rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
9166,ERR2788341,ERX2797590,ERS2709706,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7292228,SAMEA4890710,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890710|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7292228|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:pool 4|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7292228|scientific name:Danio rerio|sex:2 female  1 male|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7292228 p,5149STDY7292228 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP|Experimental Factor: infect:n1,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7292228.bam 5149STDY7292228.bam.bai,bam bam,37970494940.0,387454030.0,E MTAB 7159:5149STDY7292228,0:98,A:11476520187;C:7571635167;G:8189594199;T:10701044279;N:31701108,98,,,,11476520187,7571635167,8189594199,10701044279,31701108,ERX2797590,ERS2709706,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.87568,,0.2122,,0.82582,,0.5259,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9167,ERR2788340,ERX2797589,ERS2709705,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7274848,SAMEA4890709,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890709|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274848|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 3|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274848|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274848 p,5149STDY7274848 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Vibrio Anguillarum,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7274848.bam 5149STDY7274848.bam.bai,bam bam,34517322840.0,352217580.0,E MTAB 7159:5149STDY7274848,0:98,A:10635243399;C:6658515314;G:7525079510;T:9695995344;N:2489273,98,,,,10635243399,6658515314,7525079510,9695995344,2489273,ERX2797589,ERS2709705,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.86206,,0.18065,,0.83514,,0.53609,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9168,ERR2788339,ERX2797588,ERS2709704,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7274847,SAMEA4890708,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890708|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274847|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 2|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274847|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274847 p,5149STDY7274847 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Anisakis simplex,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7274847.bam 5149STDY7274847.bam.bai,bam bam,34467649678.0,351710711.0,E MTAB 7159:5149STDY7274847,0:98,A:10609988948;C:6722093635;G:7464497879;T:9667814950;N:3254266,98,,,,10609988948,6722093635,7464497879,9667814950,3254266,ERX2797588,ERS2709704,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.88751,,0.21835,,0.83771,,0.53927,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9169,ERR2788338,ERX2797587,ERS2709703,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7274846,SAMEA4890707,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890707|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274846|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 1|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274846|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274846 p,5149STDY7274846 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:n1,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7274846.bam 5149STDY7274846.bam.bai,bam bam,35052538472.0,357678964.0,E MTAB 7159:5149STDY7274846,0:98,A:10698116265;C:6858102477;G:7626019661;T:9866905792;N:3394277,98,,,,10698116265,6858102477,7626019661,9866905792,3394277,ERX2797587,ERS2709703,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.88916,,0.21537,,0.83802,,0.5336,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
25107,SRR25605432,SRX21332628,SRS18578260,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,gfp enriched rep3,GSM7702835,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,gfp enriched rep3,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702835,GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq,GSM7702835 r1,GSM7702835,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,2707_GFP_pos_S4_L001_R2_001.fastq.gz 2707_GFP_pos_S4_L001_R1_001.fastq.gz 2707_GFP_pos_S4_L001_I2_001.fastq.gz 2707_GFP_pos_S4_L001_I1_001.fastq.gz,fastq fastq fastq fastq,21603309774.0,156545723.0,GSM7702835 r1,0:10 1:10 2:28 3:90,A:3960451458;C:3105338977;G:3480072824;T:3541218595;N:2033216,10,10,28,90,3960451458,3105338977,3480072824,3541218595,2033216,SRX21332628,SRS18578260,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.94286,,0.14175,,0.78395,,0.51541,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25108,SRR25605433,SRX21332628,SRS18578260,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,gfp enriched rep3,GSM7702835,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,gfp enriched rep3,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702835,GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq,GSM7702835 r1,GSM7702835,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,2707_GFP_pos_S4_L002_I1_001.fastq.gz 2707_GFP_pos_S4_L002_I2_001.fastq.gz 2707_GFP_pos_S4_L002_R1_001.fastq.gz 2707_GFP_pos_S4_L002_R2_001.fastq.gz,fastq fastq fastq fastq,22413465270.0,162416415.0,GSM7702835 r2,0:10 1:10 2:28 3:90,A:4104405257;C:3220235633;G:3625448968;T:3667329471;N:58021,10,10,28,90,4104405257,3220235633,3625448968,3667329471,58021,SRX21332628,SRS18578260,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.94239,,0.14234,,0.78338,,0.50616,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25109,SRR25822232,SRX21332628,SRS18578260,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,gfp enriched rep3,GSM7702835,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,gfp enriched rep3,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702835,GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq,GSM7702835 r1,GSM7702835,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,2707_GFP_pos_S4_L001_R2_002.fastq.gz 2707_GFP_pos_S4_L001_R1_002.fastq.gz 2707_GFP_pos_S4_L001_I2_002.fastq.gz 2707_GFP_pos_S4_L001_I1_002.fastq.gz,fastq fastq fastq fastq,21424338264.0,155248828.0,GSM7702835 r3,0:10 1:10 2:28 3:90,A:3928077020;C:3077672525;G:3451667186;T:3513734857;N:1242932,10,10,28,90,3928077020,3077672525,3451667186,3513734857,1242932,SRX21332628,SRS18578260,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.9433,,0.14242,,0.78328,,0.52384,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25110,SRR25822233,SRX21332628,SRS18578260,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,gfp enriched rep3,GSM7702835,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,gfp enriched rep3,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702835,GSM7702835: gfp enriched rep3; Danio rerio; RNA Seq,GSM7702835 r1,GSM7702835,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,2707_GFP_pos_S4_L002_I1_002.fastq.gz 2707_GFP_pos_S4_L002_I2_002.fastq.gz 2707_GFP_pos_S4_L002_R1_002.fastq.gz 2707_GFP_pos_S4_L002_R2_002.fastq.gz,fastq fastq fastq fastq,22542479952.0,163351304.0,GSM7702835 r4,0:10 1:10 2:28 3:90,A:4130174287;C:3235362228;G:3643457599;T:3691295761;N:1327485,10,10,28,90,4130174287,3235362228,3643457599,3691295761,1327485,SRX21332628,SRS18578260,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.94183,,0.14124,,0.78301,,0.50517,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25111,SRR25605434,SRX21332627,SRS18578259,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,mcherry enriched rep3,GSM7702834,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,mcherry enriched rep3,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702834,GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq,GSM7702834 r1,GSM7702834,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,2707_pos_Mcherry_S3_L001_R2_001.fastq.gz 2707_pos_Mcherry_S3_L001_R1_001.fastq.gz 2707_pos_Mcherry_S3_L001_I2_001.fastq.gz 2707_pos_Mcherry_S3_L001_I1_001.fastq.gz,fastq fastq fastq fastq,20161522758.0,146097991.0,GSM7702834 r1,0:10 1:10 2:28 3:90,A:3649819934;C:2958286158;G:3267504300;T:3271384686;N:1824112,10,10,28,90,3649819934,2958286158,3267504300,3271384686,1824112,SRX21332627,SRS18578259,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.94851,,0.1483,,0.80012,,0.52549,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25112,SRR25605435,SRX21332627,SRS18578259,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,mcherry enriched rep3,GSM7702834,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,mcherry enriched rep3,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702834,GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq,GSM7702834 r1,GSM7702834,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,2707_pos_Mcherry_S3_L002_I1_001.fastq.gz 