379,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Pancreas 3 exo mRNA,GSM3032165,,source name:Pancreas except primary islet  liver|strain/background:Zebrabow M|tissue:Pancreas except primary islet  liver|developmental stage:Adult,Pancreas 3 exo mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Pancreas except primary islet  liver,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Pancreas except primary islet  liver|developmental stage:Adult,GSM3032165,GSM3032165: Pancreas 3 exo mRNA; Danio rerio; RNA Seq,GSM3032165,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032165,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,P7exo_wt_R1.fastq.gz P7exo_wt_R2.fastq.gz,fastq fastq,38574026764.0,311080861.0,GSM3032165 r1,0:26 1:98,A:10751580091;C:8744299142;G:9264760851;T:9795905887;N:17480793,26,98,,,10751580091,8744299142,9264760851,9795905887,17480793,SRX3768862,SRS3023379,SRA623333,GEO,Max Delbrück Center,2,0.00463,0.93239,0.00336,0.04555,0.99671,0.87207,0.46341,0.57662,26,98,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Adult,Adult,Multi-tissue,Multi-system
43994,SRR6811821,SRX3768861,SRS3023378,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Pancreas 3 endo mRNA,GSM3032164,,source name:Primary pancreatic islet|strain/background:Zebrabow M|tissue:Primary pancreatic islet|developmental stage:Adult,Pancreas 3 endo mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Primary pancreatic islet,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Primary pancreatic islet|developmental stage:Adult,GSM3032164,GSM3032164: Pancreas 3 endo mRNA; Danio rerio; RNA Seq,GSM3032164,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032164,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,P7endo_wt_R1.fastq.gz P7endo_wt_R2.fastq.gz,fastq fastq,41593781900.0,335433725.0,GSM3032164 r1,0:26 1:98,A:11833690021;C:9547054378;G:9724089290;T:10470148302;N:18799909,26,98,,,11833690021,9547054378,9724089290,10470148302,18799909,SRX3768861,SRS3023378,SRA623333,GEO,Max Delbrück Center,2,0.00308,0.92936,0.00192,0.05695,0.9973,0.8686,0.45945,0.58814,26,98,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Adult,Adult,Pancreas,Endocrine System
43995,SRR6811820,SRX3768860,SRS3023377,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Heart 3 mRNA,GSM3032163,,source name:Heart and blood|strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult,Heart 3 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Heart and blood,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult,GSM3032163,GSM3032163: Heart 3 mRNA; Danio rerio; RNA Seq,GSM3032163,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032163,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,H7_wt_R2.fastq.gz H7_wt_R1.fastq.gz,fastq fastq,45826897248.0,369571752.0,GSM3032163 r1,0:26 1:98,A:12856871948;C:10721924215;G:10335821801;T:11891517482;N:20761802,26,98,,,12856871948,10721924215,10335821801,11891517482,20761802,SRX3768860,SRS3023377,SRA623333,GEO,Max Delbrück Center,2,0.00303,0.90293,0.00206,0.05991,0.99746,0.86918,0.3421,0.66847,26,98,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Adult,Adult,Multi-tissue,Multi-system
43996,SRR6811819,SRX3768859,SRS3023375,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Brain 3 mRNA,GSM3032162,,source name:Brain|strain/background:Zebrabow M|tissue:Brain|developmental stage:Adult,Brain 3 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Brain,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Brain|developmental stage:Adult,GSM3032162,GSM3032162: Brain 3 mRNA; Danio rerio; RNA Seq,GSM3032162,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032162,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,B7_wt_R2.fastq.gz B7_wt_R1.fastq.gz,fastq fastq,35200219264.0,283872736.0,GSM3032162 r1,0:26 1:98,A:10338159874;C:7412176847;G:7655217994;T:9778922063;N:15742486,26,98,,,10338159874,7412176847,7655217994,9778922063,15742486,SRX3768859,SRS3023375,SRA623333,GEO,Max Delbrück Center,2,0.00528,0.88902,0.00406,0.20497,0.99573,0.78595,0.42436,0.62912,26,98,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Adult,Adult,Brain,Nervous System
43997,SRR6811818,SRX3768858,SRS3023376,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva 5 mRNA,GSM3032161,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva 5 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM3032161,GSM3032161: Larva 5 mRNA; Danio rerio; RNA Seq,GSM3032161,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032161,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,Z5_wt_R1.fastq.gz Z5_wt_R2.fastq.gz,fastq fastq,27409556812.0,221044813.0,GSM3032161 r1,0:26 1:98,A:7637677199;C:6210942203;G:6438364980;T:7117667800;N:4904630,26,98,,,7637677199,6210942203,6438364980,7117667800,4904630,SRX3768858,SRS3023376,SRA623333,GEO,Max Delbrück Center,2,0.00523,0.92734,0.0008,0.0687,0.98916,0.81479,0.44117,0.50243,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Larval,Larval,Trunk,Surface Structure
