run_metadata
888 rows where devstage_curation = "Adult" and technology = "10x"
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| Link | 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 |
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| 9166 | 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 … | 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. B… | 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 | 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 … | 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. B… | 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 | 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 … | 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. B… | 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 | 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 … | 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. B… | 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 | |||||||||||||||||||
| 10163 | 10163 | ERR5714657 | ERX5430029 | ERS6251768 | ERP128324 | PRJEB44291 | Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows | E-MTAB-10360 | Transcriptome Analysis | Macrophage colony stimulating factor receptor M CSFR/CSF1R signaling is crucial for the differentiation proliferation and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human related diseases. Here we investigate the roles of zebrafish csf1ra and csf1rb in adult myelopoiesis using single cell RNA sequencing. Our analysis of adult whole kidney marrow WKM hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease mostly in cancerogenesis. | ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14 | Protocols: Whole kidney marrow was collected from 6 mpf zebrafish wt csf1raΔ5bp or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1 16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1 16 rxns PN 1000121 was used for library preparation. | WT | SAMEA8567093 | Institute of Molecular Genetics of the Czech Academy of Sciences | ENA first public:2021 04 24|ENA last update:2021 04 14|External Id:SAMEA8567093|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 04 24T00:22:33Z|INSDC last update:2021 04 14T14:09:18Z|INSDC status:public|Submitter Id:E MTAB 10360:WT|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:head kidney|sample name:E MTAB 10360:WT|strain:AB | NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows | E MTAB 10360:WT p | WT p | Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows | Whole kidney marrow was collected from 6 mpf zebrafish wt csf1raΔ5bp or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1 16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1 16 rxns PN 1000121 was used for library preparation. | Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | PAIRED | ILLUMINA | NextSeq 500 | ERP128324 | NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows | ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14 | WT.bam | bam | 1041394032.0 | 18596322.0 | E MTAB 10360:WT | 0:56 | A:284652376;C:244349479;G:255850754;T:255536179;N:1005244 | 56 | 284652376 | 244349479 | 255850754 | 255536179 | 1005244 | ERX5430029 | ERS6251768 | ERA3959104 | Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive | Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive | 1 | 0.9192 | 0.10547 | 0.84782 | 0.53778 | 56 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Czech Republic | 2021-04-14 | Adult | Adult | Multi-tissue | Multi-system | ||||||||||||||||||||
| 10164 | 10164 | ERR5714656 | ERX5430028 | ERS6251767 | ERP128324 | PRJEB44291 | Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows | E-MTAB-10360 | Transcriptome Analysis | Macrophage colony stimulating factor receptor M CSFR/CSF1R signaling is crucial for the differentiation proliferation and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human related diseases. Here we investigate the roles of zebrafish csf1ra and csf1rb in adult myelopoiesis using single cell RNA sequencing. Our analysis of adult whole kidney marrow WKM hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease mostly in cancerogenesis. | ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14 | Protocols: Whole kidney marrow was collected from 6 mpf zebrafish wt csf1raΔ5bp or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1 16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1 16 rxns PN 1000121 was used for library preparation. | Rb | SAMEA8567092 | Institute of Molecular Genetics of the Czech Academy of Sciences | ENA first public:2021 04 24|ENA last update:2021 04 14|External Id:SAMEA8567092|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 04 24T00:22:33Z|INSDC last update:2021 04 14T14:09:18Z|INSDC status:public|Submitter Id:E MTAB 10360:Rb|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:csf1rb4bp|organism part:head kidney|sample name:E MTAB 10360:Rb|strain:AB | NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows | E MTAB 10360:Rb p | Rb p | Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows | Whole kidney marrow was collected from 6 mpf zebrafish wt csf1raΔ5bp or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1 16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1 16 rxns PN 1000121 was used for library preparation. | Experimental Factor: genotype:csf1rb4bp | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | PAIRED | ILLUMINA | NextSeq 500 | ERP128324 | NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows | ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14 | Rb.bam | bam | 1069920824.0 | 19105729.0 | E MTAB 10360:Rb | 0:56 | A:299856824;C:238947539;G:256649537;T:273433744;N:1033180 | 56 | 299856824 | 238947539 | 256649537 | 273433744 | 1033180 | ERX5430028 | ERS6251767 | ERA3959104 | Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive | Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive | 1 | 0.94145 | 0.11133 | 0.83191 | 0.52892 | 56 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Czech Republic | 2021-04-14 | Adult | Adult | Multi-tissue | Multi-system | ||||||||||||||||||||
