{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"cDNA\", experiment.library_source = \"TRANSCRIPTOMIC\" and technology = \"10x\"", "rows": [[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", null, "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 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m 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 \uf06dl 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/\u03bcl. 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\u2122 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\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min 85\u00b0C for 5 min held at 4\u00b0C. 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\u00b0C for 3 min 12 cycles of 90\u00b0C for 15 s 67\u00b0C for 20 s and 72\u00b0C for 1 min 72\u00b0C for 1 min held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 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\u00b0C for 5 min 65\u00b0C for 30 min held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m 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 \uf06dl 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/\u03bcl. 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\u2122 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\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min 85\u00b0C for 5 min held at 4\u00b0C. 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\u00b0C for 3 min 12 cycles of 90\u00b0C for 15 s 67\u00b0C for 20 s and 72\u00b0C for 1 min 72\u00b0C for 1 min held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 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\u00b0C for 5 min 65\u00b0C for 30 min held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20\u00b0C 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", "8660FApplication ReadForward11RApplication ReadReverse434", "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, null, null, null, 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 \u00e2\u20ac\u201c 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 \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.87568, null, 0.2122, null, 0.82582, null, 0.5259, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "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 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m 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 \uf06dl 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/\u03bcl. 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\u2122 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\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min 85\u00b0C for 5 min held at 4\u00b0C. 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\u00b0C for 3 min 12 cycles of 90\u00b0C for 15 s 67\u00b0C for 20 s and 72\u00b0C for 1 min 72\u00b0C for 1 min held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 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\u00b0C for 5 min 65\u00b0C for 30 min held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m 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 \uf06dl 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/\u03bcl. 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\u2122 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\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min 85\u00b0C for 5 min held at 4\u00b0C. 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\u00b0C for 3 min 12 cycles of 90\u00b0C for 15 s 67\u00b0C for 20 s and 72\u00b0C for 1 min 72\u00b0C for 1 min held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 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\u00b0C for 5 min 65\u00b0C for 30 min held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20\u00b0C 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", "8660FApplication ReadForward11RApplication ReadReverse434", "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, null, null, null, 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 \u00e2\u20ac\u201c 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 \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.86206, null, 0.18065, null, 0.83514, null, 0.53609, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "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 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m 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 \uf06dl 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/\u03bcl. 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\u2122 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\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min 85\u00b0C for 5 min held at 4\u00b0C. 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\u00b0C for 3 min 12 cycles of 90\u00b0C for 15 s 67\u00b0C for 20 s and 72\u00b0C for 1 min 72\u00b0C for 1 min held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 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\u00b0C for 5 min 65\u00b0C for 30 min held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m 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 \uf06dl 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/\u03bcl. 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\u2122 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\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min 85\u00b0C for 5 min held at 4\u00b0C. 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\u00b0C for 3 min 12 cycles of 90\u00b0C for 15 s 67\u00b0C for 20 s and 72\u00b0C for 1 min 72\u00b0C for 1 min held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 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\u00b0C for 5 min 65\u00b0C for 30 min held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20\u00b0C 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", "8660FApplication ReadForward11RApplication ReadReverse434", "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, null, null, null, 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 \u00e2\u20ac\u201c 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 \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.88751, null, 0.21835, null, 0.83771, null, 0.53927, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "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 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m 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 \uf06dl 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/\u03bcl. 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\u2122 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\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min 85\u00b0C for 5 min held at 4\u00b0C. 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\u00b0C for 3 min 12 cycles of 90\u00b0C for 15 s 67\u00b0C for 20 s and 72\u00b0C for 1 min 72\u00b0C for 1 min held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 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\u00b0C for 5 min 65\u00b0C for 30 min held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20\u00b0C 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", null, null, null, null, null, null, null, null, "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 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m 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 \uf06dl 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/\u03bcl. 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\u2122 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\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min 85\u00b0C for 5 min held at 4\u00b0C. 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\u00b0C for 3 min 12 cycles of 90\u00b0C for 15 s 67\u00b0C for 20 s and 72\u00b0C for 1 min 72\u00b0C for 1 min held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 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\u00b0C for 5 min 65\u00b0C for 30 min held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20\u00b0C 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", "8660FApplication ReadForward11RApplication ReadReverse434", "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, null, null, null, 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 \u00e2\u20ac\u201c 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 \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.88916, null, 0.21537, null, 0.83802, null, 0.5336, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2018-09-11", "Adult", "Adult", "Gut", "Digestive 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.", null, "pubmed:39101673", null, "Zebrafish EC 24hpf Aktmutant", "GSM8004755", null, "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\u2019 Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3\u2019 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP482328", null, "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, null, 4703583066, 3702175361, 3998796644, 4271932211, 5512871, "SRX23122487", "SRS20076037", "SRA1780571", "Nicoli lab, School of Medicine, Yale University", "Nicoli lab, School of Medicine, Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:39101673", null, "Zebrafish EC 24hpf Aktmutant", "GSM8004755", null, "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\u2019 Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3\u2019 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP482328", null, "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, null, 4231955850, 3363548064, 3603913589, 3849411287, 5091364, "SRX23122487", "SRS20076037", "SRA1780571", "Nicoli lab, School of Medicine, Yale University", "Nicoli lab, School of Medicine, Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:39101673", null, "Zebrafish EC 24hpf WT", "GSM8004754", null, "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\u2019 Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3\u2019 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP482328", null, "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, null, 4475749188, 3578353646, 3836029871, 4055646794, 5211557, "SRX23122486", "SRS20076036", "SRA1780571", "Nicoli lab, School of Medicine, Yale University", "Nicoli lab, School of Medicine, Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:39101673", null, "Zebrafish