43998,SRR6811817,SRX3768857,SRS3023374,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva 4 mRNA,GSM3032160,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva 4 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM3032160,GSM3032160: Larva 4 mRNA; Danio rerio; RNA Seq,GSM3032160,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032160,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,Z4_wt_R2.fastq.gz Z4_wt_R1.fastq.gz,fastq fastq,19775711456.0,159481544.0,GSM3032160 r1,0:26 1:98,A:5483727144;C:4548396363;G:4737957565;T:5002119078;N:3511306,26,98,,,5483727144,4548396363,4737957565,5002119078,3511306,SRX3768857,SRS3023374,SRA623333,GEO,Max Delbrück Center,2,0.00331,0.93006,0.00057,0.05973,0.99253,0.82369,0.38666,0.48899,26,98,T,B,sc-like readlen,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Larval,Larval,Trunk,Surface Structure
43999,SRR6811816,SRX3768856,SRS3023373,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva 3 mRNA,GSM3032159,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva 3 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM3032159,GSM3032159: Larva 3 mRNA; Danio rerio; RNA Seq,GSM3032159,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM3032159,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,Z3_wt_R1.fastq.gz Z3_wt_R2.fastq.gz Z3_wt_R3.fastq.gz,fastq fastq fastq,8016913120.0,50105707.0,GSM3032159 r1,0:130 1:14 2:16,A:2047850756;C:1318672327;G:1403772432;T:1743394108;N:52287,130,14,16,,2047850756,1318672327,1403772432,1743394108,52287,SRX3768856,SRS3023373,SRA623333,GEO,Max Delbrück Center,1,0.87661,,0.06466,,0.86614,,0.53364,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2018-03-06,Larval,Larval,Trunk,Surface Structure
44000,SRR6211492,SRX3320767,SRS2626340,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Heart 2 mRNA,GSM2830062,,source name:Heart and blood|strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult,Heart 2 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode  a UMI  and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment  we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode  we counted the number of molecules mapped to each gene  using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t =  K ln1 – k o/K  with t the final number of transcripts  k o the observed UMIs  and K the total number of UMIs possible. As protection against barcode sequencing errors  we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore  we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Heart and blood,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult,GSM2830062,GSM2830062: Heart 2 mRNA; Danio rerio; RNA Seq,GSM2830062,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830062,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,H6_wt_R2.fastq.gz H6_wt_R1.fastq.gz,fastq fastq,19466673438.0,141062851.0,GSM2830062 r1,0:28 1:110,A:5788453893;C:4266605110;G:4479895656;T:4930437501;N:1281278,28,110,,,5788453893,4266605110,4479895656,4930437501,1281278,SRX3320767,SRS2626340,SRA623333,GEO,Max Delbrück Center,2,0.00114,0.94531,0.00026,0.06835,0.99819,0.88308,0.68098,0.70993,28,110,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Adult,Adult,Multi-tissue,Multi-system
44001,SRR6211491,SRX3320766,SRS2626339,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Pancreas 2 mRNA,GSM2830061,,source name:Pancreas and liver|strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult,Pancreas 2 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode  a UMI  and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment  we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode  we counted the number of molecules mapped to each gene  using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t =  K ln1 – k o/K  with t the final number of transcripts  k o the observed UMIs  and K the total number of UMIs possible. As protection against barcode sequencing errors  we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore  we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Pancreas and liver,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult,GSM2830061,GSM2830061: Pancreas 2 mRNA; Danio rerio; RNA Seq,GSM2830061,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830061,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,P6_wt_R1.fastq.gz P6_wt_R2.fastq.gz,fastq fastq,17563278078.0,127270131.0,GSM2830061 r1,0:28 1:110,A:5146142876;C:3830859355;G:4368254000;T:4216873712;N:1148135,28,110,,,5146142876,3830859355,4368254000,4216873712,1148135,SRX3320766,SRS2626339,SRA623333,GEO,Max Delbrück Center,2,0.0023,0.93516,0.00062,0.07613,0.99667,0.8798,0.62666,0.6399,28,110,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Adult,Adult,Multi-tissue,Multi-system
44002,SRR6211490,SRX3320765,SRS2626338,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Heart 1 mRNA,GSM2830060,,source name:Heart and blood|strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult,Heart 1 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode  a UMI  and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment  we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode  we counted the number of molecules mapped to each gene  using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t =  K ln1 – k o/K  with t the final number of transcripts  k o the observed UMIs  and K the total number of UMIs possible. As protection against barcode sequencing errors  we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore  we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Heart and blood,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult,GSM2830060,GSM2830060: Heart 1 mRNA; Danio rerio; RNA Seq,GSM2830060,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830060,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,H5_wt_R1.fastq.gz H5_wt_R2.fastq.gz,fastq fastq,11175332616.0,88693116.0,GSM2830060 r1,0:26 1:100,A:3373517159;C:2470603501;G:2531314673;T:2798372007;N:1525276,26,100,,,3373517159,2470603501,2531314673,2798372007,1525276,SRX3320765,SRS2626338,SRA623333,GEO,Max Delbrück Center,2,0.00264,0.95153,0.00046,0.05429,0.99669,0.88958,0.57635,0.67876,26,100,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Adult,Adult,Multi-tissue,Multi-system