| 10165 | 10165 | ERR5714655 | ERX5430027 | ERS6251766 | ERP128324 | PRJEB44291 | Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows | E-MTAB-10360 | Transcriptome Analysis | Macrophage colony stimulating factor receptor M CSFR/CSF1R signaling is crucial for the differentiation proliferation and survival of myeloid cells. Therapeutic targeting of the CSF1R pathway is a promising strategy in many human diseases including neurological disorders or cancer. Zebrafish are commonly used for human disease modeling and preclinical therapeutic screening. Therefore it is necessary to understand the proper function of cytokine signaling in zebrafish to reliably model human related diseases. Here we investigate the roles of zebrafish csf1ra and csf1rb in adult myelopoiesis using single cell RNA sequencing. Our analysis of adult whole kidney marrow WKM hematopoietic cells suggests that csf1rb is expressed mainly by blood and myeloid progenitors and that the expression of csf1ra and csf1rb is non overlapping. We point out differentially expressed genes important in hematopoietic cell differentiation and immune response in selected WKM populations. Our findings could improve the understanding of myeloid cell function and lead to the further study of CSF1R pathway deregulation in disease mostly in cancerogenesis. | ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14 | Protocols: Whole kidney marrow was collected from 6 mpf zebrafish wt csf1raΔ5bp or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1 16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1 16 rxns PN 1000121 was used for library preparation. | Ra | SAMEA8567091 | Institute of Molecular Genetics of the Czech Academy of Sciences | ENA first public:2021 04 24|ENA last update:2021 04 14|External Id:SAMEA8567091|INSDC center alias:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC center name:Institute of Molecular Genetics of the Czech Academy of Sciences|INSDC first public:2021 04 24T00:22:33Z|INSDC last update:2021 04 14T14:09:18Z|INSDC status:public|Submitter Id:E MTAB 10360:Ra|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:csf1ra5bp|organism part:head kidney|sample name:E MTAB 10360:Ra|strain:AB | NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows | E MTAB 10360:Ra p | Ra p | Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows | Whole kidney marrow was collected from 6 mpf zebrafish wt csf1raΔ5bp or csf1rbΔ4bp mutant zebrafish animals. Kidney marrow tissue was dissociated by pipetting washed once with PBS and fractionated using Ficoll Hypaque/Biocoll density 1.077 g/ml centrifugation at 500g for 10 minutes to remove unwanted mature erythrocytes and dead cells. Further total cell concentration and viability were determined using a TC20 Automated Cell Counter Bio Rad. Samples were then resuspended in 1XPBS with 10% BSA at a concentration between 800 3000 per ml and loaded on the 10XChromium system. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1 16 rxns PN 1000121 was used for library preparation. Samples were loaded on the 10x Chromium system with a target of 4 000 cells. Chromium Single Cell 3ʹ GEM Library & Gel Bead Kit v3.1 16 rxns PN 1000121 was used for library preparation. | Experimental Factor: genotype:csf1ra5bp | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | Oligo-dT | PAIRED | ILLUMINA | NextSeq 500 | ERP128324 | NextSeq 500 paired end sequencing; Single cell RNA seq 10x Chromium V3 of zebrafish csf1ra and csf1rb mutant whole kidney marrows | ENA FIRST PUBLIC:2021 04 24|ENA LAST UPDATE:2021 04 14 | Ra.bam | bam | 1009240400.0 | 18022150.0 | E MTAB 10360:Ra | 0:56 | A:279849736;C:230130588;G:247312130;T:250994600;N:953346 | 56 | 279849736 | 230130588 | 247312130 | 250994600 | 953346 | ERX5430027 | ERS6251766 | ERA3959104 | Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive | Institute of Molecular Genetics of the Czech Academy of Sciences|European Nucleotide Archive | 1 | 0.95705 | 0.10915 | 0.84788 | 0.47011 | 56 | B | usable mapping rate | illumina | nextseq | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Czech Republic | 2021-04-14 | Adult | Adult | Multi-tissue | Multi-system | ||||||||||||||||||||
| 10166 | 10166 | ERR5762357 | ERX5471113 | ERS6291553 | ERP128548 | PRJEB44492 | scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish | E-MTAB-10370 | Transcriptome Analysis | GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice its role during adult hematopoiesis is incompletely understood. In zebrafish mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs. | ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2. | wt2 gata2b | SAMEA8606934 | Erasmus Medical Center | ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606934|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:wt2 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:wt2 gata2b|sampling site:kidney marrow|sex:female|strain:AB | Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish | E MTAB 10370:wt2 gata2b p | wt2 gata2b p | scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2. | Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP128548 | Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish | ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09 | wt2_gata2b.bam | bam | 25266437196.0 | 277653156.0 | E MTAB 10370:wt2 gata2b | 0:91 | A:7555470312;C:5144518052;G:5682746714;T:6882396490;N:1305628 | 91 | 7555470312 | 5144518052 | 5682746714 | 6882396490 | 1305628 | ERX5471113 | ERS6291553 | ERA4089475 | Erasmus Medical Center|European Nucleotide Archive | Erasmus Medical Center|European Nucleotide Archive | 1 | 0.90876 | 0.18424 | 0.84017 | 0.55508 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Netherlands | 2022-04-09 | Adult | Adult | Kidney | Renal System | ||||||||||||||||||||