EC 24hpf WT", "GSM8004754", null, "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\u2019 Library Construction Kit V3.1 CG000204 was used to generate libraires according to manufacturer intructions 10X Genomics Chromium Next GEM Single Cell 3\u2019 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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP482328", null, "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, null, 4028678970, 3250176957, 3455600305, 3651884457, 4840115, "SRX23122486", "SRS20076036", "SRA1780571", "Nicoli lab, School of Medicine, Yale University", "Nicoli lab, School of Medicine, Yale University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, "10x Genomics multiplexing CMO", "scRNA seq wild type and hamp / 36 hpf CMO", "Zebrafish embryo scRNA seq wild type and hamp / 36 hpf CMO", null, "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", null, null, null, null, null, null, null, null, "scRNA seq wild type and hamp / 36 hpf CMO", "C 3", "C 3", "10x Genomics multiplexing CMO", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "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, null, null, 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, null, null, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, "10x Genomics multiplexing CMO", "scRNA seq wild type and hamp / 24 hpf CMO", "Zebrafish embryo scRNA seq wild type and hamp / 24 hpf CMO", null, "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", null, null, null, null, null, null, null, null, "scRNA seq wild type and hamp / 24 hpf CMO", "C 2", "C 2", "10x Genomics multiplexing CMO", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "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, null, null, 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, null, null, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, "10x Genomics multiplexing CMO", "scRNA seq wild type and hamp / 12 hpf CMO", "Zebrafish embryo scRNA seq wild type and hamp / 12 hpf CMO", null, "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", null, null, null, null, null, null, null, null, "scRNA seq wild type and hamp / 12 hpf CMO", "C 1", "C 1", "10x Genomics multiplexing CMO", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "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, null, null, 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, null, null, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, "10x Genomics multiplexing GEX", "scRNA seq wild type and hamp / 36 hpf GEX", "Zebrafish embryo scRNA seq wild type and hamp / 36 hpf GEX", null, "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", null, null, null, null, null, null, null, null, "scRNA seq wild type and hamp / 36 hpf GEX", "G 3", "G 3", "10x Genomics multiplexing GEX", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "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, null, null, 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", null, "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.", null, null, "10x Genomics multiplexing GEX", "scRNA seq wild type and hamp / 24 hpf GEX", "Zebrafish embryo scRNA seq wild type and hamp / 24 hpf GEX", null, "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", null, null, null, null, null, null, null, null, "scRNA seq wild type and hamp / 24 hpf GEX", "G 2", "G 2", "10x Genomics multiplexing GEX", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "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, null, null, 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", null, "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.", null, null, "10x Genomics multiplexing GEX", "scRNA seq wild type and hamp / 12 hpf GEX", "Zebrafish embryo scRNA seq wild type and hamp / 12 hpf GEX", null, "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", null, null, null, null, null, null, null, null, "scRNA seq wild type and hamp / 12 hpf GEX", "G 1", "G 1", "10x Genomics multiplexing GEX", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP485064", null, null, "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, null, null, 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", null, "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.", null, "pubmed:39846194", null, "Zebra PS", "GSM8334032", null, "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", null, "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\u2122 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\u2019s guidelines. Following the guidelines of the 10x Chromium Single Cell 5\u2019 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\u2019 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\u2032 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\u2019 Gene Expression Library the amplified cDNA underwent a series of steps including enzymatic fragmentation end repair A tailing adapter ligation and index PCR.", null, "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\u2122 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\u2032 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP514388", null, null, "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, null, null, 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", null, "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.", null, "pubmed:39846194", null, "Zebra Control", "GSM8334031", null, "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", null, "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\u2122 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\u2019s guidelines. Following the guidelines of the 10x Chromium Single Cell 5\u2019 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\u2019 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\u2032 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\u2019 Gene Expression Library the amplified cDNA underwent a series of steps including enzymatic fragmentation end repair A tailing adapter ligation and index PCR.", null, "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\u2122 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\u2032 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP514388", null, null, "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, null, null, 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", null, "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.", null, null, null, "adult zebrafish retinal ganglion cells day 7 uninjured fish set #3", "GSM8691398", null, "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 K\u00f6lsch 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\u2019s 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\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "adult zebrafish retinal ganglion cells day 7 uninjured fish set #2", "GSM8691397", null, "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 K\u00f6lsch 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\u2019s 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\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "adult zebrafish retinal ganglion cells day 7 uninjured fish set #1", "GSM8691396", null, "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 K\u00f6lsch 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\u2019s 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\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "adult zebrafish retinal ganglion cells 7 xxx post injury fish set #3", "GSM8691395", null, "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 K\u00f6lsch 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\u2019s 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\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "adult zebrafish retinal ganglion cells 7 xxx post injury fish set #2", "GSM8691394", null, "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 K\u00f6lsch 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\u2019s 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\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "adult zebrafish retinal ganglion cells 7 xxx post injury fish set #1", "GSM8691393", null, "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 K\u00f6lsch 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\u2019s 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\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "adult zebrafish retinal ganglion cells day 1 uninjured fish set #3", "GSM8691392", null, "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 K\u00f6lsch 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\u2019s 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\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "adult zebrafish retinal ganglion cells day 1 uninjured fish set #2", "GSM8691391", null, "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 K\u00f6lsch 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\u2019s 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\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "adult zebrafish retinal ganglion cells day 1 uninjured fish set #1", "GSM8691390", null, "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 K\u00f6lsch 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\u2019s 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\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "adult zebrafish retinal ganglion cells 1 xxx post injury fish set #4", "GSM8691389", null, "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 K\u00f6lsch 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\u2019s 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\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "adult zebrafish retinal ganglion cells 1 xxx post injury fish set #3", "GSM8691388", null, "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 K\u00f6lsch 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\u2019s 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\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "adult zebrafish retinal ganglion cells 1 xxx post injury fish set #2", "GSM8691387", null, "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 K\u00f6lsch 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\u2019s 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\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, null, null, "adult