44003,SRR6211489,SRX3320764,SRS2626337,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Brain 1 mRNA,GSM2830059,,source name:Brain|strain/background:Zebrabow M|tissue:Brain|developmental stage:Adult,Brain 1 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode  a UMI  and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment  we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode  we counted the number of molecules mapped to each gene  using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t =  K ln1 – k o/K  with t the final number of transcripts  k o the observed UMIs  and K the total number of UMIs possible. As protection against barcode sequencing errors  we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore  we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Brain,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Brain|developmental stage:Adult,GSM2830059,GSM2830059: Brain 1 mRNA; Danio rerio; RNA Seq,GSM2830059,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830059,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina MiniSeq,,SRP121343,,,B5_wt_R1.fastq.gz B5_wt_R2.fastq.gz,fastq fastq,4538898000.0,36023000.0,GSM2830059 r1,0:26 1:100,A:1403578459;C:926366830;G:979609921;T:1228675807;N:666983,26,100,,,1403578459,926366830,979609921,1228675807,666983,SRX3320764,SRS2626337,SRA623333,GEO,Max Delbrück Center,2,0.0031,0.90951,0.00167,0.32324,0.99582,0.82834,0.46718,0.66863,26,100,T,B,sc-like readlen,illumina,miseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Adult,Adult,Brain,Nervous System
44004,SRR6211488,SRX3320763,SRS2626336,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Pancreas 1 mRNA,GSM2830058,,source name:Pancreas and liver|strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult,Pancreas 1 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode  a UMI  and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment  we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode  we counted the number of molecules mapped to each gene  using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t =  K ln1 – k o/K  with t the final number of transcripts  k o the observed UMIs  and K the total number of UMIs possible. As protection against barcode sequencing errors  we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore  we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Pancreas and liver,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult,GSM2830058,GSM2830058: Pancreas 1 mRNA; Danio rerio; RNA Seq,GSM2830058,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830058,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,P5_wt_R1.fastq.gz P5_wt_R2.fastq.gz,fastq fastq,18116725914.0,143783539.0,GSM2830058 r1,0:26 1:100,A:5348935548;C:3950936592;G:4404689151;T:4409667387;N:2497236,26,100,,,5348935548,3950936592,4404689151,4409667387,2497236,SRX3320763,SRS2626336,SRA623333,GEO,Max Delbrück Center,2,0.00319,0.93498,0.00092,0.08656,0.9947,0.86097,0.45652,0.53817,26,100,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Adult,Adult,Multi-tissue,Multi-system
44005,SRR6211487,SRX3320762,SRS2626335,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva 2 mRNA,GSM2830057,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva 2 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode  a UMI  and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment  we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode  we counted the number of molecules mapped to each gene  using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t =  K ln1 – k o/K  with t the final number of transcripts  k o the observed UMIs  and K the total number of UMIs possible. As protection against barcode sequencing errors  we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore  we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM2830057,GSM2830057: Larva 2 mRNA; Danio rerio; RNA Seq,GSM2830057,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830057,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,Z1_wt_R3.fastq.gz Z1_wt_R2.fastq.gz Z1_wt_R1.fastq.gz,fastq fastq fastq,28368351950.0,232527475.0,GSM2830057 r1,0:98 1:14 2:10,A:6582076349;C:4985163175;G:5131319282;T:6085835988;N:3297756,98,14,10,,6582076349,4985163175,5131319282,6085835988,3297756,SRX3320762,SRS2626335,SRA623333,GEO,Max Delbrück Center,1,0.9378,,0.05825,,0.79687,,0.50342,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Larval,Larval,Trunk,Surface Structure