| 10167 | 10167 | ERR5762356 | ERX5471112 | ERS6291552 | ERP128548 | PRJEB44492 | scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish | E-MTAB-10370 | Transcriptome Analysis | GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice its role during adult hematopoiesis is incompletely understood. In zebrafish mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs. | ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2. | wt1 gata2b | SAMEA8606933 | Erasmus Medical Center | ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606933|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:wt1 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:wt1 gata2b|sampling site:kidney marrow|sex:female|strain:AB | Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish | E MTAB 10370:wt1 gata2b p | wt1 gata2b p | scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2. | Experimental Factor: genotype:wild type genotype | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP128548 | Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish | ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09 | wt1_gata2b.bam | bam | 36376708095.0 | 399744045.0 | E MTAB 10370:wt1 gata2b | 0:91 | A:10397161431;C:8128518427;G:8799445454;T:9049686061;N:1896722 | 91 | 10397161431 | 8128518427 | 8799445454 | 9049686061 | 1896722 | ERX5471112 | ERS6291552 | ERA4089475 | Erasmus Medical Center|European Nucleotide Archive | Erasmus Medical Center|European Nucleotide Archive | 1 | 0.94708 | 0.08938 | 0.85449 | 0.52917 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Netherlands | 2022-04-09 | Adult | Adult | Kidney | Renal System | ||||||||||||||||||||
| 10168 | 10168 | ERR5762355 | ERX5471111 | ERS6291551 | ERP128548 | PRJEB44492 | scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish | E-MTAB-10370 | Transcriptome Analysis | GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice its role during adult hematopoiesis is incompletely understood. In zebrafish mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs. | ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2. | hom2 gata2b | SAMEA8606932 | Erasmus Medical Center | ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606932|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:hom2 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:gata2b / |isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:hom2 gata2b|sampling site:kidney marrow|sex:female|strain:AB | Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish | E MTAB 10370:hom2 gata2b p | hom2 gata2b p | scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2. | Experimental Factor: genotype:gata2b / | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP128548 | Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish | ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09 | hom2_gata2b.bam | bam | 22416887402.0 | 246339422.0 | E MTAB 10370:hom2 gata2b | 0:91 | A:6732382430;C:4540586585;G:4933684272;T:6209137814;N:1096301 | 91 | 6732382430 | 4540586585 | 4933684272 | 6209137814 | 1096301 | ERX5471111 | ERS6291551 | ERA4089475 | Erasmus Medical Center|European Nucleotide Archive | Erasmus Medical Center|European Nucleotide Archive | 1 | 0.91306 | 0.21566 | 0.83469 | 0.53782 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Netherlands | 2022-04-09 | Adult | Adult | Kidney | Renal System | ||||||||||||||||||||
| 10169 | 10169 | ERR5762354 | ERX5471110 | ERS6291550 | ERP128548 | PRJEB44492 | scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish | E-MTAB-10370 | Transcriptome Analysis | GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice its role during adult hematopoiesis is incompletely understood. In zebrafish mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs. | ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2. | hom1 gata2b | SAMEA8606931 | Erasmus Medical Center | ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606931|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:hom1 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:gata2b / |isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:hom1 gata2b|sampling site:kidney marrow|sex:female|strain:AB | Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish | E MTAB 10370:hom1 gata2b p | hom1 gata2b p | scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2. | Experimental Factor: genotype:gata2b / | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP128548 | Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish | ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09 | hom1_gata2b.bam | bam | 18004290759.0 | 197849349.0 | E MTAB 10370:hom1 gata2b | 0:91 | A:5232521408;C:3876317502;G:4287902596;T:4606191653;N:1357600 | 91 | 5232521408 | 3876317502 | 4287902596 | 4606191653 | 1357600 | ERX5471110 | ERS6291550 | ERA4089475 | Erasmus Medical Center|European Nucleotide Archive | Erasmus Medical Center|European Nucleotide Archive | 1 | 0.94131 | 0.08871 | 0.83465 | 0.52792 | 91 | B | usable mapping rate | illumina | novaseq_era | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | Netherlands | 2022-04-09 | Adult | Adult | Kidney | Renal System | ||||||||||||||||||||
| 10403 | 10403 | ERR8527374 | ERX8137561 | ERS10539829 | ERP135430 | PRJEB50826 | scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | E-MTAB-11079_2 | Transcriptome Analysis | Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted from pooled kidneys of ren+/+ or ren / zebrafish which carried ren:RFP and acta2:EGFP reporter genes allowing the isolation of renin expressing cells and smooth muscle cells. | ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 | Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. | ZF2 | SAMEA12941033 | University Of Edinburgh | ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941033|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF2|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP; ren / |individual:9 12 kidneys pooled|inferred cell type:recruited RLC|organism part:kidney|phenotype:ren knockout|sample name:E MTAB 11079 2:ZF2|sex:mixed|strain:WIK | NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | E MTAB 11079 2:ZF2 p | ZF2 p | scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. | Experimental Factor: phenotype:ren knockout | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | size fractionation | PAIRED | ILLUMINA | NextSeq 500 | ERP135430 | NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 | ZF2_S2_L002_I1_001.fastq.gz ZF2_S2_L002_R1_001.fastq.gz ZF2_S2_L002_R2_001.fastq.gz | fastq fastq fastq | 38557081640.0 | 125185330.0 | E MTAB 11079 2:ZF2 S2 L002 | 0:8 1:150 2:150 | A:13781315856;C:6436030786;G:6578059630;T:10759631611;N:561117 | 8 | 150 | 150 | 13781315856 | 6436030786 | 6578059630 | 10759631611 | 561117 | ERX8137561 | ERS10539829 | ERA9016154 | University Of Edinburgh|European Nucleotide Archive | University Of Edinburgh|European Nucleotide Archive | 2 | 0.0 | 0.84449 | 0.0 | 0.09657 | 1.0 | 0.8242 | 0.52635 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | size_fractionation | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2022-06-10 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 10404 | 10404 | ERR8527377 | ERX8137561 | ERS10539829 | ERP135430 | PRJEB50826 | scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | E-MTAB-11079_2 | Transcriptome Analysis | Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted from pooled kidneys of ren+/+ or ren / zebrafish which carried ren:RFP and acta2:EGFP reporter genes allowing the isolation of renin expressing cells and smooth muscle cells. | ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 | Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. | ZF2 | SAMEA12941033 | University Of Edinburgh | ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941033|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF2|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP; ren / |individual:9 12 kidneys pooled|inferred cell type:recruited RLC|organism part:kidney|phenotype:ren knockout|sample name:E MTAB 11079 2:ZF2|sex:mixed|strain:WIK | NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | E MTAB 11079 2:ZF2 p | ZF2 p | scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. | Experimental Factor: phenotype:ren knockout | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | size fractionation | PAIRED | ILLUMINA | NextSeq 500 | ERP135430 | NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 | ZF2_S2_L001_I1_001.fastq.gz ZF2_S2_L001_R1_001.fastq.gz ZF2_S2_L001_R2_001.fastq.gz | fastq fastq fastq | 38872269128.0 | 126208666.0 | E MTAB 11079 2:ZF2 S2 L001 | 0:8 1:150 2:150 | A:15151865400;C:6355030057;G:6591732598;T:9763441371;N:530374 | 8 | 150 | 150 | 15151865400 | 6355030057 | 6591732598 | 9763441371 | 530374 | ERX8137561 | ERS10539829 | ERA9016154 | University Of Edinburgh|European Nucleotide Archive | University Of Edinburgh|European Nucleotide Archive | 2 | 0.0 | 0.84526 | 0.0 | 0.09779 | 1.0 | 0.82609 | 0.54388 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | size_fractionation | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2022-06-10 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 10405 | 10405 | ERR8527376 | ERX8137560 | ERS10539828 | ERP135430 | PRJEB50826 | scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | E-MTAB-11079_2 | Transcriptome Analysis | Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted from pooled kidneys of ren+/+ or ren / zebrafish which carried ren:RFP and acta2:EGFP reporter genes allowing the isolation of renin expressing cells and smooth muscle cells. | ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 | Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. | ZF1 | SAMEA12941032 | University Of Edinburgh | ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941032|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF1|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP|individual:9 12 kidneys pooled|inferred cell type:juxtaglomerular cell|organism part:kidney|phenotype:wild type|sample name:E MTAB 11079 2:ZF1|sex:mixed|strain:WIK | NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | E MTAB 11079 2:ZF1 p | ZF1 p | scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. | Experimental Factor: phenotype:wild type | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | size fractionation | PAIRED | ILLUMINA | NextSeq 500 | ERP135430 | NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 | ZF1_S1_L002_I1_001.fastq.gz ZF1_S1_L002_R1_001.fastq.gz ZF1_S1_L002_R2_001.fastq.gz | fastq fastq fastq | 39415722500.0 | 127973125.0 | E MTAB 11079 2:ZF1 S1 L002 | 0:8 1:150 2:150 | A:14261012964;C:6339158428;G:6467430919;T:11323758989;N:576200 | 8 | 150 | 150 | 14261012964 | 6339158428 | 6467430919 | 11323758989 | 576200 | ERX8137560 | ERS10539828 | ERA9016154 | University Of Edinburgh|European Nucleotide Archive | University Of Edinburgh|European Nucleotide Archive | 2 | 0.0 | 0.81065 | 0.0 | 0.08289 | 1.0 | 0.82434 | 0.52903 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | size_fractionation | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2022-06-10 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 10406 | 10406 | ERR8527375 | ERX8137560 | ERS10539828 | ERP135430 | PRJEB50826 | scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | E-MTAB-11079_2 | Transcriptome Analysis | Libraries were made to compare the transcriptome of renin lineage cells RLCs from wild type versus ren knockout zebrafish kidneys. RLCs were FAC sorted from pooled kidneys of ren+/+ or ren / zebrafish which carried ren:RFP and acta2:EGFP reporter genes allowing the isolation of renin expressing cells and smooth muscle cells. | ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 | Protocols: Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. | ZF1 | SAMEA12941032 | University Of Edinburgh | ENA first public:2022 06 10|ENA last update:2022 06 10|External Id:SAMEA12941032|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2022 06 10T00:18:52Z|INSDC last update:2022 06 10T00:18:52Z|INSDC status:public|Submitter Id:E MTAB 11079 2:ZF1|age:6|broker name:ArrayExpress|cell type:renin lineage cell|common name:zebrafish|developmental stage:adult|genotype:ren:RFP; acta2:EGFP|individual:9 12 kidneys pooled|inferred cell type:juxtaglomerular cell|organism part:kidney|phenotype:wild type|sample name:E MTAB 11079 2:ZF1|sex:mixed|strain:WIK | NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | E MTAB 11079 2:ZF1 p | ZF1 p | scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | Mesonephric kidneys were isolated into ice cold Leibowitz medium. Cells were dissociated in medium supplemented with cold activated protease 20mg/ml DNAse 400units/ml Liberase 0.085mg/ml collagenase 2mg/ml and CaCl2 5mM at 6oC for 20 mins with frequent triturition. Samples were transferred to 28.5oC for an additional 10 mins to complete digestion. Digested kidneys were passed through a 40micron sieve prior to centrifugation. Cells were resuspended in PBS with 2% FCS for FAC sorting. A WIK mesonephric kidney was used to control for autofluorescence and DAPI was used for the live/dead cell count. Samples were sorted for red and green fluorescence in order