2707_pos_Mcherry_S3_L002_I2_001.fastq.gz 2707_pos_Mcherry_S3_L002_R1_001.fastq.gz 2707_pos_Mcherry_S3_L002_R2_001.fastq.gz,fastq fastq fastq fastq,20708273928.0,150059956.0,GSM7702834 r2,0:10 1:10 2:28 3:90,A:3746088654;C:3037032642;G:3368938151;T:3353289242;N:47351,10,10,28,90,3746088654,3037032642,3368938151,3353289242,47351,SRX21332627,SRS18578259,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.94778,,0.14581,,0.80028,,0.52885,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25113,SRR25822230,SRX21332627,SRS18578259,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,mcherry enriched rep3,GSM7702834,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,mcherry enriched rep3,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702834,GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq,GSM7702834 r1,GSM7702834,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,2707_pos_Mcherry_S3_L001_I1_002.fastq.gz 2707_pos_Mcherry_S3_L001_I2_002.fastq.gz 2707_pos_Mcherry_S3_L001_R1_002.fastq.gz 2707_pos_Mcherry_S3_L001_R2_002.fastq.gz,fastq fastq fastq fastq,20078121078.0,145493631.0,GSM7702834 r3,0:10 1:10 2:28 3:90,A:3634984131;C:2943891505;G:3255149272;T:3259243920;N:1157962,10,10,28,90,3634984131,2943891505,3255149272,3259243920,1157962,SRX21332627,SRS18578259,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.94884,,0.14622,,0.80099,,0.52572,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25114,SRR25822231,SRX21332627,SRS18578259,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,mcherry enriched rep3,GSM7702834,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,mcherry enriched rep3,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702834,GSM7702834: mcherry enriched rep3; Danio rerio; RNA Seq,GSM7702834 r1,GSM7702834,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,2707_pos_Mcherry_S3_L002_I1_002.fastq.gz 2707_pos_Mcherry_S3_L002_I2_002.fastq.gz 2707_pos_Mcherry_S3_L002_R1_002.fastq.gz 2707_pos_Mcherry_S3_L002_R2_002.fastq.gz,fastq fastq fastq fastq,20884392978.0,151336181.0,GSM7702834 r4,0:10 1:10 2:28 3:90,A:3779370721;C:3059502508;G:3396295214;T:3383865877;N:1221970,10,10,28,90,3779370721,3059502508,3396295214,3383865877,1221970,SRX21332627,SRS18578259,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.94896,,0.14559,,0.8002,,0.51418,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25115,SRR25605436,SRX21332626,SRS18578258,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,gfp enriched rep2,GSM7702833,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,gfp enriched rep2,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702833,GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq,GSM7702833 r1,GSM7702833,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py|options:  allowEarlyFileEnd,1907_GFP_pos_S2_L001_I1_001.fastq.gz 1907_GFP_pos_S2_L001_I2_001.fastq.gz 1907_GFP_pos_S2_L001_R1_001.fastq.gz 1907_GFP_pos_S2_L001_R2_001.fastq.gz,fastq fastq fastq fastq,22174775364.0,160686778.0,GSM7702833 r1,0:10 1:10 2:28 3:90,A:4207510387;C:3050740898;G:3362227609;T:3839333241;N:1997885,10,10,28,90,4207510387,3050740898,3362227609,3839333241,1997885,SRX21332626,SRS18578258,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.93287,,0.11844,,0.81087,,0.55264,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25116,SRR25605437,SRX21332626,SRS18578258,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,gfp enriched rep2,GSM7702833,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,gfp enriched rep2,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702833,GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq,GSM7702833 r1,GSM7702833,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py|options:  allowEarlyFileEnd,1907_GFP_pos_S2_L002_I1_001.fastq.gz 1907_GFP_pos_S2_L002_I2_001.fastq.gz 1907_GFP_pos_S2_L002_R1_001.fastq.gz 1907_GFP_pos_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,22047847518.0,159767011.0,GSM7702833 r2,0:10 1:10 2:28 3:90,A:4174013532;C:3033959926;G:3357962867;T:3813042664;N:52001,10,10,28,90,4174013532,3033959926,3357962867,3813042664,52001,SRX21332626,SRS18578258,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.93359,,0.11585,,0.81087,,0.55705,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25117,SRR25822228,SRX21332626,SRS18578258,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,gfp enriched rep2,GSM7702833,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,gfp enriched rep2,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702833,GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq,GSM7702833 r1,GSM7702833,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,1907_GFP_pos_S2_L001_I1_002.fastq.gz 1907_GFP_pos_S2_L001_I2_002.fastq.gz 1907_GFP_pos_S2_L001_R1_002.fastq.gz 1907_GFP_pos_S2_L001_R2_002.fastq.gz,fastq fastq fastq fastq,22010894568.0,159499236.0,GSM7702833 r3,0:10 1:10 2:28 3:90,A:4176090595;C:3026940106;G:3336506731;T:3814128890;N:1264918,10,10,28,90,4176090595,3026940106,3336506731,3814128890,1264918,SRX21332626,SRS18578258,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.93457,,0.11733,,0.81032,,0.55203,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25118,SRR25822229,SRX21332626,SRS18578258,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,gfp enriched rep2,GSM7702833,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,gfp enriched rep2,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702833,GSM7702833: gfp enriched rep2; Danio rerio; RNA Seq,GSM7702833 r1,GSM7702833,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,1907_GFP_pos_S2_L002_I1_002.fastq.gz 1907_GFP_pos_S2_L002_I2_002.fastq.gz 1907_GFP_pos_S2_L002_R1_002.fastq.gz 1907_GFP_pos_S2_L002_R2_002.fastq.gz,fastq fastq fastq fastq,22227220746.0,161066817.0,GSM7702833 r4,0:10 1:10 2:28 3:90,A:4209198596;C:3055507768;G:3382717459;T:3847294849;N:1294858,10,10,28,90,4209198596,3055507768,3382717459,3847294849,1294858,SRX21332626,SRS18578258,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.93428,,0.11629,,0.81014,,0.56014,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25119,SRR25605438,SRX21332625,SRS18578257,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,mcherry enriched rep2,GSM7702832,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,mcherry enriched rep2,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702832,GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq,GSM7702832 r1,GSM7702832,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,1907_pos_pos_S1_L001_I1_001.fastq.gz 1907_pos_pos_S1_L001_I2_001.fastq.gz 1907_pos_pos_S1_L001_R1_001.fastq.gz 1907_pos_pos_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,25141955454.0,182188083.0,GSM7702832 r1,0:10 1:10 2:28 3:90,A:4942067104;C:3446689328;G:3778138998;T:4227670796;N:2361244,10,10,28,90,4942067104,3446689328,3778138998,4227670796,2361244,SRX21332625,SRS18578257,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.90803,,0.11273,,0.81872,,0.54345,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25120,SRR25605439,SRX21332625,SRS18578257,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,mcherry enriched rep2,GSM7702832,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,mcherry enriched rep2,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702832,GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq,GSM7702832 r1,GSM7702832,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,1907_pos_pos_S1_L002_R2_001.fastq.gz 1907_pos_pos_S1_L002_R1_001.fastq.gz 1907_pos_pos_S1_L002_I2_001.fastq.gz 1907_pos_pos_S1_L002_I1_001.fastq.gz,fastq fastq fastq fastq,25433730786.0,184302397.0,GSM7702832 r2,0:10 1:10 2:28 3:90,A:4980326106;C:3488986366;G:3842594871;T:4275245265;N:63122,10,10,28,90,4980326106,3488986366,3842594871,4275245265,63122,SRX21332625,SRS18578257,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.91035,,0.11175,,0.82016,,0.52814,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25121,SRR25822226,SRX21332625,SRS18578257,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,mcherry enriched rep2,GSM7702832,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,mcherry enriched rep2,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702832,GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq,GSM7702832 r1,GSM7702832,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,1907_pos_pos_S1_L001_R2_002.fastq.gz 1907_pos_pos_S1_L001_R1_002.fastq.gz 1907_pos_pos_S1_L001_I2_002.fastq.gz 1907_pos_pos_S1_L001_I1_002.fastq.gz,fastq fastq fastq fastq,24834656088.0,179961276.0,GSM7702832 r3,0:10 1:10 2:28 3:90,A:4878672093;C:3403443000;G:3732878174;T:4180051888;N:1469685,10,10,28,90,4878672093,3403443000,3732878174,4180051888,1469685,SRX21332625,SRS18578257,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.90776,,0.11325,,0.81852,,0.54011,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