44006,SRR6211485,SRX3320760,SRS2626333,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva 1 mRNA,GSM2830056,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva 1 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode  a UMI  and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment  we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode  we counted the number of molecules mapped to each gene  using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t =  K ln1 – k o/K  with t the final number of transcripts  k o the observed UMIs  and K the total number of UMIs possible. As protection against barcode sequencing errors  we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore  we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM2830056,GSM2830056: Larva 1 mRNA; Danio rerio; RNA Seq,GSM2830056,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830056,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,Z2_1_wt_R1.fastq.gz Z2_1_wt_R2.fastq.gz Z2_1_wt_R3.fastq.gz,fastq fastq fastq,36065037280.0,225406483.0,GSM2830056 r1,0:130 1:14 2:16,A:9121762570;C:5889322717;G:6251660049;T:8039869338;N:228116,130,14,16,,9121762570,5889322717,6251660049,8039869338,228116,SRX3320760,SRS2626333,SRA623333,GEO,Max Delbrück Center,1,0.88569,,0.08353,,0.86016,,0.53379,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Larval,Larval,Trunk,Surface Structure
44007,SRR6211486,SRX3320760,SRS2626333,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva 1 mRNA,GSM2830056,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva 1 mRNA,Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2. Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication. Every sequencing read consists of a cellular barcode  a UMI  and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting ' q 50' to a reference transcriptome constructed from Ensembl release 74 www.ensembl.org with extended three prime UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. post alignment  we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules. For each cellular barcode  we counted the number of molecules mapped to each gene  using the UMI correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t =  K ln1 – k o/K  with t the final number of transcripts  k o the observed UMIs  and K the total number of UMIs possible. As protection against barcode sequencing errors  we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore  we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts. Genome build: GRCz10   release 90 Supplementary files format and content: * matrix.mtx: Single cell transcript count table; * barcodes.tsv: List of cell barcodes.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM2830056,GSM2830056: Larva 1 mRNA; Danio rerio; RNA Seq,GSM2830056,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830056,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,Z2_2_wt_R1.fastq.gz Z2_2_wt_R2.fastq.gz Z2_2_wt_R3.fastq.gz,fastq fastq fastq,7700646560.0,48129041.0,GSM2830056 r2,0:130 1:14 2:16,A:1890861891;C:1307860042;G:1403340071;T:1654667424;N:45902,130,14,16,,1890861891,1307860042,1403340071,1654667424,45902,SRX3320760,SRS2626333,SRA623333,GEO,Max Delbrück Center,1,0.89198,,0.07477,,0.87288,,0.49519,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Larval,Larval,Trunk,Surface Structure
44008,SRR6211484,SRX3320759,SRS2626332,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Heart 2 scar,GSM2830055,,source name:Heart and blood|strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult,Heart 2 scar,Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode  a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors  we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step  we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step  we aimed to remove easily recognizable sequencing errors. To this end  we consecutively considered scar sequences that have the same cellular barcode and UMI  UMIs that have the same cellular barcode and scar sequence  and cellular barcodes that have the same UMI and scar sequence. In each step  we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI  or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus  but information about scar expression levels was not required in our downstream analysis. In the third filtering step  we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. In the fourth filtering step  we determined the distribution of reads for the scars we had kept so far. Based on this distribution  we set a cut off and filtered out the scars that did not have at least this number of reads. Finally  for each cell type  we determined the distribution of different scars seen per cell and set a maximum number of scars a cell of that type can have. We filtered out cells in which we observed more than this maximum number as possible doublets. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.,Heart and blood,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult,GSM2830055,GSM2830055: Heart 2 scar; Danio rerio; OTHER,GSM2830055,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830055,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,H6_scar_R1.fastq.gz H6_scar_R2.fastq.gz,fastq fastq,2079107172.0,15065994.0,GSM2830055 r1,0:28 1:110,A:580640871;C:641740953;G:501505035;T:355092832;N:127481,28,110,,,580640871,641740953,501505035,355092832,127481,SRX3320759,SRS2626332,SRA623333,GEO,Max Delbrück Center,2,5e-05,0.00253,4e-05,0.00023,1.0,0.99778,,0.58419,28,110,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Adult,Adult,Multi-tissue,Multi-system