to sort renin expressing cells and smooth muscle cells respectively. Zebrafish were terminally anaesthetised tricaine methanesulphonate; MS 222 and decapitated. Lower abdomen was removed to expose kidney which was carefully teased away from the spine. Zebrafish were maintained in a Home Office approved establishment at 28.5oC under standard feeding and light regimen. Renin gene was targetted using CRISPR Cas9 technology. Briefly an sgRNA specifically targeting exon 2 of the renin gene was complexed with tracr RNA and Cas9 protein and injected into a one cell embryo. Surviving fish were genotyped by tail clip and targeted fish were crossed onto WIKs. The genotype of F1 progeny was determined by sequencing across the target site and fish heterozygous for an 8bp deletion in renin exon 2 were crossed to generate ren / knockout fish. Nucleic acid was extracted using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. Nucleic acid library was constructed using the Chromium Single Cell three prime Library and Gel Bead kit v2 10X Genomics PN 120237 and the Chromium Single Cell A Chip kit 10X Genomics PN 120236 according to manufacturers instructions. | Experimental Factor: phenotype:wild type | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | size fractionation | PAIRED | ILLUMINA | NextSeq 500 | ERP135430 | NextSeq 500 paired end sequencing; scRNAseq libraries of pooled kidney samples from wild type ZF1 versus CRISPR targeted renin knockout ZF2 zebrafish | ENA FIRST PUBLIC:2022 06 10|ENA LAST UPDATE:2022 06 10 | ZF1_S1_L001_I1_001.fastq.gz ZF1_S1_L001_R1_001.fastq.gz ZF1_S1_L001_R2_001.fastq.gz | fastq fastq fastq | 39744721324.0 | 129041303.0 | E MTAB 11079 2:ZF1 S1 L001 | 0:8 1:150 2:150 | A:15670316830;C:6278039908;G:6505806971;T:10257683184;N:544007 | 8 | 150 | 150 | 15670316830 | 6278039908 | 6505806971 | 10257683184 | 544007 | ERX8137560 | ERS10539828 | ERA9016154 | University Of Edinburgh|European Nucleotide Archive | University Of Edinburgh|European Nucleotide Archive | 2 | 0.0 | 0.81031 | 0.0 | 0.08495 | 1.0 | 0.82169 | 0.51724 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | size_fractionation | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2022-06-10 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||
| 11017 | 11017 | ERR9750937 | ERX9298876 | ERS12023662 | ERP137743 | PRJEB52989 | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E-MTAB-10643 | Transcriptome Analysis | Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells. | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Expt 2 Uninjured | SAMEA14418104 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France. | ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418104|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 2 Uninjured|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:heart|sample name:E MTAB 10643:Expt 2 Uninjured|sex:male|strain:AB | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E MTAB 10643:Expt 2 Uninjured p | Expt 2 Uninjured p | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Experimental Factor: injury:n1|Experimental Factor: treatment:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | ERP137743 | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | E2_Uninjured_S2_L002_I1_001.fastq.gz E2_Uninjured_S2_L002_I2_001.fastq.gz E2_Uninjured_S2_L002_R1_001.fastq.gz E2_Uninjured_S2_L002_R2_001.fastq.gz | fastq fastq fastq fastq | 9325673775.0 | 69079065.0 | E MTAB 10643:Expt 2 Uninjured | 0:10 1:10 2:28 3:87 | A:1619571910;C:1420805235;G:1471531128;T:1496998088;N:972294 | 10 | 10 | 28 | 87 | 1619571910 | 1420805235 | 1471531128 | 1496998088 | 972294 | ERX9298876 | ERS12023662 | ERA14538536 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | 1 | 0.93798 | 0.11364 | 0.84843 | 0.53531 | 87 | B | usable mapping rate | illumina | novaseq_era | 3prime | poly_a | unknown | sc | single_cell_droplet | 10x | France | 2022-05-20 | Adult | Adult | Heart | Cardiovascular System | |||||||||||||||||
| 11018 | 11018 | ERR9750936 | ERX9298875 | ERS12023661 | ERP137743 | PRJEB52989 | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E-MTAB-10643 | Transcriptome Analysis | Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells. | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Expt 2 Sham | SAMEA14418103 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France. | ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418103|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 2 Sham|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:sham surgery|organism part:heart|sample name:E MTAB 10643:Expt 2 Sham|sex:male|strain:AB | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E MTAB 10643:Expt 2 Sham p | Expt 2 Sham p | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Experimental Factor: injury:sham surgery|Experimental Factor: time:3|Experimental Factor: treatment:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | ERP137743 | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | E2_Sham_S1_L002_I1_001.fastq.gz E2_Sham_S1_L002_I2_001.fastq.gz E2_Sham_S1_L002_R1_001.fastq.gz E2_Sham_S1_L002_R2_001.fastq.gz | fastq fastq fastq fastq | 11328674040.0 | 83916104.0 | E MTAB 10643:Expt 2 Sham | 0:10 1:10 2:28 3:87 | A:1955327720;C:1746332187;G:1777122701;T:1820705338;N:1213102 | 10 | 10 | 28 | 87 | 1955327720 | 1746332187 | 1777122701 | 1820705338 | 1213102 | ERX9298875 | ERS12023661 | ERA14538536 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | 1 | 0.92847 | 0.09981 | 0.85707 | 0.46947 | 87 | B | usable mapping rate | illumina | novaseq_era | 3prime | poly_a | unknown | sc | single_cell_droplet | 10x | France | 2022-05-20 | Adult | Adult | Heart | Cardiovascular System | |||||||||||||||||