zebrafish retinal ganglion cells 1 xxx post injury fish set #1", "GSM8691386", null, "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 K\u00f6lsch 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\u2019s 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\u2019 v2 kit 10X genomics Single cell libraries were prepared using the single cell gene expression 3\u2019 v2 kit on the Chromium platform 10X Genomics Pleasanton CA following the manufacturer\u2019s 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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP552478", null, null, "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, null, null, 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", null, null, null, null, null, null, null, null, null, null, null, "T", "B", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-12-18", "Adult", "Adult", "Eye", "Sensory System"], [34508, "SRR32041235", "SRX27390499", "SRS23823272", "SRP558202", "PRJNA1212333", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212333", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr[VI]+VC 3 group", "Cr+VC 3", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 14|health state:health|sample type:tissue|lep:Cr+VC 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "EHK0300476", "EHK0300476", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558202", null, null, "Cr+VC-3.R1.raw.fastq.gz Cr+VC-3.R2.raw.fastq.gz", "fastq fastq", 6579236402.0, 21785551.0, "Cr+VC 3.R1.raw.fastq.gz", "0:151 1:151", "A:1950296368;C:1342383640;G:1373591474;T:1912893257;N:71663", 151, 151, null, null, 1950296368, 1342383640, 1373591474, 1912893257, 71663, "SRX27390499", "SRS23823272", "SRA2054545", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-18", "Adult", "Adult", "Brain", "Nervous System"], [34509, "SRR32041236", "SRX27390498", "SRS23823271", "SRP558202", "PRJNA1212333", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212333", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr[VI]+VC 2 group", "Cr+VC 2", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 14|health state:health|sample type:tissue|lep:Cr+VC 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "EHK0300475", "EHK0300475", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558202", null, null, "Cr+VC-2.R1.raw.fastq.gz Cr+VC-2.R2.raw.fastq.gz", "fastq fastq", 7431192898.0, 24606599.0, "Cr+VC 2.R1.raw.fastq.gz", "0:151 1:151", "A:2185434880;C:1533450452;G:1567401090;T:2144825061;N:81415", 151, 151, null, null, 2185434880, 1533450452, 1567401090, 2144825061, 81415, "SRX27390498", "SRS23823271", "SRA2054545", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-18", "Adult", "Adult", "Brain", "Nervous System"], [34510, "SRR32041237", "SRX27390497", "SRS23823270", "SRP558202", "PRJNA1212333", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212333", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr[VI]+VC 1 group", "Cr+VC 1", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 14|health state:health|sample type:tissue|lep:Cr+VC 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "EHK0300474", "EHK0300474", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558202", null, null, "Cr+VC-1.R1.raw.fastq.gz Cr+VC-1.R2.raw.fastq.gz", "fastq fastq", 6385666180.0, 21144590.0, "Cr+VC 1.R1.raw.fastq.gz", "0:151 1:151", "A:1864936934;C:1329491594;G:1363211111;T:1827956599;N:69942", 151, 151, null, null, 1864936934, 1329491594, 1363211111, 1827956599, 69942, "SRX27390497", "SRS23823270", "SRA2054545", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-18", "Adult", "Adult", "Brain", "Nervous System"], [34511, "SRR32041238", "SRX27390496", "SRS23823269", "SRP558202", "PRJNA1212333", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212333", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr[VI] 3 group", "Cr 3", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 13|health state:health|sample type:tissue|lep:Cr 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "EHK0300473", "EHK0300473", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558202", null, null, "Cr-3.R1.raw.fastq.gz Cr-3.R2.raw.fastq.gz", "fastq fastq", 6339933716.0, 20993158.0, "Cr 3.R1.raw.fastq.gz", "0:151 1:151", "A:1873178321;C:1296125569;G:1333622723;T:1836939106;N:67997", 151, 151, null, null, 1873178321, 1296125569, 1333622723, 1836939106, 67997, "SRX27390496", "SRS23823269", "SRA2054545", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-18", "Adult", "Adult", "Brain", "Nervous System"], [34512, "SRR32041239", "SRX27390495", "SRS23823268", "SRP558202", "PRJNA1212333", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212333", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr[VI] 2 group", "Cr 2", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 13|health state:health|sample type:tissue|lep:Cr 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "EHK0300472", "EHK0300472", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558202", null, null, "Cr-2.R1.raw.fastq.gz Cr-2.R2.raw.fastq.gz", "fastq fastq", 6461518010.0, 21395755.0, "Cr 2.R1.raw.fastq.gz", "0:151 1:151", "A:1878799067;C:1352321588;G:1386809443;T:1843520259;N:67653", 151, 151, null, null, 1878799067, 1352321588, 1386809443, 1843520259, 67653, "SRX27390495", "SRS23823268", "SRA2054545", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-18", "Adult", "Adult", "Brain", "Nervous System"], [34513, "SRR32041240", "SRX27390494", "SRS23823267", "SRP558202", "PRJNA1212333", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212333", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr[VI] 1 group", "Cr 1", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 13|health state:health|sample type:tissue|lep:Cr 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "EHK0300471", "EHK0300471", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558202", null, null, "Cr-1.R1.raw.fastq.gz Cr-1.R2.raw.fastq.gz", "fastq fastq", 7143701582.0, 23654641.0, "Cr 1.R1.raw.fastq.gz", "0:151 1:151", "A:1955056767;C:1615392059;G:1650478323;T:1922695182;N:79251", 151, 151, null, null, 1955056767, 1615392059, 1650478323, 1922695182, 79251, "SRX27390494", "SRS23823267", "SRA2054545", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-18", "Adult", "Adult", "Brain", "Nervous System"], [34514, "SRR32041241", "SRX27390493", "SRS23823266", "SRP558202", "PRJNA1212333", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212333", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "control 3 group", "Con 3", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 12|health state:health|sample type:tissue|lep:Con 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "EHK0300470", "EHK0300470", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558202", null, null, "Con-3.R1.raw.fastq.gz Con-3.R2.raw.fastq.gz", "fastq fastq", 6474159730.0, 21437615.0, "Con 3.R1.raw.fastq.gz", "0:151 1:151", "A:1937289968;C:1298659806;G:1337603954;T:1900535989;N:70013", 151, 151, null, null, 1937289968, 1298659806, 1337603954, 1900535989, 70013, "SRX27390493", "SRS23823266", "SRA2054545", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-18", "Adult", "Adult", "Brain", "Nervous System"], [34515, "SRR32041242", "SRX27390492", "SRS23823265", "SRP558202", "PRJNA1212333", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212333", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "control 2 group", "Con 2", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 12|health state:health|sample type:tissue|lep:Con 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "EHK0300469", "EHK0300469", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558202", null, null, "Con-2.R1.raw.fastq.gz Con-2.R2.raw.fastq.gz", "fastq fastq", 8372440828.0, 27723314.0, "Con 2.R1.raw.fastq.gz", "0:151 1:151", "A:2235968446;C:1933538809;G:1977416201;T:2225425413;N:91959", 151, 151, null, null, 2235968446, 1933538809, 1977416201, 2225425413, 91959, "SRX27390492", "SRS23823265", "SRA2054545", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-18", "Adult", "Adult", "Brain", "Nervous System"], [34516, "SRR32041243", "SRX27390491", "SRS23823264", "SRP558202", "PRJNA1212333", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212333", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating brain hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "control 1 group", "Con 1", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:brain|death date:2023 8 12|health state:health|sample type:tissue|lep:Con 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "EHK0300468", "EHK0300468", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558202", null, null, "Con-1.R1.raw.fastq.gz Con-1.R2.raw.fastq.gz", "fastq fastq", 6527063486.0, 21612793.0, "Con 1.R1.raw.fastq.gz", "0:151 1:151", "A:1939230604;C:1326702799;G:1357063348;T:1903995450;N:71285", 151, 151, null, null, 1939230604, 1326702799, 1357063348, 1903995450, 71285, "SRX27390491", "SRS23823264", "SRA2054545", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-18", "Adult", "Adult", "Brain", "Nervous System"], [34517, "SRR32044795", "SRX27393953", "SRS23824014", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr+VC 3", "I", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Cr+VC 3", "Cr+VC 3", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, null, "Cr+VC-3.R1.raw.fastq.gz Cr+VC-3.R2.raw.fastq.gz", "fastq fastq", 6773536558.0, 22428929.0, "Cr+VC 3.R1.raw.fastq.gz", "0:151 1:151", "A:1792253952;C:1581454013;G:1629330621;T:1770470694;N:27278", 151, 151, null, null, 1792253952, 1581454013, 1629330621, 1770470694, 27278, "SRX27393953", "SRS23824014", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive System"], [34518, "SRR32044796", "SRX27393952", "SRS23824013", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr+VC 2", "H", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Cr+VC 2", "Cr+VC 2", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, null, "Cr+VC-2.R1.raw.fastq.gz Cr+VC-2.R2.raw.fastq.gz", "fastq fastq", 7449518862.0, 24667281.0, "Cr+VC 2.R1.raw.fastq.gz", "0:151 1:151", "A:1969693675;C:1748150730;G:1771267240;T:1960378098;N:29119", 151, 151, null, null, 1969693675, 1748150730, 1771267240, 1960378098, 29119, "SRX27393952", "SRS23824013", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive System"], [34519, "SRR32044797", "SRX27393951", "SRS23824012", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr+VC 1", "G", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Cr+VC 1", "Cr+VC 1", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, "loader:fastq load.py|options: doNotUseSharq", "Cr+VC-1.R1.raw.fastq Cr+VC-1.R2.raw.fastq", "fastq fastq", 6865491179.0, 45466829.0, "Cr+VC 1.R1.raw.fastq.gz", "0:151", "A:1830069736;C:1600281531;G:1626303427;T:1808809011;N:27474", 151, null, null, null, 1830069736, 1600281531, 1626303427, 1808809011, 27474, "SRX27393951", "SRS23824012", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive System"], [34520, "SRR32044798", "SRX27393950", "SRS23824011", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr 3", "F", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Cr 3", "Cr 3", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, null, "Cr-3.R1.raw.fastq.gz Cr-3.R2.raw.fastq.gz", "fastq fastq", 6069804078.0, 20098689.0, "Cr 3.R1.raw.fastq.gz", "0:151 1:151", "A:1603886661;C:1431213970;G:1440806224;T:1593873144;N:24079", 151, 151, null, null, 1603886661, 1431213970, 1440806224, 1593873144, 24079, "SRX27393950", "SRS23824011", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive System"], [34521, "SRR32044799", "SRX27393949", "SRS23824010", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr 2", "E", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Cr 2", "Cr 2", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, "loader:fastq load.py|options: doNotUseSharq", "Cr-2.R1.raw.fastq Cr-2.R2.raw.fastq", "fastq fastq", 8327156985.0, 55146735.0, "Cr 2.R1.raw.fastq.gz", "0:151", "A:2181317777;C:1974793526;G:2003240106;T:2167771431;N:34145", 151, null, null, null, 2181317777, 1974793526, 2003240106, 2167771431, 34145, "SRX27393949", "SRS23824010", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive System"], [34522, "SRR32044800", "SRX27393948", "SRS23824009", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr 1", "D", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Cr 1", "Cr 1", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, null, "Cr-1.R1.raw.fastq.gz Cr-1.R2.raw.fastq.gz", "fastq fastq", 7322067614.0, 24245257.0, "Cr 1.R1.raw.fastq.gz", "0:151 1:151", "A:1927213281;C:1727973559;G:1748866497;T:1917985720;N:28557", 151, 151, null, null, 1927213281, 1727973559, 1748866497, 1917985720, 28557, "SRX27393948", "SRS23824009", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive System"], [34523, "SRR32044801", "SRX27393947", "SRS23824008", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Con 3", "C", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Con 3", "Con 3", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, null, "Con-3.R1.raw.fastq.gz Con-3.R2.raw.fastq.gz", "fastq fastq", 10329187314.0, 34202607.0, "Con 3.R1.raw.fastq.gz", "0:151 1:151", "A:2805764955;C:2343400161;G:2421657823;T:2758323021;N:41354", 151, 151, null, null, 2805764955, 2343400161, 2421657823, 2758323021, 41354, "SRX27393947", "SRS23824008", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive System"], [34524, "SRR32044802", "SRX27393946", "SRS23824007", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Con 2", "B", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Con 2", "Con 2", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, null, "Con-2.R1.raw.fastq.gz Con-2.R2.raw.fastq.gz", "fastq fastq", 10789961398.0, 35728349.0, "Con 2.R1.raw.fastq.gz", "0:151 1:151", "A:2983305704;C:2396592872;G:2488165589;T:2921853880;N:43353", 151, 151, null, null, 2983305704, 2396592872, 2488165589, 2921853880, 43353, "SRX27393946", "SRS23824007", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive System"], [34525, "SRR32044803", "SRX27393945", "SRS23824006", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Con 1", "A", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Con 1", "Con 1", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, null, "Con-1.R1.raw.fastq.gz Con-1.R2.raw.fastq.gz", "fastq fastq", 7118179260.0, 23570130.0, "Con 1.R1.raw.fastq.gz", "0:151 1:151", "A:1874284939;C:1673861890;G:1718740497;T:1851263659;N:28275", 151, 151, null, null, 1874284939, 1673861890, 1718740497, 1851263659, 28275, "SRX27393945", "SRS23824006", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive 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", null, null, null, "Zebrafish Adult Pachymeninges scRNA seq", "GSM8902567", null, "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", null, "Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. 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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. 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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. 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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. 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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", null, null, null, "Zebrafish Adult Pachymeninges scRNA seq", "GSM8902567", null, "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", null, "Cell suspension prepared from 20 leptomeningeal linings 10 from females 10 from males removed from zebrafish comprising 10 000 cells. 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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. 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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. 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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. 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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. 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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. 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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. 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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. 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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. 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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. 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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. 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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. 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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. 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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. 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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. 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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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM3032172", "GSM3032172: Larva F1 1 mRNA; Danio rerio; RNA Seq", "GSM3032172", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032172", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, null, 7365353958, 6068313931, 6251004125, 6996410946, 4793112, "SRX3768869", "SRS3023385", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "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.", null, "pubmed:29644996", null, "Pancreas 3 exo mRNA", "GSM3032165", null, "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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Pancreas except primary islet liver|developmental stage:Adult", "GSM3032165", "GSM3032165: Pancreas 3 exo mRNA; Danio rerio; RNA Seq", "GSM3032165", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032165", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "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, null, null, 10751580091, 8744299142, 9264760851, 9795905887, 17480793, "SRX3768862", "SRS3023379", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "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.", null, "pubmed:29644996", null, "Pancreas 3 endo mRNA", "GSM3032164", null, "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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Primary pancreatic islet|developmental stage:Adult", "GSM3032164", "GSM3032164: Pancreas 3 endo mRNA; Danio rerio; RNA Seq", "GSM3032164", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032164", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "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, null, null, 11833690021, 9547054378, 9724089290, 10470148302, 18799909, "SRX3768861", "SRS3023378", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "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.", null, "pubmed:29644996", null, "Heart 3 mRNA", "GSM3032163", null, "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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult", "GSM3032163", "GSM3032163: Heart 3 mRNA; Danio rerio; RNA Seq", "GSM3032163", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032163", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "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, null, null, 12856871948, 10721924215, 10335821801, 11891517482, 20761802, "SRX3768860", "SRS3023377", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "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.", null, "pubmed:29644996", null, "Brain 3 mRNA", "GSM3032162", null, "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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Brain|developmental stage:Adult", "GSM3032162", "GSM3032162: Brain 3 mRNA; Danio rerio; RNA Seq", "GSM3032162", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032162", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "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, null, null, 10338159874, 7412176847, 7655217994, 9778922063, 15742486, "SRX3768859", "SRS3023375", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "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.", null, "pubmed:29644996", null, "Larva 5 mRNA", "GSM3032161", null, "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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM3032161", "GSM3032161: Larva 5 mRNA; Danio rerio; RNA Seq", "GSM3032161", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032161", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, null, 7637677199, 6210942203, 6438364980, 7117667800, 4904630, "SRX3768858", "SRS3023376", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "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.", null, "pubmed:29644996", null, "Larva 4 mRNA", "GSM3032160", null, "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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM3032160", "GSM3032160: Larva 4 mRNA; Danio rerio; RNA Seq", "GSM3032160", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032160", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, null, 5483727144, 4548396363, 4737957565, 5002119078, 3511306, "SRX3768857", "SRS3023374", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "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.", null, "pubmed:29644996", null, "Larva 3 mRNA", "GSM3032159", null, "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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM3032159", "GSM3032159: Larva 3 mRNA; Danio rerio; RNA Seq", "GSM3032159", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM3032159", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, 2047850756, 1318672327, 1403772432, 1743394108, 52287, "SRX3768856", "SRS3023373", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 1, 0.87661, null, 0.06466, null, 0.86614, null, 0.53364, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:29644996", null, "Heart 2 mRNA", "GSM2830062", null, "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 Gr\u00fcn 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 \u2013 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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult", "GSM2830062", "GSM2830062: Heart 2 mRNA; Danio rerio; RNA Seq", "GSM2830062", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830062", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "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, null, null, 5788453893, 4266605110, 4479895656, 4930437501, 1281278, "SRX3320767", "SRS2626340", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "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.", null, "pubmed:29644996", null, "Pancreas 2 mRNA", "GSM2830061", null, "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 Gr\u00fcn 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 \u2013 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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult", "GSM2830061", "GSM2830061: Pancreas 2 mRNA; Danio rerio; RNA Seq", "GSM2830061", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830061", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "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, null, null, 5146142876, 3830859355, 4368254000, 4216873712, 1148135, "SRX3320766", "SRS2626339", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "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.", null, "pubmed:29644996", null, "Heart 1 mRNA", "GSM2830060", null, "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 Gr\u00fcn 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 \u2013 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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Heart and blood|developmental stage:Adult", "GSM2830060", "GSM2830060: Heart 1 mRNA; Danio rerio; RNA Seq", "GSM2830060", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830060", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "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, null, null, 3373517159, 2470603501, 2531314673, 2798372007, 1525276, "SRX3320765", "SRS2626338", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "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.", null, "pubmed:29644996", null, "Brain 1 mRNA", "GSM2830059", null, "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 Gr\u00fcn 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 \u2013 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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Brain|developmental stage:Adult", "GSM2830059", "GSM2830059: Brain 1 mRNA; Danio rerio; RNA Seq", "GSM2830059", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830059", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina MiniSeq", null, "SRP121343", null, null, "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, null, null, 1403578459, 926366830, 979609921, 1228675807, 666983, "SRX3320764", "SRS2626337", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "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.", null, "pubmed:29644996", null, "Pancreas 1 mRNA", "GSM2830058", null, "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 Gr\u00fcn 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 \u2013 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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Pancreas and liver|developmental stage:Adult", "GSM2830058", "GSM2830058: Pancreas 1 mRNA; Danio rerio; RNA Seq", "GSM2830058", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830058", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP121343", null, null, "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, null, null, 5348935548, 3950936592, 4404689151, 4409667387, 2497236, "SRX3320763", "SRS2626336", "SRA623333", "GEO", "Max Delbr\u00fcck 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", null, "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.", null, "pubmed:29644996", null, "Larva 2 mRNA", "GSM2830057", null, "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 Gr\u00fcn 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 \u2013 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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM2830057", "GSM2830057: Larva 2 mRNA; Danio rerio; RNA Seq", "GSM2830057", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830057", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, 6582076349, 4985163175, 5131319282, 6085835988, 3297756, "SRX3320762", "SRS2626335", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 1, 0.9378, null, 0.05825, null, 0.79687, null, 0.50342, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:29644996", null, "Larva 1 mRNA", "GSM2830056", null, "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 Gr\u00fcn 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 \u2013 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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM2830056", "GSM2830056: Larva 1 mRNA; Danio rerio; RNA Seq", "GSM2830056", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830056", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, 9121762570, 5889322717, 6251660049, 8039869338, 228116, "SRX3320760", "SRS2626333", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 1, 0.88569, null, 0.08353, null, 0.86016, null, 0.53379, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:29644996", null, "Larva 1 mRNA", "GSM2830056", null, "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 Gr\u00fcn 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 \u2013 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", null, "Single cell dissociation. 10X Genomics Chromium", null, "strain/background:Zebrabow M|tissue:Whole body|developmental stage:Larva", "GSM2830056", "GSM2830056: Larva 1 mRNA; Danio rerio; RNA Seq", "GSM2830056", null, "1", "Single cell dissociation. 10X Genomics Chromium", "GEO Accession:GSM2830056", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP121343", null, null, "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, null, 1890861891, 1307860042, 1403340071, 1654667424, 45902, "SRX3320760", "SRS2626333", "SRA623333", "GEO", "Max Delbr\u00fcck Center", 1, 0.89198, null, 0.07477, null, 0.87288, null, 0.49519, null, 130, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "HabenulaR2", "GSM2818523", null, "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 \u201ccellranger count\u201d 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", null, "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/", null, "developmental stage:Adult|tissue:Brain|tissue subtype:adult habenula", "GSM2818523", "GSM2818523: HabenulaR2; Danio rerio; RNA Seq", "GSM2818523 2", null, "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", null, "SRP131047", null, "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, null, null, null, 13883773158, 9254138795, 10071286557, 14206806013, 8632149, "SRX3586252", "SRS2608612", "SRA650466", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.89145, null, 0.21966, null, 0.80417, null, 0.4925, null, 98, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "HabenulaR1", "GSM2818522", null, "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 \u201ccellranger count\u201d 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", null, "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/", null, "developmental stage:Adult|tissue:Brain|tissue subtype:adult habenula", "GSM2818522", "GSM2818522: HabenulaR1; Danio rerio; RNA Seq", "GSM2818522 2", null, "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", null, "SRP131047", null, null, "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, null, null, null, 10793327710, 6125333298, 6353453321, 10947283926, 1770594, "SRX3586251", "SRS2608614", "SRA650466", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.84773, null, 0.23824, null, 0.816, null, 0.51567, null, 59, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2017-10-18", "Adult", "Adult", "Brain", "Nervous System"], [45061, "SRR6497181", "SRX3586250", "SRS2608613", "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", null, "larvalR2", "GSM2818521", null, "tissue:larval habenula|developmental stage:10 dpf subtype:larval habenula", "larvalR2", "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 \u201ccellranger count\u201d 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", "larval habenula", null, "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/", null, "developmental stage:10 dpf subtype:larval habenula", "GSM2818521", "GSM2818521: larvalR2; Danio rerio; RNA Seq", "GSM2818521 