25122,SRR25822227,SRX21332625,SRS18578257,SRP454539,PRJNA1004255,Unique activities of two overlapping PAX6 retinal enhancers,GSE240575,Transcriptome Analysis,Enhancers play a critical role in development by precisely modulating spatial  temporal  and cell type specific gene expression. Sequence variants in enhancers have been implicated in disease  however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active. PAX6 is the master regulator of eye development  with a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive  redundant  or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of two PAX6 retinal enhancers  HS5 and NRE. Using a unique combination of live imaging and single cell RNA sequencing in dual enhancer reporter zebrafish embryos  we uncover differences in the spatiotemporal activity of these enhancers. Our results show that although overlapping  these enhancers have distinct activities in different cell types and therefore likely non redundant functions. This work demonstrates that unique cell type specific activities can be uncovered for apparently similar enhancers when investigated at high resolution in vivo. Overall design: In order to define the precise cell types within the retina where the PAX6 enhancers HS5 and NRE are active  we carried out scRNA seq on eyes from NRE eGFP/HS5 mCherry zebrafish reporter embryos. With this technique  we aimed to uncover cell type or transcriptional differences between the two enhancer active populations. We dissected eyes from 48 hpf NRE eGFP/HS5 mCherry embryos and used FACS to enrich for either mCherry positive/HS5 active cells or eGFP positive/NRE active cells. Three samples for each population were processed for scRNA seq using the 10x Genomics Chromium single cell three prime gene expression technology.,,pubmed:37643867,,mcherry enriched rep2,GSM7702832,,source name:Eye|tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf|geo loc name:missing|collection date:missing,mcherry enriched rep2,Cell Ranger v6.1.2 was used to perform alignment  filtering  barcode counting  and UMI counting. A custom reference genome was created for alignment using cellranger mkref  combining the Danio rerio GRCz11 genome assembly with manually annotated eGFP and mCherry sequences. Cell calling and QC: The emptyDrops function from DropletUtils was used to filter out empty droplets/barcodes not corresponding to cells Lun et al.  2019. Mitochondrial and ribosomal genes were excluded from the emptyDrops analysis to improve the filtering of droplets containing ambient RNA or cell fragments. The scater package was used to filter cells based on the QC metrics of library size  detected genes  and mitochondrial reads McCarthy et al.  2017. Cells with detected genes ≥ 500  library size ≥ 800  and mitochondrial reads ≤ 10% were retained. Within the processed dataset  mean reads per cell = 11239  and median genes per cell = 1554. Reference mapping and filtering: The SingleR package was used to annotate cell types based on mapping to the zebrafish single cell transcriptome atlas Aran et al.  2019; Farnsworth et al.  2019. Expression matrix and cell annotation data were downloaded from the UCSC cell browser http://zebrafish dev.cells.ucsc.edu; only the 2 dpf data were used for mapping. Erroneously sorted cells of non retinal identity for example pigmented cell types such as melanocytes with high autofluorescence were filtered out at this stage. This was carried out to improve the resolution of clustering for retinal cell types.  Clustering and cell type annotation: Seurat v4 was used for clustering and further analysis for a total of 6 288 cells Butler et al.  2018. SCTransform was used to perform log normalisation  scaling  and highly variable gene HVG detection on a dataset consisting of the 6 samples merged into one. Standard SCTransform options were used  with regression of mitochondrial expression and cell cycle stage using ‘vars.to.regress’. We performed Principle Component Analysis PCA on the normalized counts matrix restricted to HVGs  using Seurat's RunPCA function with number of PCs = 50. To enable integration of the samples  we then used Harmony to generate PCs corrected for batch effects between libraries Korsunsky et al.  2019. The Harmony PCs were then used to perform K nearest neighbour analysis k=20 and Louvain clustering using Seurat 15 dimensions and resolution 0.6. Clusters were annotated as retinal cell types based on the highest expressed marker genes  and other known genes for each cell type  using information from the literature and ZFIN Sprague et al.  2008. Cell cycle scoring was performed using the Seurat CellCycleScoring function  using zebrafish genes homologous to the ‘s.features’ and ‘g2m.features’ genes provided by Seurat. Assembly: GRCz11 Supplementary files format and content: Tab separated values files  matrix files  Seurat object RDS file,Eye,,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell 3’ gene expression technology v3.1.,,tissue:Eye|genotype:NRE eGFP/HS5 mCherry|developmental stage:48 hpf,GSM7702832,GSM7702832: mcherry enriched rep2; Danio rerio; RNA Seq,GSM7702832 r1,GSM7702832,1,NRE eGFP/HS5 mCherry embryos were collected and treated with PTU from 12 hpf. At 48 hpf  embryos were anaesthetised with Tricaine 20–30 mg/l and placed into Danieau's solution. Eyes were dissected from 100 150 embryos using fine forceps Dumont #5SF  and immediately placed into Danieau's solution on ice. Samples were centrifuged at 300g for 1 minute at 4°C  then washed with Danieau's solution. Washing step was carried out three times with Danieau's solution  and once with FACSmax Amsbio. In a final 500 µl FACSmax  the samples were passed through a 35 µm cell strainer to obtain single cell suspension on ice. Samples were sorted for mCherry and eGFP fluorescence using a FACS Aria II BD or CytoFLEX SRT Beckman Coulter machine. Forward and side scatter sorting was used to select single cells from clumps and debris  and DAPI staining was used to exclude dead cells. Libraries were prepared using the 10x Genomics Chromium single cell three prime gene expression technology v3.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP454539,,loader:fastq load.py,1907_pos_pos_S1_L002_I1_002.fastq.gz 1907_pos_pos_S1_L002_I2_002.fastq.gz 1907_pos_pos_S1_L002_R1_002.fastq.gz 1907_pos_pos_S1_L002_R2_002.fastq.gz,fastq fastq fastq fastq,25609437216.0,185575632.0,GSM7702832 r4,0:10 1:10 2:28 3:90,A:5015380345;C:3509305882;G:3867598814;T:4308011415;N:1510424,10,10,28,90,5015380345,3509305882,3867598814,4308011415,1510424,SRX21332625,SRS18578257,SRA1702612,"Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh","Wendy Bickmore, MRC Human Genetics Unit, University of Edinburgh",1,0.90907,,0.11192,,0.81994,,0.50902,,90,,B,,usable mapping rate,illumina,nextseq_v2,3prime,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2023-08-10,Hatching,Embryo,Eye,Sensory System
68149,SRR17630939,SRX13799350,SRS11681639,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 3 compared to intact control testes,GSM5820567,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 3 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820567,GSM5820567: dissociated bulk seq control testes   rep 3 compared to intact control testes; Danio rerio; RNA Seq,GSM5820567 r1,GSM5820567,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C3_S14_L001_R1_001.fastq.gz,fastq,1847371623.0,36222973.0,GSM5820567 r1,0:51 1:0,A:535632392;C:366862698;G:429979337;T:514873991;N:23205,51,0,,,535632392,366862698,429979337,514873991,23205,SRX13799350,SRS11681639,SRA1357269,University of Florida,University of Florida,1,0.87212,,0.1857,,0.69372,,0.56886,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68150,SRR17630940,SRX13799350,SRS11681639,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 3 compared to intact control testes,GSM5820567,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 3 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820567,GSM5820567: dissociated bulk seq control testes   rep 3 compared to intact control testes; Danio rerio; RNA Seq,GSM5820567 r1,GSM5820567,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C3_S14_L002_R1_001.fastq.gz,fastq,1823230824.0,35749624.0,GSM5820567 r2,0:51 1:0,A:529009592;C:361883074;G:424030274;T:508289743;N:18141,51,0,,,529009592,361883074,424030274,508289743,18141,SRX13799350,SRS11681639,SRA1357269,University of Florida,University of Florida,1,0.8708,,0.18714,,0.6955,,0.5716,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68151,SRR17630941,SRX13799349,SRS11681638,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 2 compared to intact control testes,GSM5820566,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 2 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820566,GSM5820566: dissociated bulk seq control testes   rep 2 compared to intact control testes; Danio rerio; RNA Seq,GSM5820566 r1,GSM5820566,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C2_S13_L001_R1_001.fastq.gz,fastq,536561208.0,10520808.0,GSM5820566 r1,0:51 1:0,A:163430759;C:106016694;G:122059136;T:145048023;N:6596,51,0,,,163430759,106016694,122059136,145048023,6596,SRX13799349,SRS11681638,SRA1357269,University of Florida,University of Florida,1,0.83573,,0.2005,,0.71056,,0.52825,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68152,SRR17630942,SRX13799349,SRS11681638,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 2 compared to intact control testes,GSM5820566,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 2 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820566,GSM5820566: dissociated bulk seq control testes   rep 2 compared to intact control testes; Danio rerio; RNA Seq,GSM5820566 r1,GSM5820566,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C2_S13_L002_R1_001.fastq.gz,fastq,530978238.0,10411338.0,GSM5820566 r2,0:51 1:0,A:161875304;C:104815309;G:120705456;T:143576873;N:5296,51,0,,,161875304,104815309,120705456,143576873,5296,SRX13799349,SRS11681638,SRA1357269,University of Florida,University of Florida,1,0.83663,,0.19964,,0.71104,,0.54143,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68153,SRR17630943,SRX13799348,SRS11681637,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 1 compared to intact control testes,GSM5820565,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 1 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820565,GSM5820565: dissociated bulk seq control testes   rep 1 compared to intact control testes; Danio rerio; RNA Seq,GSM5820565 r1,GSM5820565,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C1_S12_L001_R1_001.fastq.gz,fastq,523779282.0,10270182.0,GSM5820565 r1,0:51 1:0,A:155891194;C:103400919;G:120028554;T:144451616;N:6999,51,0,,,155891194,103400919,120028554,144451616,6999,SRX13799348,SRS11681637,SRA1357269,University of Florida,University of Florida,1,0.85957,,0.19557,,0.69501,,0.56637,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68154,SRR17630944,SRX13799348,SRS11681637,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 1 compared to intact control testes,GSM5820565,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 1 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820565,GSM5820565: dissociated bulk seq control testes   rep 1 compared to intact control testes; Danio rerio; RNA Seq,GSM5820565 r1,GSM5820565,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C1_S12_L002_R1_001.fastq.gz,fastq,516901983.0,10135333.0,GSM5820565 r2,0:51 1:0,A:153923180;C:101966413;G:118359254;T:142647450;N:5686,51,0,,,153923180,101966413,118359254,142647450,5686,SRX13799348,SRS11681637,SRA1357269,University of Florida,University of Florida,1,0.85795,,0.19403,,0.69627,,0.57159,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68155,SRR17630945,SRX13799347,SRS11681636,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 3,GSM5820564,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 3,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820564,GSM5820564: bulk seq intact control testes   rep 3; Danio rerio; RNA Seq,GSM5820564 r1,GSM5820564,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C3_S16_L001_R1_001.fastq.gz,fastq,1673456880.0,32812880.0,GSM5820564 r1,0:51 1:0,A:496655744;C:334242155;G:387205466;T:455330132;N:23383,51,0,,,496655744,334242155,387205466,455330132,23383,SRX13799347,SRS11681636,SRA1357269,University of Florida,University of Florida,1,0.8707,,0.22045,,0.71078,,0.60605,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68156,SRR17630946,SRX13799347,SRS11681636,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 3,GSM5820564,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 3,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820564,GSM5820564: bulk seq intact control testes   rep 3; Danio rerio; RNA Seq,GSM5820564 r1,GSM5820564,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C3_S16_L002_R1_001.fastq.gz,fastq,1647184587.0,32297737.0,GSM5820564 r2,0:51 1:0,A:489182217;C:328774657;G:380849646;T:448358863;N:19204,51,0,,,489182217,328774657,380849646,448358863,19204,SRX13799347,SRS11681636,SRA1357269,University of Florida,University of Florida,1,0.87032,,0.22081,,0.71261,,0.60917,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68157,SRR17630947,SRX13799346,SRS11681635,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes,GSM5820561,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq TCDD testes rep 2to be compared  to scRNA seq TCDD testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820561,GSM5820561: bulk seq TCDD testes rep 2to be compared  to scRNA seq TCDD testes; Danio rerio; RNA Seq,GSM5820561 r1,GSM5820561,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_T2_S7_L001_R1_001.fastq.gz,fastq,1583815608.0,31055208.0,GSM5820561 r1,0:51 1:0,A:447529477;C:312467507;G:374130013;T:449667219;N:21392,51,0,,,447529477,312467507,374130013,449667219,21392,SRX13799346,SRS11681635,SRA1357269,University of Florida,University of Florida,1,0.86982,,0.25275,,0.70774,,0.5721,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68158,SRR17630948,SRX13799346,SRS11681635,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes,GSM5820561,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq TCDD testes rep 2to be compared  to scRNA seq TCDD testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820561,GSM5820561: bulk seq TCDD testes rep 2to be compared  to scRNA seq TCDD testes; Danio rerio; RNA Seq,GSM5820561 r1,GSM5820561,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_T2_S7_L002_R1_001.fastq.gz,fastq,1564087941.0,30668391.0,GSM5820561 r2,0:51 1:0,A:442209708;C:308400147;G:369229792;T:444230646;N:17648,51,0,,,442209708,308400147,369229792,444230646,17648,SRX13799346,SRS11681635,SRA1357269,University of Florida,University of Florida,1,0.87035,,0.2527,,0.70682,,0.57673,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68159,SRR17630949,SRX13799345,SRS11681634,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 2,GSM5820563,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 2,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820563,GSM5820563: bulk seq intact control testes   rep 2; Danio rerio; RNA Seq,GSM5820563 r1,GSM5820563,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C2_S15_L001_R1_001.fastq.gz,fastq,1493724669.0,29288719.0,GSM5820563 r1,0:51 1:0,A:445588125;C:289131502;G:340459665;T:418525850;N:19527,51,0,,,445588125,289131502,340459665,418525850,19527,SRX13799345,SRS11681634,SRA1357269,University of Florida,University of Florida,1,0.85779,,0.20343,,0.69887,,0.56808,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68160,SRR17630950,SRX13799345,SRS11681634,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 2,GSM5820563,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 2,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820563,GSM5820563: bulk seq intact control testes   rep 2; Danio rerio; RNA Seq,GSM5820563 r1,GSM5820563,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C2_S15_L002_R1_001.fastq.gz,fastq,1475012565.0,28921815.0,GSM5820563 r2,0:51 1:0,A:440339743;C:285301590;G:335922618;T:413432380;N:16234,51,0,,,440339743,285301590,335922618,413432380,16234,SRX13799345,SRS11681634,SRA1357269,University of Florida,University of Florida,1,0.85783,,0.20221,,0.70102,,0.57116,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68161,SRR17630957,SRX13799344,SRS11681633,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 1,GSM5820562,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 1,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820562,GSM5820562: bulk seq intact control testes   rep 1; Danio rerio; RNA Seq,GSM5820562 r1,GSM5820562,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C1_S2_L001_R1_001.fastq.gz,fastq,1783515696.0,34970896.0,GSM5820562 r1,0:51 1:0,A:503613569;C:361648917;G:420357217;T:497872153;N:23840,51,0,,,503613569,361648917,420357217,497872153,23840,SRX13799344,SRS11681633,SRA1357269,University of Florida,University of Florida,1,0.88797,,0.22692,,0.69522,,0.57676,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68162,SRR17630958,SRX13799344,SRS11681633,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 1,GSM5820562,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 1,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820562,GSM5820562: bulk seq intact control testes   rep 1; Danio rerio; RNA Seq,GSM5820562 r1,GSM5820562,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C1_S2_L002_R1_001.fastq.gz,fastq,1758067563.0,34471913.0,GSM5820562 r2,0:51 1:0,A:496669418;C:356271536;G:414028881;T:491077933;N:19795,51,0,,,496669418,356271536,414028881,491077933,19795,SRX13799344,SRS11681633,SRA1357269,University