| 11019 | 11019 | ERR9750935 | ERX9298874 | ERS12023660 | ERP137743 | PRJEB52989 | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E-MTAB-10643 | Transcriptome Analysis | Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells. | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Expt 2 3d post amputation | SAMEA14418102 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France. | ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418102|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 2 3d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 2 3d post amputation|sex:male|strain:AB | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E MTAB 10643:Expt 2 3d post amputation p | Expt 2 3d post amputation p | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:3|Experimental Factor: treatment:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | ERP137743 | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | E2_3dpa_S3_L002_I1_001.fastq.gz E2_3dpa_S3_L002_I2_001.fastq.gz E2_3dpa_S3_L002_R1_001.fastq.gz E2_3dpa_S3_L002_R2_001.fastq.gz | fastq fastq fastq fastq | 16111486440.0 | 119344344.0 | E MTAB 10643:Expt 2 3d post amputation | 0:10 1:10 2:28 3:87 | A:2610144058;C:2617445332;G:2496763759;T:2656876552;N:1728227 | 10 | 10 | 28 | 87 | 2610144058 | 2617445332 | 2496763759 | 2656876552 | 1728227 | ERX9298874 | ERS12023660 | ERA14538536 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | 1 | 0.94868 | 0.07071 | 0.89221 | 0.54333 | 87 | B | usable mapping rate | illumina | novaseq_era | 3prime | poly_a | unknown | sc | single_cell_droplet | 10x | France | 2022-05-20 | Adult | Adult | Heart | Cardiovascular System | |||||||||||||||||
| 11020 | 11020 | ERR9750934 | ERX9298873 | ERS12023659 | ERP137743 | PRJEB52989 | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E-MTAB-10643 | Transcriptome Analysis | Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells. | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Expt 3 3d post amputation + MMP inhibitor | SAMEA14418101 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France. | ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418101|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor|sex:male|strain:AB|treatment:matrix metalloproteinase inhibitor | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor p | Expt 3 3d post amputation + MMP inhibitor p | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:3|Experimental Factor: treatment:matrix metalloproteinase inhibitor | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | ERP137743 | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | E2_3dpa_inhibitor_S4_L002_I1_001.fastq.gz E2_3dpa_inhibitor_S4_L002_I2_001.fastq.gz E2_3dpa_inhibitor_S4_L002_R1_001.fastq.gz E2_3dpa_inhibitor_S4_L002_R2_001.fastq.gz | fastq fastq fastq fastq | 8621019270.0 | 63859402.0 | E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor | 0:10 1:10 2:28 3:87 | A:1438763050;C:1365497247;G:1350808021;T:1399773154;N:926502 | 10 | 10 | 28 | 87 | 1438763050 | 1365497247 | 1350808021 | 1399773154 | 926502 | ERX9298873 | ERS12023659 | ERA14538536 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | 1 | 0.92796 | 0.08671 | 0.87176 | 0.55088 | 87 | B | usable mapping rate | illumina | novaseq_era | 3prime | poly_a | unknown | sc | single_cell_droplet | 10x | France | 2022-05-20 | Adult | Adult | Heart | Cardiovascular System | |||||||||||||||||
| 11021 | 11021 | ERR9750933 | ERX9298872 | ERS12023658 | ERP137743 | PRJEB52989 | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E-MTAB-10643 | Transcriptome Analysis | Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells. | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Expt 1 Uninjured | SAMEA14418100 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France. | ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418100|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 Uninjured|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:heart|sample name:E MTAB 10643:Expt 1 Uninjured|sex:male|strain:AB | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E MTAB 10643:Expt 1 Uninjured p | Expt 1 Uninjured p | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Experimental Factor: injury:n1|Experimental Factor: treatment:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | ERP137743 | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | E1_Uninjured_S1_L002_I1_001.fastq.gz E1_Uninjured_S1_L002_R1_001.fastq.gz E1_Uninjured_S1_L002_R2_001.fastq.gz | fastq fastq fastq | 8575585211.0 | 67524293.0 | E MTAB 10643:Expt 1 Uninjured | 0:8 1:28 2:91 | A:1801503847;C:1312196506;G:1367890726;T:1663053783;N:65801 | 8 | 28 | 91 | 1801503847 | 1312196506 | 1367890726 | 1663053783 | 65801 | ERX9298872 | ERS12023658 | ERA14538536 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | 1 | 0.9169 | 0.11202 | 0.81576 | 0.54253 | 91 | B | usable mapping rate | illumina | novaseq_era | 3prime | poly_a | unknown | sc | single_cell_droplet | 10x | France | 2022-05-20 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||||||||
| 11022 | 11022 | ERR9750932 | ERX9298871 | ERS12023657 | ERP137743 | PRJEB52989 | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E-MTAB-10643 | Transcriptome Analysis | Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells. | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Expt 1 7d post amputation | SAMEA14418099 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France. | ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418099|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 7d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 1 7d post amputation|sex:male|strain:AB | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E MTAB 10643:Expt 1 7d post amputation p | Expt 1 7d post amputation p | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:7|Experimental Factor: treatment:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | ERP137743 | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | E1_7d_S3_L002_I1_001.fastq.gz E1_7d_S3_L002_R1_001.fastq.gz E1_7d_S3_L002_R2_001.fastq.gz | fastq fastq fastq | 17341796660.0 | 136549580.0 | E MTAB 10643:Expt 1 7d post amputation | 0:8 1:28 2:91 | A:3506600812;C:2774617588;G:2814960106;T:3329701112;N:132162 | 8 | 28 | 91 | 3506600812 | 2774617588 | 2814960106 | 3329701112 | 132162 | ERX9298871 | ERS12023657 | ERA14538536 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | 1 | 0.90616 | 0.09608 | 0.82446 | 0.46632 | 91 | B | usable mapping rate | illumina | novaseq_era | 3prime | poly_a | unknown | sc | single_cell_droplet | 10x | France | 2022-05-20 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||||||||