44009,SRR6211483,SRX3320758,SRS2626348,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Pancreas 2 scar,GSM2830054,,source name:Pancreas and liver|strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult,Pancreas 2 scar,Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode  a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors  we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step  we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step  we aimed to remove easily recognizable sequencing errors. To this end  we consecutively considered scar sequences that have the same cellular barcode and UMI  UMIs that have the same cellular barcode and scar sequence  and cellular barcodes that have the same UMI and scar sequence. In each step  we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI  or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus  but information about scar expression levels was not required in our downstream analysis. In the third filtering step  we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. In the fourth filtering step  we determined the distribution of reads for the scars we had kept so far. Based on this distribution  we set a cut off and filtered out the scars that did not have at least this number of reads. Finally  for each cell type  we determined the distribution of different scars seen per cell and set a maximum number of scars a cell of that type can have. We filtered out cells in which we observed more than this maximum number as possible doublets. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.,Pancreas and liver,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult,GSM2830054,GSM2830054: Pancreas 2 scar; Danio rerio; OTHER,GSM2830054,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830054,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,P6_scar_R1.fastq.gz P6_scar_R2.fastq.gz,fastq fastq,1026715860.0,7439970.0,GSM2830054 r1,0:28 1:110,A:287816843;C:320879355;G:243598630;T:174359452;N:61580,28,110,,,287816843,320879355,243598630,174359452,61580,SRX3320758,SRS2626348,SRA623333,GEO,Max Delbrück Center,2,0.00029,0.00123,0.00028,6e-05,1.0,0.99914,,0.25714,28,110,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Adult,Adult,Multi-tissue,Multi-system
44010,SRR6211482,SRX3320757,SRS2626331,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Heart 1 scar,GSM2830053,,source name:Heart and blood|strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult,Heart 1 scar,Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode  a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors  we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step  we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step  we aimed to remove easily recognizable sequencing errors. To this end  we consecutively considered scar sequences that have the same cellular barcode and UMI  UMIs that have the same cellular barcode and scar sequence  and cellular barcodes that have the same UMI and scar sequence. In each step  we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI  or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus  but information about scar expression levels was not required in our downstream analysis. In the third filtering step  we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. In the fourth filtering step  we determined the distribution of reads for the scars we had kept so far. Based on this distribution  we set a cut off and filtered out the scars that did not have at least this number of reads. Finally  for each cell type  we determined the distribution of different scars seen per cell and set a maximum number of scars a cell of that type can have. We filtered out cells in which we observed more than this maximum number as possible doublets. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.,Heart and blood,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult,GSM2830053,GSM2830053: Heart 1 scar; Danio rerio; OTHER,GSM2830053,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830053,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,H5_scar_R1.fastq.gz H5_scar_R2.fastq.gz,fastq fastq,1287546624.0,10218624.0,GSM2830053 r1,0:26 1:100,A:365272675;C:413037677;G:296495693;T:212570153;N:170426,26,100,,,365272675,413037677,296495693,212570153,170426,SRX3320757,SRS2626331,SRA623333,GEO,Max Delbrück Center,2,0.00023,0.00044,0.00022,3e-05,1.0,0.99955,,0.32653,26,100,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Adult,Adult,Multi-tissue,Multi-system
44011,SRR6211481,SRX3320756,SRS2626330,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Brain 1 scar,GSM2830052,,source name:Brain|strain/background:Zebrabow M|tissue:Brain|developmental stage:Adult,Brain 1 scar,Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode  a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors  we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step  we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step  we aimed to remove easily recognizable sequencing errors. To this end  we consecutively considered scar sequences that have the same cellular barcode and UMI  UMIs that have the same cellular barcode and scar sequence  and cellular barcodes that have the same UMI and scar sequence. In each step  we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI  or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus  but information about scar expression levels was not required in our downstream analysis. In the third filtering step  we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. In the fourth filtering step  we determined the distribution of reads for the scars we had kept so far. Based on this distribution  we set a cut off and filtered out the scars that did not have at least this number of reads. Finally  for each cell type  we determined the distribution of different scars seen per cell and set a maximum number of scars a cell of that type can have. We filtered out cells in which we observed more than this maximum number as possible doublets. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.,Brain,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Brain|developmental stage:Adult,GSM2830052,GSM2830052: Brain 1 scar; Danio rerio; OTHER,GSM2830052,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830052,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,B5_scar_R1.fastq.gz B5_scar_R2.fastq.gz,fastq fastq,438883452.0,3483202.0,GSM2830052 r1,0:26 1:100,A:125829044;C:139532010;G:100613706;T:72846911;N:61781,26,100,,,125829044,139532010,100613706,72846911,61781,SRX3320756,SRS2626330,SRA623333,GEO,Max Delbrück Center,2,0.00072,0.0013,0.00069,0.00011,0.99991,0.99878,0.75,0.36879,26,100,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Adult,Adult,Brain,Nervous System
44012,SRR6211480,SRX3320755,SRS2626329,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Pancreas 1 scar,GSM2830051,,source name:Pancreas and liver|strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult,Pancreas 1 scar,Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode  a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors  we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step  we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step  we aimed to remove easily recognizable sequencing errors. To this end  we consecutively considered scar sequences that have the same cellular barcode and UMI  UMIs that have the same cellular barcode and scar sequence  and cellular barcodes that have the same UMI and scar sequence. In each step  we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI  or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus  but information about scar expression levels was not required in our downstream analysis. In the third filtering step  we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. In the fourth filtering step  we determined the distribution of reads for the scars we had kept so far. Based on this distribution  we set a cut off and filtered out the scars that did not have at least this number of reads. Finally  for each cell type  we determined the distribution of different scars seen per cell and set a maximum number of scars a cell of that type can have. We filtered out cells in which we observed more than this maximum number as possible doublets. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.,Pancreas and liver,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult,GSM2830051,GSM2830051: Pancreas 1 scar; Danio rerio; OTHER,GSM2830051,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830051,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,NextSeq 500,,SRP121343,,,P5_scar_R1.fastq.gz P5_scar_R2.fastq.gz,fastq fastq,1192602600.0,9465100.0,GSM2830051 r1,0:26 1:100,A:346841760;C:383266222;G:268916933;T:193424756;N:152929,26,100,,,346841760,383266222,268916933,193424756,152929,SRX3320755,SRS2626329,SRA623333,GEO,Max Delbrück Center,2,0.00021,0.00091,0.00014,2e-05,0.99997,0.99892,0.0,0.23931,26,100,T,T,mates < 9% mapping rate,illumina,nextseq,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Adult,Adult,Multi-tissue,Multi-system
44013,SRR6211477,SRX3320753,SRS2626327,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva 1 scar,GSM2830049,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva 1 scar,Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode  a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors  we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step  we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step  we aimed to remove easily recognizable sequencing errors. To this end  we consecutively considered scar sequences that have the same cellular barcode and UMI  UMIs that have the same cellular barcode and scar sequence  and cellular barcodes that have the same UMI and scar sequence. In each step  we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI  or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus  but information about scar expression levels was not required in our downstream analysis. In the third filtering step  we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. In the fourth filtering step  we determined the distribution of reads for the scars we had kept so far. Based on this distribution  we set a cut off and filtered out the scars that did not have at least this number of reads. Finally  for each cell type  we determined the distribution of different scars seen per cell and set a maximum number of scars a cell of that type can have. We filtered out cells in which we observed more than this maximum number as possible doublets. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM2830049,GSM2830049: Larva 1 scar; Danio rerio; OTHER,GSM2830049,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830049,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,Z2_1_scar_R1.fastq.gz Z2_1_scar_R2.fastq.gz Z2_1_scar_R3.fastq.gz,fastq fastq fastq,1358915680.0,8493223.0,GSM2830049 r1,0:130 1:14 2:16,A:286107087;C:390283378;G:268551180;T:159171790;N:5555,130,14,16,,286107087,390283378,268551180,159171790,5555,SRX3320753,SRS2626327,SRA623333,GEO,Max Delbrück Center,1,0.00515,,8e-05,,0.99959,,0.24561,,130,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Larval,Larval,Trunk,Surface Structure