of Florida,University of Florida,1,0.88843,,0.22792,,0.69619,,0.57488,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68163,SRR17630951,SRX13799343,SRS11681632,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes,GSM5820560,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820560,GSM5820560: bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes; Danio rerio; RNA Seq,GSM5820560 r1,GSM5820560,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_T1_S6_L001_R1_001.fastq.gz,fastq,3525780042.0,69132942.0,GSM5820560 r1,0:51 1:0,A:1025376436;C:691776192;G:829134506;T:979443851;N:49057,51,0,,,1025376436,691776192,829134506,979443851,49057,SRX13799343,SRS11681632,SRA1357269,University of Florida,University of Florida,1,0.86505,,0.30929,,0.72074,,0.6373,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68164,SRR17630952,SRX13799343,SRS11681632,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes,GSM5820560,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820560,GSM5820560: bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes; Danio rerio; RNA Seq,GSM5820560 r1,GSM5820560,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_T1_S6_L002_R1_001.fastq.gz,fastq,3479799156.0,68231356.0,GSM5820560 r2,0:51 1:0,A:1012622841;C:682305804;G:817948602;T:966881210;N:40699,51,0,,,1012622841,682305804,817948602,966881210,40699,SRX13799343,SRS11681632,SRA1357269,University of Florida,University of Florida,1,0.86392,,0.30933,,0.71863,,0.63706,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68165,SRR17630953,SRX13799342,SRS11681631,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 2  to be compared to scRNA seq control testes,GSM5820558,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 2  to be compared to  scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820558,GSM5820558: bulk seq control testes rep 2  to be compared to  scRNA seq control testes; Danio rerio; RNA Seq,GSM5820558 r1,GSM5820558,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C2_S8_L001_R1_001.fastq.gz,fastq,1264687137.0,24797787.0,GSM5820558 r1,0:51 1:0,A:361072135;C:254984535;G:302043978;T:346569617;N:16872,51,0,,,361072135,254984535,302043978,346569617,16872,SRX13799342,SRS11681631,SRA1357269,University of Florida,University of Florida,1,0.86972,,0.31888,,0.71561,,0.6242,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68166,SRR17630954,SRX13799342,SRS11681631,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 2  to be compared to scRNA seq control testes,GSM5820558,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 2  to be compared to  scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820558,GSM5820558: bulk seq control testes rep 2  to be compared to  scRNA seq control testes; Danio rerio; RNA Seq,GSM5820558 r1,GSM5820558,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C2_S8_L002_R1_001.fastq.gz,fastq,1247134620.0,24453620.0,GSM5820558 r2,0:51 1:0,A:356333809;C:251264657;G:297639103;T:341883185;N:13866,51,0,,,356333809,251264657,297639103,341883185,13866,SRX13799342,SRS11681631,SRA1357269,University of Florida,University of Florida,1,0.8683,,0.31544,,0.71332,,0.62605,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68167,SRR17630955,SRX13799341,SRS11681630,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 3  to be compared to scRNA seq control testes,GSM5820559,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 3  to be compared to  scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820559,GSM5820559: bulk seq control testes rep 3  to be compared to  scRNA seq control testes; Danio rerio; RNA Seq,GSM5820559 r1,GSM5820559,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C3_S5_L001_R1_001.fastq.gz,fastq,1298470557.0,25460207.0,GSM5820559 r1,0:51 1:0,A:370125548;C:258465981;G:307735443;T:362125609;N:17976,51,0,,,370125548,258465981,307735443,362125609,17976,SRX13799341,SRS11681630,SRA1357269,University of Florida,University of Florida,1,0.87017,,0.23168,,0.7049,,0.43404,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68168,SRR17630956,SRX13799341,SRS11681630,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 3  to be compared to scRNA seq control testes,GSM5820559,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 3  to be compared to  scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820559,GSM5820559: bulk seq control testes rep 3  to be compared to  scRNA seq control testes; Danio rerio; RNA Seq,GSM5820559 r1,GSM5820559,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C3_S5_L002_R1_001.fastq.gz,fastq,1282277445.0,25142695.0,GSM5820559 r2,0:51 1:0,A:365706822;C:255117242;G:303741803;T:357696714;N:14864,51,0,,,365706822,255117242,303741803,357696714,14864,SRX13799341,SRS11681630,SRA1357269,University of Florida,University of Florida,1,0.86967,,0.23412,,0.70447,,0.60084,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68169,SRR17630959,SRX13799340,SRS11681629,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 1 to be compared to scRNA seq control testes,GSM5820557,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 1 to be compared to scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820557,GSM5820557: bulk seq control testes rep 1 to be compared to scRNA seq control testes; Danio rerio; RNA Seq,GSM5820557 r1,GSM5820557,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C1_S4_L001_R1_001.fastq.gz,fastq,363711651.0,7131601.0,GSM5820557 r1,0:51 1:0,A:101645255;C:77359657;G:89895787;T:94805817;N:5135,51,0,,,101645255,77359657,89895787,94805817,5135,SRX13799340,SRS11681629,SRA1357269,University of Florida,University of Florida,1,0.86049,,0.29611,,0.72293,,0.54071,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68170,SRR17630960,SRX13799340,SRS11681629,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 1 to be compared to scRNA seq control testes,GSM5820557,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 1 to be compared to scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820557,GSM5820557: bulk seq control testes rep 1 to be compared to scRNA seq control testes; Danio rerio; RNA Seq,GSM5820557 r1,GSM5820557,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C1_S4_L002_R1_001.fastq.gz,fastq,358349460.0,7026460.0,GSM5820557 r2,0:51 1:0,A:100176173;C:76199709;G:88532838;T:93436578;N:4162,51,0,,,100176173,76199709,88532838,93436578,4162,SRX13799340,SRS11681629,SRA1357269,University of Florida,University of Florida,1,0.86034,,0.29588,,0.72346,,0.54277,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
76372,SRR24954201,SRX20712237,SRS18004425,SRP444513,PRJNA981358,Danio rerio Genome sequencing and assembly,PRJNA981358,Whole Genome Sequencing,To explore the source of Csf1a and Csf1b in embryonic zebrafish  we carried out a single cell RNA sequencing scRNA seq. We collected the trunks from 28 hpf embryos and performed 10X Genomics scRNA seq.,,,This sample contained cells isolated from trunks of 40 zebrafish embryos at 28hpf.,Cells isolated from trunks of wildtype danio rerio at 28hpf,WT 1,,strain:ABSR|dev stage:28 hpf date:2019 11 18|geo loc name:China: Guangzhou|sex:not determined|tissue:Trunk|BioSampleModel:Model organism or animal,,,,,,,,,scRNA seq of 28hpfWT trunk,28hpfWT 1,28hpfWT 1,Cellular suspensions were loaded on a 10X Genomics GemCode Single cell instrument that generates single cell Gel Bead In EMlusion GEMs. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3 Reagent Kits v3.1. Upon dissolution of the Gel Bead in a GEM  primers containing i an Illumina R1 sequence read 1 sequencing primer  ii a 16nt 10x Barcode  iii a 10nt Unique Molecular Identifier UMI  and iv a poly dT primer sequence were released and mixed with cell lysate and Master Mix. Barcoded  full length cDNAs were then reverse transcribed from poly adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full length  barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction. R1 were added to the molecules during GEM incubation. P5  P7  a sample index  and R2 were added during library construction via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification.,,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP444513,,,J1911072-ATGCTCCG_BKDL192544560-1a-AK949_2.fq.gz J1911072-CACTCGGA_BKDL192544560-1a-AK946_1.fq.gz J1911072-CACTCGGA_BKDL192544560-1a-AK946_2.fq.gz J1911072-GCTGAATT_BKDL192544560-1a-AK947_1.fq.gz J1911072-GCTGAATT_BKDL192544560-1a-AK947_2.fq.gz J1911072-TGAAGTAC_BKDL192544560-1a-AK948_1.fq.gz J1911072-TGAAGTAC_BKDL192544560-1a-AK948_2.fq.gz J1911072-ATGCTCCG_BKDL192544560-1a-AK949_1.fq.gz,fastq fastq fastq fastq fastq fastq fastq fastq,144260432400.0,480868108.0,J1911072 ATGCTCCG BKDL192544560 1a AK949 1.fq.gz,0:150 1:150,A:57113710706;C:25903289244;G:24836065109;T:36405707402;N:1659939,150,150,,,57113710706,25903289244,24836065109,36405707402,1659939,SRX20712237,SRS18004425,SRA1657728,South China University of Technology|School of Medicine,South China University of Technology,2,0.0,0.92449,0.0,0.12055,1.0,0.77806,,0.51028,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,full_length,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2023-06-17,Pharyngula,Embryo,Trunk,Surface Structure