| 11023 | 11023 | ERR9750931 | ERX9298870 | ERS12023656 | ERP137743 | PRJEB52989 | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E-MTAB-10643 | Transcriptome Analysis | Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells. | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Expt 1 3d post amputation | SAMEA14418098 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France. | ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418098|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 3d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 1 3d post amputation|sex:male|strain:AB | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E MTAB 10643:Expt 1 3d post amputation p | Expt 1 3d post amputation p | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:3|Experimental Factor: treatment:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | ERP137743 | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | E1_3d_S2_L002_I1_001.fastq.gz E1_3d_S2_L002_R1_001.fastq.gz E1_3d_S2_L002_R2_001.fastq.gz | fastq fastq fastq | 8183008018.0 | 64433134.0 | E MTAB 10643:Expt 1 3d post amputation | 0:8 1:28 2:91 | A:1630460899;C:1330248096;G:1326144211;T:1576499358;N:62630 | 8 | 28 | 91 | 1630460899 | 1330248096 | 1326144211 | 1576499358 | 62630 | ERX9298870 | ERS12023656 | ERA14538536 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | 1 | 0.88759 | 0.08679 | 0.82948 | 0.47863 | 91 | B | usable mapping rate | illumina | novaseq_era | 3prime | poly_a | unknown | sc | single_cell_droplet | 10x | France | 2022-05-20 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||||||||
| 11024 | 11024 | ERR9750930 | ERX9298869 | ERS12023655 | ERP137743 | PRJEB52989 | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E-MTAB-10643 | Transcriptome Analysis | Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells. | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Expt 1 14d post amputation | SAMEA14418097 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France. | ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418097|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 14d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 1 14d post amputation|sex:male|strain:AB | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | E MTAB 10643:Expt 1 14d post amputation p | Expt 1 14d post amputation p | scRNAseq of post amputation regenerating zebrafish cardiac ventricle | Zebrafish were euthanized in tricaine and hearts were extracted in PBS "Hearts were pooled and ""pre digested"" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum." The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics. | Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:14|Experimental Factor: treatment:n1 | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | ERP137743 | Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle | ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20 | E1_14d_S4_L002_I1_001.fastq.gz E1_14d_S4_L002_R1_001.fastq.gz E1_14d_S4_L002_R2_001.fastq.gz | fastq fastq fastq | 12911908390.0 | 101668570.0 | E MTAB 10643:Expt 1 14d post amputation | 0:8 1:28 2:91 | A:2700371496;C:1971281481;G:2062280628;T:2517806408;N:99857 | 8 | 28 | 91 | 2700371496 | 1971281481 | 2062280628 | 2517806408 | 99857 | ERX9298869 | ERS12023655 | ERA14538536 | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive | 1 | 0.90771 | 0.11048 | 0.81523 | 0.53024 | 91 | B | usable mapping rate | illumina | novaseq_era | 3prime | poly_a | unknown | sc | single_cell_droplet | 10x | France | 2022-05-20 | Adult | Adult | Heart | Cardiovascular System | ||||||||||||||||||
| 11813 | 11813 | ERR11788863 | ERX11187331 | ERS16221143 | ERP149944 | PRJEB64780 | A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain | E-MTAB-13223 | Transcriptome Analysis | To understand the cellular basis of the immune compartment of the zebrafish brain we have established reliable protocols for dissociation and prospective isolation of brain leukocytes using fluorescent transgenic lines. By combining this approach with single cell RNA sequencing we have generated a gene expression atlas composed of the distinct immune cells present in the homeostatic brain. These analyses revealed the presence of subpopulations of mononuclear phagocytes and other leukocytes including cell types that have not been or have been poorly characterized so far. Here we present the characterization of a new mononuclear phagocyte population that represents an important fraction among all brain leukocytes. Adult brain single cell suspensions were prepared from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 and a total of 14 000 cd45:DsRed+ cells were processed for single cell profiling using the 10x Genomics platform. | ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 | Protocols: FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 were dissected in 0.9X Dulbecco′s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33°C for 30 45 minutes fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4ºC 10 min and filtered through a 40µm nylon mesh. Just before flow cytometry analysis using calcein violet to exclude dead cells 1µM Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson. RNA Illumina | Sample 1 | SAMEA114235870 | Universite Libre de Bruxelles | ENA FIRST PUBLIC:2023 12 25T01:15:29Z|ENA LAST UPDATE:2023 12 25T01:15:29Z|External Id:SAMEA114235870|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:29Z|INSDC last update:2023 12 25T01:15:29Z|INSDC status:public|Submitter Id:E MTAB 13223:Sample 1|age:5|broker name:ArrayExpress|cell type:leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:pool of 3 fish|isolate:not applicable|organism part:brain|sample name:E MTAB 13223:Sample 1|scientific name:Danio rerio|sex:male and female|strain:AB | A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain | E MTAB 13223:Sample 1 p | Sample 1 p | A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain | FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 were dissected in 0.9X Dulbecco′s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33°C for 30 45 minutes fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4ºC 10 min and filtered through a 40µm nylon mesh. Just before flow cytometry analysis using calcein violet to exclude dead cells 1µM Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson. RNA Illumina | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | PAIRED | ILLUMINA | NextSeq 550 | ERP149944 | NextSeq 550 paired end sequencing; A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain | ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 | L41805_Track-81843_R1.fastq.gz L41805_Track-81843_R2.fastq.gz | fastq fastq | 5545444464.0 | 66017196.0 | E MTAB 13223:L41805 Track 81843 | 0:28 1:56 | A:1576174024;C:1193175858;G:1221776615;T:1551009004;N:3308963 | 28 | 56 | 1576174024 | 1193175858 | 1221776615 | 1551009004 | 3308963 | ERX11187331 | ERS16221143 | ERA26318932 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.00738 | 0.90151 | 0.00285 | 0.20553 | 0.99072 | 0.82402 | 0.4645 | 0.53817 | 28 | 56 | T | B | sc-like readlen | illumina | nextseq | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2023-12-25 | Adult | Adult | Brain | Nervous System | ||||||||||||||