2", null, "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:GSM2818521", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP131047", null, "dangling references:treat as unmapped", "larva_possorted_genome_bam.bam", "10X Genomics bam file", 28345528526.0, 289240087.0, "GSM2818521 r11", "0:98", "A:8402517943;C:5487086955;G:5983229058;T:8461684002;N:11010568", 98, null, null, null, 8402517943, 5487086955, 5983229058, 8461684002, 11010568, "SRX3586250", "SRS2608613", "SRA650466", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.89549, null, 0.27435, null, 0.78127, null, 0.49496, null, 98, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2017-10-18", "Larval", "Larval", "Undetermined", "Undetermined"], [48048, "SRR6956074", "SRX3899097", "SRS3136394", "SRP137889", "PRJNA449093", "10x analysis of wild type TLAB and MZoep zebrafish embryos at 6 somite stage", "GSE112824", "Transcriptome Analysis", "Wild type and MZoep zebrafish embryos were mechanically dissociated and profiled using 10x Genomics pipeline. Overall design: 10x scRNA seq was performed on visually staged mechanically dissociated embryos. Samples were combined and sequenced in one batch.", "parent bioproject:PRJNA417291", "pubmed:29700225", null, "MZoep zebrafish embryo 6 somite", "GSM3084403", null, "tissue:Maternal Zygotic oep tz57 Mutant Embryo|genotype/variation:MZoep mutant|developmental stage:6 somite|hpf", "MZoep zebrafish embryo 6 somite", "Data was processed using Cell Ranger 2.0.2 following the pipeline posted on 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. Command \"cellranger mkfastq\" was called to generate demultiplexed FASTQ files from the Illumina BCL output files. Command \"cellranger count\" was used to align the reads to generate the bam files provided as raw data. Single cell gene barcode counts were calculated by \"cellranger count\" and were filtered to eliminate non cellular barcodes filtered gene barcode counts are provided as processed data. Genome build: dr82 Supplementary files format and content: Compressed folder containing filtered gene barcode matrices in Market Exchange Format MEX as outputted by \"cellranger count\".", "Maternal Zygotic oep tz57 Mutant Embryo", null, "Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated and lysed in droplets using the 10X Chromium controller. Libraries were prepared using the 10X Chromium Single Cell three prime Reagent Kit. Libraries for the two genotypes were prepared separately to incorporate different read indices. Libraries were pooled together and sequenced in one batch.", "Wild type Tupful longfin / AB or MZoep tz57 fish were incrossed embryos were collected and grown at 28\u00b0C in chorions until they reached the desired stage confirmed via visual morphological staging.", "genotype/variation:MZoep mutant|developmental stage:6 somite|hpf", "GSM3084403", "GSM3084403: MZoep zebrafish embryo 6 somite; Danio rerio; RNA Seq", "GSM3084403", null, "1", "Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated and lysed in droplets using the 10X Chromium controller. Libraries were prepared using the 10X Chromium Single Cell three prime Reagent Kit. Libraries for the two genotypes were prepared separately to incorporate different read indices. Libraries were pooled together and sequenced in one batch.", "GEO Accession:GSM3084403", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP137889", null, "dangling references:treat as unmapped", "10xMZoep6S_possorted_genome_bam.bam", "10X Genomics bam file", 6798121188.0, 117208986.0, "GSM3084403 r1", "0:58", "A:1967536512;C:1404909465;G:1675749247;T:1735311022;N:14614942", 58, null, null, null, 1967536512, 1404909465, 1675749247, 1735311022, 14614942, "SRX3899097", "SRS3136394", "SRA683448", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.9431, null, 0.07175, null, 0.84439, null, 0.49587, null, 58, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2018-04-06", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [48049, "SRR6956073", "SRX3899096", "SRS3136393", "SRP137889", "PRJNA449093", "10x analysis of wild type TLAB and MZoep zebrafish embryos at 6 somite stage", "GSE112824", "Transcriptome Analysis", "Wild type and MZoep zebrafish embryos were mechanically dissociated and profiled using 10x Genomics pipeline. Overall design: 10x scRNA seq was performed on visually staged mechanically dissociated embryos. Samples were combined and sequenced in one batch.", "parent bioproject:PRJNA417291", "pubmed:29700225", null, "WT zebrafish embryo 6 somite", "GSM3084402", null, "tissue:Wild type TLAB Embryo|genotype/variation:wild type TLAB|developmental stage:6 somite|hpf", "WT zebrafish embryo 6 somite", "Data was processed using Cell Ranger 2.0.2 following the pipeline posted on 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. Command \"cellranger mkfastq\" was called to generate demultiplexed FASTQ files from the Illumina BCL output files. Command \"cellranger count\" was used to align the reads to generate the bam files provided as raw data. Single cell gene barcode counts were calculated by \"cellranger count\" and were filtered to eliminate non cellular barcodes filtered gene barcode counts are provided as processed data. Genome build: dr82 Supplementary files format and content: Compressed folder containing filtered gene barcode matrices in Market Exchange Format MEX as outputted by \"cellranger count\".", "Wild type TLAB Embryo", null, "Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated and lysed in droplets using the 10X Chromium controller. Libraries were prepared using the 10X Chromium Single Cell three prime Reagent Kit. Libraries for the two genotypes were prepared separately to incorporate different read indices. Libraries were pooled together and sequenced in one batch.", "Wild type Tupful longfin / AB or MZoep tz57 fish were incrossed embryos were collected and grown at 28\u00b0C in chorions until they reached the desired stage confirmed via visual morphological staging.", "genotype/variation:wild type TLAB|developmental stage:6 somite|hpf", "GSM3084402", "GSM3084402: WT zebrafish embryo 6 somite; Danio rerio; RNA Seq", "GSM3084402", null, "1", "Embryos were dechorionated and deyolked manually mechanically dissociated washed and resuspended in PBS + 0.1% BSA + 20% Optiprep filtered through a cell sieve and encapsulated and lysed in droplets using the 10X Chromium controller. Libraries were prepared using the 10X Chromium Single Cell three prime Reagent Kit. Libraries for the two genotypes were prepared separately to incorporate different read indices. Libraries were pooled together and sequenced in one batch.", "GEO Accession:GSM3084402", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP137889", null, "dangling references:treat as unmapped", "10xWT6S_possorted_genome_bam.bam", "10X Genomics bam file", 9353929816.0, 161274652.0, "GSM3084402 r1", "0:58", "A:2687281275;C:1909606804;G:2337322093;T:2396497626;N:23222018", 58, null, null, null, 2687281275, 1909606804, 2337322093, 2396497626, 23222018, "SRX3899096", "SRS3136393", "SRA683448", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.94618, null, 0.07281, null, 0.8435, null, 0.501, null, 58, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2018-04-06", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [48774, "SRR7297839", "SRX4200373", "SRS3410607", "SRP150365", "PRJNA475784", "Phenotypic landscape of schizophrenia associated genes defines candidates and their shared functions", "GSE115427", "Transcriptome Analysis", "Znf536 mutant and wild types were profiled to discover cell type landscape modulated by the transcription factor. Overall design: 10x libraries of single cell transcriptomes", null, "pubmed:30929901", null, "znf mut 10x", "GSM3187949", null, "source name:zebrafish brain|tissue:Forebrain|developmental stage:6dpf|genotype/variation:znf mutant", "znf mut 10x", "Raw sequencing data was converted to matrices of expression using the cell ranger software provide by 10x genomics. Raw BCL files from Illumina nextseq were demultiplexed into paired end gzip compressed FASTQ files using cellranger mkgastq. Both FASTQs were then provided as input to cell ranger count which partitioned reads into cell of origin based on a 16 bp barcode on the left read. Reads were aligned to a zebrafish reference transcriptomeENSEMBL Zv10 release 82 reference transcriptome and transcript counts quantified for each annotated gene. 10bp UMI on th eleft read was used to collapse PCR duplicates. Genome build: GRCz10 Supplementary files format and content: CSV files for transcriptome data were generated using the cellranger pipeline. Each column in the CSV files contains a cell identifier and each row contains expression values for gene.", "zebrafish brain", null, "Single cell suspensions were processsed according to manufacturer's instructions by 10X chromium 10x chromium", null, "tissue:Forebrain|developmental stage:6dpf|genotype/variation:znf mutant", "GSM3187949", "GSM3187949: znf mut 10x; Danio rerio; RNA Seq", "GSM3187949", null, "1", "Single cell suspensions were processsed according to manufacturer's instructions by 10X chromium 10x chromium", "GEO Accession:GSM3187949", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP150365", null, null, "mut_possorted_genome_bam.bam", "10X Genomics bam file", 16531944740.0, 285033530.0, "GSM3187949 r1", "0:58", "A:5037043538;C:3032099047;G:3558921957;T:4900111360;N:3768838", 58, null, null, null, 5037043538, 3032099047, 3558921957, 4900111360, 3768838, "SRX4200373", "SRS3410607", "SRA720602", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.88667, null, 0.33708, null, 0.83102, null, 0.50699, null, 58, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2018-06-12", "Larval", "Larval", "Brain", "Nervous System"], [48775, "SRR7297838", "SRX4200372", "SRS3410606", "SRP150365", "PRJNA475784", "Phenotypic landscape of schizophrenia associated genes defines candidates and their shared functions", "GSE115427", "Transcriptome Analysis", "Znf536 mutant and wild types were profiled to discover cell type landscape modulated by the transcription factor. Overall design: 10x libraries of single cell transcriptomes", null, "pubmed:30929901", null, "znf wt 10x", "GSM3187948", null, "source name:zebrafish brain|tissue:Forebrain|developmental