76997,SRR25423053,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L001_I1_001.fastq.gz,fastq,39075288.0,4884411.0,GSM7660980 r1,0:8,A:8072562;C:6862766;G:17416494;T:5849783;N:873683,8,,,,8072562,6862766,17416494,5849783,873683,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
76998,SRR25423054,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L004_I1_001.fastq.gz,fastq,40207464.0,5025933.0,GSM7660980 r10,0:8,A:8353613;C:7111546;G:18405023;T:6056882;N:280400,8,,,,8353613,7111546,18405023,6056882,280400,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
76999,SRR25423055,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L004_R1_001.fastq.gz,fastq,140726124.0,5025933.0,GSM7660980 r11,0:28,A:37863942;C:35273460;G:29075767;T:38479070;N:33885,28,,,,37863942,35273460,29075767,38479070,33885,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00815,,0.00373,,0.98762,,0.37971,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77000,SRR25423056,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L004_R2_001.fastq.gz,fastq,653371290.0,5025933.0,GSM7660980 r12,0:130,A:197652493;C:123117545;G:153788236;T:174856024;N:3956992,130,,,,197652493,123117545,153788236,174856024,3956992,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.88819,,0.26058,,0.79498,,0.51248,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77001,SRR25423057,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L001_R1_001.fastq.gz,fastq,136763508.0,4884411.0,GSM7660980 r2,0:28,A:36700123;C:34378994;G:28311664;T:37342519;N:30208,28,,,,36700123,34378994,28311664,37342519,30208,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00746,,0.00299,,0.98782,,0.33891,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77002,SRR25423058,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L001_R2_001.fastq.gz,fastq,634973430.0,4884411.0,GSM7660980 r3,0:130,A:194231988;C:122172940;G:144200881;T:173659068;N:708553,130,,,,194231988,122172940,144200881,173659068,708553,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.89999,,0.26714,,0.78884,,0.51009,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77003,SRR25423059,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L002_I1_001.fastq.gz,fastq,40874608.0,5109326.0,GSM7660980 r4,0:8,A:8407020;C:7216140;G:18310689;T:6123507;N:817252,8,,,,8407020,7216140,18310689,6123507,817252,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77004,SRR25423060,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L002_R1_001.fastq.gz,fastq,143061128.0,5109326.0,GSM7660980 r5,0:28,A:38454355;C:35931605;G:29585361;T:39031878;N:57929,28,,,,38454355,35931605,29585361,39031878,57929,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00783,,0.00316,,0.98744,,0.37064,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77005,SRR25423061,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L002_R2_001.fastq.gz,fastq,664212380.0,5109326.0,GSM7660980 r6,0:130,A:201730540;C:125762436;G:157718531;T:178360911;N:639962,130,,,,201730540,125762436,157718531,178360911,639962,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.88361,,0.26162,,0.79529,,0.50582,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77006,SRR25423062,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L003_I1_001.fastq.gz,fastq,38381576.0,4797697.0,GSM7660980 r7,0:8,A:8075384;C:6797029;G:17490080;T:5805523;N:213560,8,,,,8075384,6797029,17490080,5805523,213560,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77007,SRR25423063,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L003_R1_001.fastq.gz,fastq,134335516.0,4797697.0,GSM7660980 r8,0:28,A:36087906;C:33767454;G:27805596;T:36644298;N:30262,28,,,,36087906,33767454,27805596,36644298,30262,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00769,,0.00317,,0.98729,,0.35107,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77008,SRR25423064,SRX21157894,SRS18420147,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane3 & lane4,GSM7660980,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660980,GSM7660980: WT s1026 rep1 lane3 & lane4; Danio rerio; RNA Seq,GSM7660980 r1,GSM7660980,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p155_S0_L003_R2_001.fastq.gz,fastq,623700610.0,4797697.0,GSM7660980 r9,0:130,A:190543769;C:119560339;G:140982942;T:169663923;N:2949637,130,,,,190543769,119560339,140982942,169663923,2949637,SRX21157894,SRS18420147,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.89981,,0.26806,,0.79026,,0.51173,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77009,SRR25423065,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L001_I1_001.fastq.gz,fastq,41579560.0,5197445.0,GSM7660979 r1,0:8,A:9428308;C:7309725;G:17762022;T:6829664;N:249841,8,,,,9428308,7309725,17762022,6829664,249841,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77010,SRR25423066,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L004_I1_001.fastq.gz,fastq,44075624.0,5509453.0,GSM7660979 r10,0:8,A:9834086;C:7713037;G:19303314;T:7170073;N:55114,8,,,,9834086,7713037,19303314,7170073,55114,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77011,SRR25423067,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L004_R1_001.fastq.gz,fastq,154264684.0,5509453.0,GSM7660979 r11,0:28,A:41220569;C:38745415;G:32338250;T:41944588;N:15862,28,,,,41220569,38745415,32338250,41944588,15862,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00988,,0.00473,,0.98632,,0.39018,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77012,SRR25423068,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L004_R2_001.fastq.gz,fastq,716228890.0,5509453.0,GSM7660979 r12,0:130,A:218476823;C:134111218;G:167891935;T:195631787;N:117127,130,,,,218476823,134111218,167891935,195631787,117127,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.88562,,0.27256,,0.79297,,0.51067,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77013,SRR25423069,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L001_R1_001.fastq.gz,fastq,145528460.0,5197445.0,GSM7660979 r2,0:28,A:38963827;C:36550891;G:30408548;T:39584512;N:20682,28,,,,38963827,36550891,30408548,39584512,20682,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00936,,0.00443,,0.98675,,0.35245,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77014,SRR25423070,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L001_R2_001.fastq.gz,fastq,675667850.0,5197445.0,GSM7660979 r3,0:130,A:208215940;C:128013993;G:151798676;T:187487780;N:151461,130,,,,208215940,128013993,151798676,187487780,151461,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.89748,,0.27631,,0.79064,,0.49734,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77015,SRR25423071,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L002_I1_001.fastq.gz,fastq,45134216.0,5641777.0,GSM7660979 r4,0:8,A:10035142;C:7986132;G:19502502;T:7387873;N:222567,8,,,,10035142,7986132,19502502,7387873,222567,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77016,SRR25423072,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L002_R1_001.fastq.gz,fastq,157969756.0,5641777.0,GSM7660979 r5,0:28,A:42059394;C:39433356;G:33728111;T:42718219;N:30676,28,,,,42059394,39433356,33728111,42718219,30676,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0132,,0.00877,,0.98829,,0.34149,,28,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77017,SRR25423073,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L002_R2_001.fastq.gz,fastq,733431010.0,5641777.0,GSM7660979 r6,0:130,A:222497848;C:136467931;G:175111806;T:199206848;N:146577,130,,,,222497848,136467931,175111806,199206848,146577,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.8786,,0.26704,,0.79433,,0.51215,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77018,SRR25423074,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L003_I1_001.fastq.gz,fastq,41837504.0,5229688.0,GSM7660979 r7,0:8,A:9528062;C:7341028;G:18072427;T:6806346;N:89641,8,,,,9528062,7341028,18072427,6806346,89641,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77019,SRR25423075,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L003_R1_001.fastq.gz,fastq,146431264.0,5229688.0,GSM7660979 r8,0:28,A:39246118;C:36825633;G:30475523;T:39867658;N:16332,28,,,,39246118,36825633,30475523,39867658,16332,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00821,,0.00344,,0.98703,,0.36121,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77020,SRR25423076,SRX21157893,SRS18420146,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,WT s1026 rep1 lane1 & lane2,GSM7660979,,source name:brain|tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1|geo loc