44014,SRR6211478,SRX3320753,SRS2626327,SRP121343,PRJNA415636,Simultaneous lineage tracing and cell type identification using CRISPR/Cas9 induced genetic scars,GSE106121,Other,A key goal of developmental biology is to understand how a single cell transforms into a full grown organism consisting of many different cell types. Single cell RNA sequencing scRNA seq has become a widely used method due to its ability to identify all cell types in a tissue or organ in a systematic manner. However  a major challenge is to organize the resulting taxonomy of cell types into lineage trees revealing the developmental origin of cells. Here  we present a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes  we reconstruct developmental lineage trees in zebrafish larvae and adult fish. In future analyses  LINNAEUS LINeage tracing by Nuclease Activated Editing of Ubiquitous Sequences can be used as a systematic approach for identifying the lineage origin of novel cell types  or of known cell types under different conditions. Overall design: Combining scRNA seq with computational analysis of lineage barcodes generated by genome editing of transgenic reporter genes.,,pubmed:29644996,,Larva 1 scar,GSM2830049,,source name:Full organism|strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,Larva 1 scar,Library strategy: Targeted amplification Scar reads have the same structure as transcript reads: they consist of a barcode  a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped  had an incorrect barcode  or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences. To correct for sequencing errors  we implemented several rounds of scar filtering Supplementary Fig. 2 in publication. We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step  we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step  we aimed to remove easily recognizable sequencing errors. To this end  we consecutively considered scar sequences that have the same cellular barcode and UMI  UMIs that have the same cellular barcode and scar sequence  and cellular barcodes that have the same UMI and scar sequence. In each step  we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI  or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus  but information about scar expression levels was not required in our downstream analysis. In the third filtering step  we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?  Do both scars occur in cells independently from each other?  Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true  the scars were kept and the sequences were placed on a list of validated scars that  if they occurred in the same cell in another library  did not have to be tested anymore. If one or zero criteria were true  the scar that had only one transcript  or the scar that did not occur independently  were filtered out. In the fourth filtering step  we determined the distribution of reads for the scars we had kept so far. Based on this distribution  we set a cut off and filtered out the scars that did not have at least this number of reads. Finally  for each cell type  we determined the distribution of different scars seen per cell and set a maximum number of scars a cell of that type can have. We filtered out cells in which we observed more than this maximum number as possible doublets. Genome build: N/A Supplementary files format and content: List of scar transcripts with cell barcode  scar name  cell type  scar probability and number of organisms that have this cell.,Full organism,,Single cell dissociation. 10X Genomics Chromium,,strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva,GSM2830049,GSM2830049: Larva 1 scar; Danio rerio; OTHER,GSM2830049,,1,Single cell dissociation. 10X Genomics Chromium,GEO Accession:GSM2830049,OTHER,TRANSCRIPTOMIC,other,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP121343,,,Z2_2_scar_R1.fastq.gz Z2_2_scar_R2.fastq.gz Z2_2_scar_R3.fastq.gz,fastq fastq fastq,1103410080.0,6896313.0,GSM2830049 r2,0:130 1:14 2:16,A:232542409;C:315925727;G:218437491;T:129610895;N:4168,130,14,16,,232542409,315925727,218437491,129610895,4168,SRX3320753,SRS2626327,SRA623333,GEO,Max Delbrück Center,1,0.00786,,0.0,,0.99922,,0.31764,,130,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,other,unknown,sc,single_cell_droplet,10x,,Germany,2017-10-24,Larval,Larval,Trunk,Surface Structure