stage:6dpf|genotype/variation:znf wild type", "znf wt 10x", "Raw sequencing data was converted to matrices of expression using the cell ranger software provide by 10x genomics. Raw BCL files from Illumina nextseq were demultiplexed into paired end gzip compressed FASTQ files using cellranger mkgastq. Both FASTQs were then provided as input to cell ranger count which partitioned reads into cell of origin based on a 16 bp barcode on the left read. Reads were aligned to a zebrafish reference transcriptomeENSEMBL Zv10 release 82 reference transcriptome and transcript counts quantified for each annotated gene. 10bp UMI on th eleft read was used to collapse PCR duplicates. Genome build: GRCz10 Supplementary files format and content: CSV files for transcriptome data were generated using the cellranger pipeline. Each column in the CSV files contains a cell identifier and each row contains expression values for gene.", "zebrafish brain", null, "Single cell suspensions were processsed according to manufacturer's instructions by 10X chromium 10x chromium", null, "tissue:Forebrain|developmental stage:6dpf|genotype/variation:znf wild type", "GSM3187948", "GSM3187948: znf wt 10x; Danio rerio; RNA Seq", "GSM3187948", null, "1", "Single cell suspensions were processsed according to manufacturer's instructions by 10X chromium 10x chromium", "GEO Accession:GSM3187948", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP150365", null, null, "wt_possorted_genome_bam.bam", "10X Genomics bam file", 10334856266.0, 178187177.0, "GSM3187948 r1", "0:58", "A:3176662073;C:1883843325;G:2216500039;T:3055499601;N:2351228", 58, null, null, null, 3176662073, 1883843325, 2216500039, 3055499601, 2351228, "SRX4200372", "SRS3410606", "SRA720602", "GEO", "Schier Lab, Molecular and Cellular Biology, Harvard University", 1, 0.89165, null, 0.36096, null, 0.83372, null, 0.49416, null, 58, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2018-06-12", "Larval", "Larval", "Brain", "Nervous System"], [49093, "SRR7723466", "SRX4579978", "SRS3674265", "SRP157997", "PRJNA486153", "Single cell analyses of Amyloid beta42 and Interleukin 4 on neural stem cell plasticity I", "GSE118577", "Transcriptome Analysis", "The neural stem cell NSC reservoir can be harnessed for stem cell based regenerative therapies. Zebrafish remarkably regenerate their brain by inducing NSC plasticity in a Amyloid \u00df 42 A\u00df42 induced experimental Alzheimer's disease AD model. Interleukin 4 IL 4 is also critical for AD induced NSC proliferation. However the mechanisms of this response have remained unknown. Using single cell transcriptomics in the adult zebrafish brain we identify distinct subtypes of NSCs and neurons and differentially regulated pathways and their gene ontologies and investigate how cell cell communication is altered through ligand receptor pairs in AD conditions. Our results propose the existence of heterogeneous and spatially organized stem cell populations that react distinctly to amyloid toxicity. This resource article provides an extensive database for the molecular basis of NSC plasticity in the AD model of the adult zebrafish brain. Further analyses of stem cell heterogeneity and neuro regenerative ability at single cell resolution could yield drug targets for mobilizing NSCs for endogenous neuro regeneration in humans. Overall design: Single cell analyses of zebrafish telencephalon by 10X Genomics", null, "pubmed:31018142;pubmed:34685728;pubmed:35681503", null, "PBS Control", "GSM3334110", null, "tissue:Telencephalon|treatment:PBS Control", "PBS Control", "The fastq files were aligned to zebrafish transcript Ensembl Version 91by using STAR. The BAM files were as input for Cell Ranger 10X genmoics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Genome build: danRer10 Supplementary files format and content: tab delimited file with gene names in rows and cell names and counts in columns.", "Telencephalon", "Fish were injected PBS by CVMI.", "Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol", "Fish were kept at 28 \u00b0C water system with 14/10 hours light/dark cycles", "treatment:PBS Control", "GSM3334110", "GSM3334110: PBS Control; Danio rerio; RNA Seq", "GSM3334110 2", null, "1", "Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol", "GEO Accession:GSM3334110", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP157997", null, "dangling references:treat as unmapped", "PBS_possorted_genome_bam.bam", "10X Genomics bam file", 6292411773.0, 110393189.0, "GSM3334110 r11", "0:57", "A:1933363206;C:1158155764;G:1296886350;T:1901320452;N:2686001", 57, null, null, null, 1933363206, 1158155764, 1296886350, 1901320452, 2686001, "SRX4579978", "SRS3674265", "SRA759092", "GEO", "AG KIZIL, German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association", 1, 0.87993, null, 0.28191, null, 0.77861, null, 0.50645, null, 57, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2018-08-15", "Undetermined", "Adult", "Brain", "Nervous System"], [49094, "SRR7723465", "SRX4579977", "SRS3672878", "SRP157997", "PRJNA486153", "Single cell analyses of Amyloid beta42 and Interleukin 4 on neural stem cell plasticity I", "GSE118577", "Transcriptome Analysis", "The neural stem cell NSC reservoir can be harnessed for stem cell based regenerative therapies. Zebrafish remarkably regenerate their brain by inducing NSC plasticity in a Amyloid \u00df 42 A\u00df42 induced experimental Alzheimer's disease AD model. Interleukin 4 IL 4 is also critical for AD induced NSC proliferation. However the mechanisms of this response have remained unknown. Using single cell transcriptomics in the adult zebrafish brain we identify distinct subtypes of NSCs and neurons and differentially regulated pathways and their gene ontologies and investigate how cell cell communication is altered through ligand receptor pairs in AD conditions. Our results propose the existence of heterogeneous and spatially organized stem cell populations that react distinctly to amyloid toxicity. This resource article provides an extensive database for the molecular basis of NSC plasticity in the AD model of the adult zebrafish brain. Further analyses of stem cell heterogeneity and neuro regenerative ability at single cell resolution could yield drug targets for mobilizing NSCs for endogenous neuro regeneration in humans. Overall design: Single cell analyses of zebrafish telencephalon by 10X Genomics", null, "pubmed:31018142;pubmed:34685728;pubmed:35681503", null, "interleukin 4", "GSM3333764", null, "tissue:Telencephalon|treatment:interleukin 4", "interleukin 4", "The fastq files were aligned to zebrafish transcript Ensembl Version 91by using STAR. The BAM files were as input for Cell Ranger 10X genmoics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Genome build: danRer10 Supplementary files format and content: tab delimited file with gene names in rows and cell names and counts in columns.", "Telencephalon", "Fish were injected interleukin 4 by CVMI.", "Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol", "Fish were kept at 28 \u00b0C water system with 14/10 hours light/dark cycles", "treatment:interleukin 4", "GSM3333764", "GSM3333764: interleukin 4; Danio rerio; RNA Seq", "GSM3333764 2", null, "1", "Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol", "GEO Accession:GSM3333764", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP157997", null, "dangling references:treat as unmapped", "IL4_possorted_genome_bam.bam", "10X Genomics bam file", 7136552532.0, 125202676.0, "GSM3333764 r11", "0:57", "A:2212558326;C:1297976520;G:1461158205;T:2161803665;N:3055816", 57, null, null, null, 2212558326, 1297976520, 1461158205, 2161803665, 3055816, "SRX4579977", "SRS3672878", "SRA759092", "GEO", "AG KIZIL, German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association", 1, 0.87473, null, 0.30099, null, 0.77828, null, 0.49122, null, 57, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2018-08-15", "Undetermined", "Adult", "Brain", "Nervous System"], [49095, "SRR7697065", "SRX4555360", "SRS3672366", "SRP157997", "PRJNA486153", "Single cell analyses of Amyloid beta42 and Interleukin 4 on neural stem cell plasticity I", "GSE118577", "Transcriptome Analysis", "The neural stem cell NSC reservoir can be harnessed for stem cell based regenerative therapies. Zebrafish remarkably regenerate their brain by inducing NSC plasticity in a Amyloid \u00df 42 A\u00df42 induced experimental Alzheimer's disease AD model. Interleukin 4 IL 4 is also critical for AD induced NSC proliferation. However the mechanisms of this response have remained unknown. Using single cell transcriptomics in the adult zebrafish brain we identify distinct subtypes of NSCs and neurons and differentially regulated pathways and their gene ontologies and investigate how cell cell communication is altered through ligand receptor pairs in AD conditions. Our results propose the existence of heterogeneous and spatially organized stem cell populations that react distinctly to amyloid toxicity. This resource article provides an extensive database for the molecular basis of NSC plasticity in the AD model of the adult zebrafish brain. Further analyses of stem cell heterogeneity and neuro regenerative ability at single cell resolution could yield drug targets for mobilizing NSCs for endogenous neuro regeneration in humans. Overall design: Single cell analyses of zebrafish telencephalon by 10X Genomics", null, "pubmed:31018142;pubmed:34685728;pubmed:35681503", null, "amyloid beta 42", "GSM3333461", null, "tissue:Telencephalon|treatment:amyloid beta 42", "amyloid beta 42", "The fastq files were aligned to zebrafish transcript Ensembl Version 91by using STAR. The BAM files were as input for Cell Ranger 10X genmoics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Genome build: danRer10 Supplementary files format and content: tab delimited file with gene names in rows and cell names and counts in columns.", "Telencephalon", "Fish were injected amyloid beta 42 by CVMI.", "Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol", "Fish were kept at 28 \u00b0C water system with 14/10 hours light/dark cycles", "treatment:amyloid beta 42", "GSM3333461", "GSM3333461: amyloid beta 42; Danio rerio; RNA