name:missing|collection date:missing,WT s1026 rep1 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:s1026 transgenic line|cell type:neurons|genotype:WT|treatment:N1,GSM7660979,GSM7660979: WT s1026 rep1 lane1 & lane2; Danio rerio; RNA Seq,GSM7660979 r1,GSM7660979,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p154_S0_L003_R2_001.fastq.gz,fastq,679859440.0,5229688.0,GSM7660979 r9,0:130,A:210099119;C:129100730;G:151835050;T:188699403;N:125138,130,,,,210099119,129100730,151835050,188699403,125138,SRX21157893,SRS18420146,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.89817,,0.27686,,0.78839,,0.50029,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77021,SRR25423077,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L001_I1_001.fastq.gz,fastq,41558296.0,5194787.0,GSM7660978 r1,0:8,A:8653956;C:7501606;G:18389913;T:6889579;N:123242,8,,,,8653956,7501606,18389913,6889579,123242,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77022,SRR25423078,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L004_I1_001.fastq.gz,fastq,44153920.0,5519240.0,GSM7660978 r10,0:8,A:9112539;C:7989581;G:19589834;T:7272691;N:189275,8,,,,9112539,7989581,19589834,7272691,189275,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77023,SRR25423079,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L004_R1_001.fastq.gz,fastq,154538720.0,5519240.0,GSM7660978 r11,0:28,A:41768269;C:38565549;G:31995336;T:42189478;N:20088,28,,,,41768269,38565549,31995336,42189478,20088,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00832,,0.00399,,0.98802,,0.387,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77024,SRR25423080,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L004_R2_001.fastq.gz,fastq,717501200.0,5519240.0,GSM7660978 r12,0:130,A:223425289;C:128869376;G:157867154;T:204364748;N:2974633,130,,,,223425289,128869376,157867154,204364748,2974633,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.86456,,0.33873,,0.80712,,0.51252,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77025,SRR25423081,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L001_R1_001.fastq.gz,fastq,145454036.0,5194787.0,GSM7660978 r2,0:28,A:39325327;C:36299242;G:30079706;T:39733166;N:16595,28,,,,39325327,36299242,30079706,39733166,16595,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00777,,0.00372,,0.98912,,0.34306,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77026,SRR25423082,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L001_R2_001.fastq.gz,fastq,675322310.0,5194787.0,GSM7660978 r3,0:130,A:211915718;C:123090340;G:143012180;T:195734602;N:1569470,130,,,,211915718,123090340,143012180,195734602,1569470,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.87849,,0.34767,,0.80056,,0.50735,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77027,SRR25423083,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L002_I1_001.fastq.gz,fastq,44049120.0,5506140.0,GSM7660978 r4,0:8,A:8944566;C:7961128;G:19746021;T:7226687;N:170718,8,,,,8944566,7961128,19746021,7226687,170718,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77028,SRR25423084,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L002_R1_001.fastq.gz,fastq,154171920.0,5506140.0,GSM7660978 r5,0:28,A:41607797;C:38479559;G:31947188;T:42108428;N:28948,28,,,,41607797,38479559,31947188,42108428,28948,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0082,,0.0037,,0.98764,,0.36041,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77029,SRR25423085,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L002_R2_001.fastq.gz,fastq,715798200.0,5506140.0,GSM7660978 r6,0:130,A:220199429;C:127429364;G:164452265;T:202077008;N:1640134,130,,,,220199429,127429364,164452265,202077008,1640134,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.86141,,0.34092,,0.80892,,0.51636,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77030,SRR25423086,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L003_I1_001.fastq.gz,fastq,41701648.0,5212706.0,GSM7660978 r7,0:8,A:8699211;C:7482837;G:18518090;T:6841716;N:159794,8,,,,8699211,7482837,18518090,6841716,159794,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77031,SRR25423087,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L003_R1_001.fastq.gz,fastq,145955768.0,5212706.0,GSM7660978 r8,0:28,A:39432715;C:36411478;G:30250823;T:39840040;N:20712,28,,,,39432715,36411478,30250823,39840040,20712,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00842,,0.00384,,0.98746,,0.37644,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77032,SRR25423088,SRX21157892,SRS18420145,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep4 lane1 & lane2,GSM7660978,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep4 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660978,GSM7660978: lakritz HGn12C rep4 lane1 & lane2; Danio rerio; RNA Seq,GSM7660978 r1,GSM7660978,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p182_S0_L003_R2_001.fastq.gz,fastq,677651780.0,5212706.0,GSM7660978 r9,0:130,A:212834801;C:123716124;G:143169759;T:196419860;N:1511236,130,,,,212834801,123716124,143169759,196419860,1511236,SRX21157892,SRS18420145,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.87783,,0.34587,,0.80004,,0.50737,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77033,SRR25423089,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L001_I1_001.fastq.gz,fastq,28230536.0,3528817.0,GSM7660977 r1,0:8,A:5846993;C:4500398;G:13413679;T:4284440;N:185026,8,,,,5846993,4500398,13413679,4284440,185026,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77034,SRR25423090,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L004_I1_001.fastq.gz,fastq,29841512.0,3730189.0,GSM7660977 r10,0:8,A:5996183;C:4745155;G:14573475;T:4491992;N:34707,8,,,,5996183,4745155,14573475,4491992,34707,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77035,SRR25423091,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L004_R1_001.fastq.gz,fastq,104445292.0,3730189.0,GSM7660977 r11,0:28,A:27569833;C:25852975;G:23011555;T:27996654;N:14275,28,,,,27569833,25852975,23011555,27996654,14275,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.028,,0.02215,,0.98616,,0.37606,,28,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77036,SRR25423092,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L004_R2_001.fastq.gz,fastq,484924570.0,3730189.0,GSM7660977 r12,0:130,A:146960114;C:85137895;G:117712649;T:135019012;N:94900,130,,,,146960114,85137895,117712649,135019012,94900,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.8426,,0.343,,0.80904,,0.51553,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77037,SRR25423093,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L001_R1_001.fastq.gz,fastq,98806876.0,3528817.0,GSM7660977 r2,0:28,A:26486103;C:24902412;G:20399917;T:26995262;N:23182,28,,,,26486103,24902412,20399917,26995262,23182,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00972,,0.00476,,0.9867,,0.37988,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77038,SRR25423094,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L001_R2_001.fastq.gz,fastq,458746210.0,3528817.0,GSM7660977 r3,0:130,A:142756416;C:83435608;G:99381174;T:132821566;N:351446,130,,,,142756416,83435608,99381174,132821566,351446,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.87492,,0.35523,,0.8005,,0.51302,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77039,SRR25423095,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L002_I1_001.fastq.gz,fastq,29813552.0,3726694.0,GSM7660977 r4,0:8,A:6023894;C:4790724;G:14323297;T:4511397;N:164240,8,,,,6023894,4790724,14323297,4511397,164240,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77040,SRR25423096,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L002_R1_001.fastq.gz,fastq,104347432.0,3726694.0,GSM7660977 r5,0:28,A:27972757;C:26292261;G:21550202;T:28495595;N:36617,28,,,,27972757,26292261,21550202,28495595,36617,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00972,,0.0048,,0.98642,,0.38768,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77041,SRR25423097,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L002_R2_001.fastq.gz,fastq,484470220.0,3726694.0,GSM7660977 r6,0:130,A:148967159;C:86626052;G:111069442;T:137592736;N:214831,130,,,,148967159,86626052,111069442,137592736,214831,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.8627,,0.3511,,0.80537,,0.51342,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77042,SRR25423098,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L003_I1_001.fastq.gz,fastq,27884800.0,3485600.0,GSM7660977 r7,0:8,A:5814876;C:4428196;G:13359658;T:4213922;N:68148,8,,,,5814876,4428196,13359658,4213922,68148,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77043,SRR25423099,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L003_R1_001.fastq.gz,fastq,97596800.0,3485600.0,GSM7660977 