45059,SRR6497183,SRX3586252,SRS2608612,SRP131047,PRJNA429936,10X genomics analysis of adult and larval habenula from the gng8 GFP transgenic line,GSE109158,Transcriptome Analysis,The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: For larval dataset  multiple gng8 GFP labeled zebrafish brains were dissociated and habenular cells FAC sorted into PBS+1%BSA and immediately loaded into 10X chromium for cell capture. For adult dataset  5 6 habenulae were cleanly dissected out  dissociated  filtered in PBS+BSA and immediately captured in droplets with 10x platform. Both libraries were then constructed using standard instrutions of the 10x plaform.,parent bioproject:PRJNA414719,pubmed:29576475,,HabenulaR2,GSM2818523,,source name:adult habenula|developmental stage:Adult|tissue:Brain|tissue subtype:adult habenula,HabenulaR2,"Raw requencing data was converted to matrizes of expression conts using cell ranger software provided by 10x genomics. Briefly raw BCL files from Illumina nExtseq were demultiplexed into compressed Fastqs for each channel using ""cellranger mkfastq"" FASTQ files were then provided as input to “cellranger count” which partitioned the reads into their cell of origin based on the 14bp cell barcode on the left read  aligned reads to a zebrafish reference transcriptome  and quantified transcript counts for each annotated gene within every cell. Here  the 10bp unique molecular identifier UMI on the left read was used to collapse PCR duplicates  and accurately quantify the number of transcript molecules captured for each gene in every cell. Supplementary files format and content: text file with tab delimiters",adult habenula,,polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform. Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform https://www.10xgenomics.com/single cell/,,developmental stage:Adult|tissue:Brain|tissue subtype:adult habenula,GSM2818523,GSM2818523: HabenulaR2; Danio rerio; RNA Seq,GSM2818523 2,,1,polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform. Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform https://www.10xgenomics.com/single cell/,GEO Accession:GSM2818523,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP131047,,dangling references:treat as unmapped,AdultR2_possorted_genome_bam.bam,10X Genomics bam file,47424636672.0,483924864.0,GSM2818523 r11,0:98,A:13883773158;C:9254138795;G:10071286557;T:14206806013;N:8632149,98,,,,13883773158,9254138795,10071286557,14206806013,8632149,SRX3586252,SRS2608612,SRA650466,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.89145,,0.21966,,0.80417,,0.4925,,98,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2017-10-18,Adult,Adult,Brain,Nervous System
45060,SRR6497182,SRX3586251,SRS2608614,SRP131047,PRJNA429936,10X genomics analysis of adult and larval habenula from the gng8 GFP transgenic line,GSE109158,Transcriptome Analysis,The identification of cell types and marker genes is critical for dissecting neural development and function  but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula  a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly  despite brain growth and functional maturation  cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: For larval dataset  multiple gng8 GFP labeled zebrafish brains were dissociated and habenular cells FAC sorted into PBS+1%BSA and immediately loaded into 10X chromium for cell capture. For adult dataset  5 6 habenulae were cleanly dissected out  dissociated  filtered in PBS+BSA and immediately captured in droplets with 10x platform. Both libraries were then constructed using standard instrutions of the 10x plaform.,parent bioproject:PRJNA414719,pubmed:29576475,,HabenulaR1,GSM2818522,,source name:adult habenula|developmental stage:Adult|tissue:Brain|tissue subtype:adult habenula,HabenulaR1,"Raw requencing data was converted to matrizes of expression conts using cell ranger software provided by 10x genomics. Briefly raw BCL files from Illumina nExtseq were demultiplexed into compressed Fastqs for each channel using ""cellranger mkfastq"" FASTQ files were then provided as input to “cellranger count” which partitioned the reads into their cell of origin based on the 14bp cell barcode on the left read  aligned reads to a zebrafish reference transcriptome  and quantified transcript counts for each annotated gene within every cell. Here  the 10bp unique molecular identifier UMI on the left read was used to collapse PCR duplicates  and accurately quantify the number of transcript molecules captured for each gene in every cell. Supplementary files format and content: text file with tab delimiters",adult habenula,,polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform. Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform https://www.10xgenomics.com/single cell/,,developmental stage:Adult|tissue:Brain|tissue subtype:adult habenula,GSM2818522,GSM2818522: HabenulaR1; Danio rerio; RNA Seq,GSM2818522 2,,1,polyA selection based RNA capture as per the manufacturer's instructions provided by 10X genomics platform. Libraries were prepared as per manufacturer's insturctions provided by 10X genomics platform https://www.10xgenomics.com/single cell/,GEO Accession:GSM2818522,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP131047,,,AdultR1_possorted_genome_bam.bam dr82_jeffspike.fasta,10X Genomics bam file fasta,34221168849.0,580019811.0,GSM2818522 r11,0:59,A:10793327710;C:6125333298;G:6353453321;T:10947283926;N:1770594,59,,,,10793327710,6125333298,6353453321,10947283926,1770594,SRX3586251,SRS2608614,SRA650466,GEO,"Schier Lab, Molecular and Cellular Biology, Harvard University",1,0.84773,,0.23824,,0.816,,0.51567,,59,,B,,usable mapping rate,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2017-10-18,Adult,Adult,Brain,Nervous System