Seq", "GSM3333461", null, "1", "Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol", "GEO Accession:GSM3333461", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP157997", null, "dangling references:treat as unmapped", "AB42_possorted_genome_bam.bam", "10X Genomics bam file", 4538914104.0, 79630072.0, "GSM3333461 r1", "0:57", "A:1398743208;C:825411025;G:924551078;T:1388288174;N:1920619", 57, null, null, null, 1398743208, 825411025, 924551078, 1388288174, 1920619, "SRX4555360", "SRS3672366", "SRA759092", "GEO", "AG KIZIL, German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association", 1, 0.88003, null, 0.26711, null, 0.78336, null, 0.50584, null, 57, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2018-08-15", "Undetermined", "Adult", "Brain", "Nervous System"], [49096, "SRR7698982", "SRX4557276", "SRS3674267", "SRP158038", "PRJNA486182", "Single cell analyses of Amyloid beta42 and Interleukin 4 on neural stem cell plasticity IV", "GSE118599", "Other", "Neural stem cells NSCs constitute the reservoir for new cells and might be harnessed for stem cell based regenerative therapies. Zebrafish has remarkable ability to regenerate its brain by inducing NSC plasticity upon Alzheimer's pathology. We recently identified that NSCs enhance their proliferation and neurogenic outcome in an Amyloid beta42 based A\u00df42 experimental Alzheimer's disease model in zebrafish brain and Interleukin 4 IL4 is a critical molecule for inducing NSC proliferation in AD conditions. However the mechanisms by which A\u00df42 and IL4 affect NSCs remained unknown. Using single cell transcriptomics we determined distinct subtypes of NSCs and neurons in adult zebrafish brain identified differentially expressed genes post A\u00df42 and IL4 treatments analyzed the gene ontology and pathways that are affected by A\u00df42 and IL4 and investigated how cell cell communication is altered through secreted molecules and their receptors. Our results constitute the most extensive resource in the Alzheimer's disease model of adult zebrafish brain are likely to provide unique insights into how A\u00df42/IL4 affects NSC plasticity and yield in novel drug targets for mobilizing neural stem cells for endogenous neuro regeneration. Overall design: Single cell analyses of zebrafish telencephalon by 10X Genomics", null, "pubmed:31905199", null, "serotonin", "GSM3334111", null, "tissue:Telencephalon|treatment:serotonin", "serotonin", "The fastq files were aligned to zebrafish transcript Ensembl Version 91by using STAR. The BAM files were as input for Cell Ranger 10X genmoics to generate processed data files that include gene names row names and cell names column names and counts. Further analysis done by using Seurat package in R. Genome build: danRer10 Supplementary files format and content: tab delimited file with gene names in rows and cell names and counts in columns.", "Telencephalon", "Fish were injected serotonin by CVMI.", "Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol", "Fish were kept at 28 \u00b0C water system with 14/10 hours light/dark cycles", "treatment:serotonin", "GSM3334111", "GSM3334111: serotonin; Danio rerio; RNA Seq", "GSM3334111", null, "1", "Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number. The library preparation was performed by 10X Genomics as per manufactur protocol", "GEO Accession:GSM3334111", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP158038", null, "dangling references:treat as unmapped", "SRT_possorted_genome_bam.bam", "10X Genomics bam file", 6880682724.0, 120713732.0, "GSM3334111 r1", "0:57", "A:2102623379;C:1264130463;G:1410616586;T:2100393658;N:2918638", 57, null, null, null, 2102623379, 1264130463, 1410616586, 2100393658, 2918638, "SRX4557276", "SRS3674267", "SRA759542", "GEO", "AG KIZIL, German Center for Neurodegenerative Diseases (DZNE) Dresden, Helmholtz Association", 1, 0.87735, null, 0.27987, null, 0.78346, null, 0.49332, null, 57, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "Germany", "2018-08-15", "Undetermined", "Adult", "Brain", "Nervous System"], [49405, "SRR7904989", "SRX4741349", "SRS3822681", "SRP162658", "PRJNA493234", "Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x]", "GSE120503", "Other", "To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics.", "parent bioproject:PRJNA493631", "pubmed:31042481;pubmed:33785593", null, "52 hpf CHT cells", "GSM3402061", null, "tissue:zebrafish embryos|region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf", "52 hpf CHT cells", "UMI tools was used to analysis our single cell data. Firstly in \u201cwhitelist\u201d step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in \u201cextract\u201d step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in \u201ccount\u201d step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts", "zebrafish embryos", null, "The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads\u00ae MyOne\u2122 Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture\u2019s introduction.", null, "region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf", "GSM3402061", "GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq", "GSM3402061", null, "1", "The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads\u00ae MyOne\u2122 Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction.", "GEO Accession:GSM3402061", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP162658", null, null, "171353A_zebrafish_HSC_mixture-1_S9_L001_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-1_S9_L001_R2_001.fastq.gz", "fastq fastq", 20612658541.0, 68497783.0, "GSM3402061 r1", "0:150.50 1:150.43", "A:5839137036;C:3293726779;G:3429783599;T:8049467865;N:543262", 150, 150, null, null, 5839137036, 3293726779, 3429783599, 8049467865, 543262, "SRX4741349", "SRS3822681", "SRA784241", "GEO", "Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)", 2, 0.04293, 0.91361, 0.0057, 0.0679, 0.97494, 0.8187, 0.48327, 0.49296, 150, 151, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2018-09-26", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [49406, "SRR7904990", "SRX4741349", "SRS3822681", "SRP162658", "PRJNA493234", "Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x]", "GSE120503", "Other", "To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics.", "parent bioproject:PRJNA493631", "pubmed:31042481;pubmed:33785593", null, "52 hpf CHT cells", "GSM3402061", null, "tissue:zebrafish embryos|region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf", "52 hpf CHT cells", "UMI tools was used to analysis our single cell data. Firstly in \u201cwhitelist\u201d step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in \u201cextract\u201d step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in \u201ccount\u201d step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts", "zebrafish embryos", null, "The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads\u00ae MyOne\u2122 Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture\u2019s introduction.", null, "region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf", "GSM3402061", "GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq", "GSM3402061", null, "1", "The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads\u00ae MyOne\u2122 Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture's introduction.", "GEO Accession:GSM3402061", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP162658", null, null, "171353A_zebrafish_HSC_mixture-1_S9_L002_R1_001.fastq.gz 171353A_zebrafish_HSC_mixture-1_S9_L002_R2_001.fastq.gz", "fastq fastq", 20253907193.0, 67305836.0, "GSM3402061 r2", "0:150.50 1:150.43", "A:5762133423;C:3217021369;G:3378178325;T:7895841084;N:732992", 150, 150, null, null, 5762133423, 3217021369, 3378178325, 7895841084, 732992, "SRX4741349", "SRS3822681", "SRA784241", "GEO", "Jing-Dong Jackie Han's Lab, CAS-MPG Partner Institute for Computational Biology (PICB)", 2, 0.04531, 0.91352, 0.006, 0.06682, 0.97486, 0.81889, 0.47811, 0.50237, 151, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2018-09-26", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [49407, "SRR7904991", "SRX4741349", "SRS3822681", "SRP162658", "PRJNA493234", "Multi dimensional transcriptome analysis of an intact hematopoietic organ for HSPC expansion [10x]", "GSE120503", "Other", "To investigate the peculiarity of CHT HSPCs as well as the interaction of CHT niche and HSPCs at higher resolution we performed scRNA seq with zebrafish CHT. Overall design: The 52 hpf transgenic embryos were cut tails for dissecting into single cell suspension with PI staining. The 50 thousand kdrl:mCherry+ cells and 50 thousand CD41:GFP+ cells plus 50 thousands double negative cells were sorted by FACS for 10X genomics.", "parent bioproject:PRJNA493631", "pubmed:31042481;pubmed:33785593", null, "52 hpf CHT cells", "GSM3402061", null, "tissue:zebrafish embryos|region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf", "52 hpf CHT cells", "UMI tools was used to analysis our single cell data. Firstly in \u201cwhitelist\u201d step we set 5000 as cell number and check quality plots. The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in \u201cextract\u201d step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in \u201ccount\u201d step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all samples measured by UMI counts", "zebrafish embryos", null, "The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads\u00ae MyOne\u2122 Silane Beads Invitrogen 37002D. Single cell RNA seq libraries were prepared using Single Cell three prime Library Gel Bead Kit V2 10x Genomics 120237 following the manufacture\u2019s introduction.", null, "region:CHT|cells:endothelial cells+hematopoietic cells+ double negative niche cells|Stage:52 hpf", "GSM3402061", "GSM3402061: 52 hpf CHT cells; Danio rerio; RNA Seq", "GSM3402061", null, "1", "The single cells were sorted by FACS and cell suspensions 300 1000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10x Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Library and Gel Bead Kit V2 10x Genomics 120237. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs Zheng et al. 2017. Barcoded cDNAs were pooled and cleanup by using DynaBeads\u00ae MyOne\u2122 Silane Beads Invitrogen 37002D. 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