r8,0:28,A:26153650;C:24561941;G:20253854;T:26610923;N:16432,28,,,,26153650,24561941,20253854,26610923,16432,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.01092,,0.00601,,0.9865,,0.37684,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77044,SRR25423100,SRX21157891,SRS18420144,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane3 & lane4,GSM7660977,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane3 & lane4,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660977,GSM7660977: lakritz HGn12C rep3 lane3 & lane4; Danio rerio; RNA Seq,GSM7660977 r1,GSM7660977,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p171_S0_L003_R2_001.fastq.gz,fastq,453128000.0,3485600.0,GSM7660977 r9,0:130,A:140968028;C:82271283;G:99033183;T:130715848;N:139658,130,,,,140968028,82271283,99033183,130715848,139658,SRX21157891,SRS18420144,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.87275,,0.3559,,0.80182,,0.51746,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77045,SRR25423101,SRX21157890,SRS18420143,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane1 & lane2,GSM7660976,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660976,GSM7660976: lakritz HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660976 r1,GSM7660976,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p170_S0_L001_I1_001.fastq.gz,fastq,29787544.0,3723443.0,GSM7660976 r1,0:8,A:6291781;C:4754023;G:14140176;T:4509077;N:92487,8,,,,6291781,4754023,14140176,4509077,92487,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77046,SRR25423102,SRX21157890,SRS18420143,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane1 & lane2,GSM7660976,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660976,GSM7660976: lakritz HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660976 r1,GSM7660976,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p170_S0_L004_I1_001.fastq.gz,fastq,31294328.0,3911791.0,GSM7660976 r10,0:8,A:6592572;C:5083904;G:14754028;T:4819225;N:44599,8,,,,6592572,5083904,14754028,4819225,44599,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",,,,,,,,,,,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77047,SRR25423103,SRX21157890,SRS18420143,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane1 & lane2,GSM7660976,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660976,GSM7660976: lakritz HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660976 r1,GSM7660976,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p170_S0_L004_R1_001.fastq.gz,fastq,109530148.0,3911791.0,GSM7660976 r11,0:28,A:29597133;C:27430169;G:22526281;T:29958507;N:18058,28,,,,29597133,27430169,22526281,29958507,18058,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00894,,0.00415,,0.98735,,0.40096,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77048,SRR25423104,SRX21157890,SRS18420143,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane1 & lane2,GSM7660976,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660976,GSM7660976: lakritz HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660976 r1,GSM7660976,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p170_S0_L004_R2_001.fastq.gz,fastq,508532830.0,3911791.0,GSM7660976 r12,0:130,A:159207324;C:90927654;G:114226247;T:144088377;N:83228,130,,,,159207324,90927654,114226247,144088377,83228,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.86494,,0.35089,,0.80965,,0.50948,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77049,SRR25423105,SRX21157890,SRS18420143,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane1 & lane2,GSM7660976,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660976,GSM7660976: lakritz HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660976 r1,GSM7660976,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p170_S0_L001_R1_001.fastq.gz,fastq,104256404.0,3723443.0,GSM7660976 r2,0:28,A:28240149;C:26091346;G:21397649;T:28513954;N:13306,28,,,,28240149,26091346,21397649,28513954,13306,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.00927,,0.00429,,0.98701,,0.38362,,28,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77050,SRR25423106,SRX21157890,SRS18420143,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane1 & lane2,GSM7660976,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660976,GSM7660976: lakritz HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660976 r1,GSM7660976,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p170_S0_L001_R2_001.fastq.gz,fastq,484047590.0,3723443.0,GSM7660976 r3,0:130,A:153076719;C:87852215;G:103323528;T:139733266;N:61862,130,,,,153076719,87852215,103323528,139733266,61862,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.87385,,0.3547,,0.80397,,0.51066,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77051,SRR25423107,SRX21157890,SRS18420143,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane1 & lane2,GSM7660976,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660976,GSM7660976: lakritz HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660976 r1,GSM7660976,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p170_S0_L002_I1_001.fastq.gz,fastq,31052016.0,3881502.0,GSM7660976 r4,0:8,A:6427800;C:4967419;G:14857276;T:4682418;N:117103,8,,,,6427800,4967419,14857276,4682418,117103,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77052,SRR25423108,SRX21157890,SRS18420143,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane1 & lane2,GSM7660976,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660976,GSM7660976: lakritz HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660976 r1,GSM7660976,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p170_S0_L002_R1_001.fastq.gz,fastq,108682056.0,3881502.0,GSM7660976 r5,0:28,A:29226161;C:27023100;G:22866742;T:29528967;N:37086,28,,,,29226161,27023100,22866742,29528967,37086,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.01532,,0.0104,,0.98768,,0.39479,,28,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System
77053,SRR25423109,SRX21157890,SRS18420143,SRP451428,PRJNA998413,Retina derived signals control pace of neurogenesis in visual brain areas but not circuit configuration,GSE238240,Transcriptome Analysis,Brain development is orchestrated by both innate and experience dependent mechanisms  but their relative contributions are often difficult to resolve. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum  thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated  the complete set of 77 neuronal types develops in apparently normal proportions  at normal locations  and along normal differentiation trajectories. Strikingly  the cell cycle exits of proliferating progenitors in these areas are delayed  and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion  we show that signals emitted by retinal axons influence the pace of neurogenesis in visual areas  but do not detectably affect the specification or wiring of downstream neurons. Overall design: TgHGn12C:GFP or [TgGal4s1026t X TgUAS:GFP] larvae were sorted for GFP expression 24 hpf All single cell experiments were performed at 6 dpf To obtain unrelated WT  pigmented larvae were used from TgHGn12C:GFP pigmented males or females crossed with WT TLN  which are homozygous mutant for mitfa. To obtain lakritz mutant and sibling WT larvae  TgHGn12C:GFP lakritz heterozygous adults were crossed with adult lakritz heterozygous. For experiments with lakritz larvae  only lakritz mutants were collected; for other experiments  they were discarded. For single cell experiments larvae were rapidly decapitated and processed for cell dissociation followed by FACS of labelled cells.,,pubmed:37758715,,lakritz HGn12C rep3 lane1 & lane2,GSM7660976,,source name:brain|tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1|geo loc name:missing|collection date:missing,lakritz HGn12C rep3 lane1 & lane2,Standard cellRanger alignment and filtering processed data files are output files from cellranger used for analysis in single cell sequencing pipelines Assembly: GRCz11 Supplementary files format and content: Standard 10x genomics cellranger output,brain,,Cell dissociation 10X genomics,,tissue:brain|cell line:HGn12C transgenic line|cell type:neurons|genotype:lakritz|treatment:N1,GSM7660976,GSM7660976: lakritz HGn12C rep3 lane1 & lane2; Danio rerio; RNA Seq,GSM7660976 r1,GSM7660976,1,Cell dissociation 10X genomics,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP451428,,,p170_S0_L002_R2_001.fastq.gz,fastq,504595260.0,3881502.0,GSM7660976 r6,0:130,A:156874723;C:89614357;G:115903779;T:142154131;N:48270,130,,,,156874723,89614357,115903779,142154131,48270,SRX21157890,SRS18420143,SRA1679726,"Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence","Baier, Genes - Circuits - Behavior, Max Planck Institute for Biological Intelligence",1,0.85688,,0.34647,,0.80915,,0.51666,,130,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Germany,2023-07-25,Undetermined,Larval,Brain,Nervous System