| 11814 | 11814 | ERR11788864 | ERX11187331 | ERS16221143 | ERP149944 | PRJEB64780 | A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain | E-MTAB-13223 | Transcriptome Analysis | To understand the cellular basis of the immune compartment of the zebrafish brain we have established reliable protocols for dissociation and prospective isolation of brain leukocytes using fluorescent transgenic lines. By combining this approach with single cell RNA sequencing we have generated a gene expression atlas composed of the distinct immune cells present in the homeostatic brain. These analyses revealed the presence of subpopulations of mononuclear phagocytes and other leukocytes including cell types that have not been or have been poorly characterized so far. Here we present the characterization of a new mononuclear phagocyte population that represents an important fraction among all brain leukocytes. Adult brain single cell suspensions were prepared from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 and a total of 14 000 cd45:DsRed+ cells were processed for single cell profiling using the 10x Genomics platform. | ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 | Protocols: FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 were dissected in 0.9X Dulbecco′s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33°C for 30 45 minutes fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4ºC 10 min and filtered through a 40µm nylon mesh. Just before flow cytometry analysis using calcein violet to exclude dead cells 1µM Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson. RNA Illumina | Sample 1 | SAMEA114235870 | Universite Libre de Bruxelles | ENA FIRST PUBLIC:2023 12 25T01:15:29Z|ENA LAST UPDATE:2023 12 25T01:15:29Z|External Id:SAMEA114235870|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:29Z|INSDC last update:2023 12 25T01:15:29Z|INSDC status:public|Submitter Id:E MTAB 13223:Sample 1|age:5|broker name:ArrayExpress|cell type:leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:pool of 3 fish|isolate:not applicable|organism part:brain|sample name:E MTAB 13223:Sample 1|scientific name:Danio rerio|sex:male and female|strain:AB | A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain | E MTAB 13223:Sample 1 p | Sample 1 p | A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain | FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 were dissected in 0.9X Dulbecco′s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33°C for 30 45 minutes fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4ºC 10 min and filtered through a 40µm nylon mesh. Just before flow cytometry analysis using calcein violet to exclude dead cells 1µM Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson. RNA Illumina | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | PolyA | PAIRED | ILLUMINA | NextSeq 550 | ERP149944 | NextSeq 550 paired end sequencing; A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain | ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25 | L41805_Track-81377_R1.fastq.gz L41805_Track-81377_R2.fastq.gz | fastq fastq | 3184137096.0 | 37906394.0 | E MTAB 13223:L41805 Track 81377 | 0:28 1:56 | A:899943184;C:685571078;G:703849582;T:889228559;N:5544693 | 28 | 56 | 899943184 | 685571078 | 703849582 | 889228559 | 5544693 | ERX11187331 | ERS16221143 | ERA26318932 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | 2 | 0.00734 | 0.90077 | 0.00293 | 0.20318 | 0.99064 | 0.82765 | 0.47994 | 0.53473 | 28 | 56 | T | B | sc-like readlen | illumina | nextseq | unknown | poly_a | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2023-12-25 | Adult | Adult | Brain | Nervous System | ||||||||||||||
| 15614 | 15614 | ERR13109732 | ERX12481366 | ERS19896183 | ERP160330 | PRJEB75769 | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E-MTAB-14075 | Transcriptome Analysis | The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | WT young | SAMEA115618603 | Department of Hematology cancer institute ErasmusMC | ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E MTAB 14075:WT young p | WT young p | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP160330 | Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | WT_young_S16_L002_I1_001.fastq.gz WT_young_S16_L002_R1_001.fastq.gz WT_young_S16_L002_R2_001.fastq.gz | fastq fastq fastq | 11547230144.0 | 90923072.0 | E MTAB 14075:WT young S16 L002 | 0:8 1:28 2:91 | A:2298760158;C:1887715706;G:1977278606;T:2109839457;N:405625 | 8 | 28 | 91 | 2298760158 | 1887715706 | 1977278606 | 2109839457 | 405625 | ERX12481366 | ERS19896183 | ERA30396266 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | usable mapping rate | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2024-11-05 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||||||||
| 15615 | 15615 | ERR13109737 | ERX12481366 | ERS19896183 | ERP160330 | PRJEB75769 | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E-MTAB-14075 | Transcriptome Analysis | The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | WT young | SAMEA115618603 | Department of Hematology cancer institute ErasmusMC | ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E MTAB 14075:WT young p | WT young p | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP160330 | Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | WT_young_run2_S10_L001_I1_001.fastq.gz WT_young_run2_S10_L001_R1_001.fastq.gz WT_young_run2_S10_L001_R2_001.fastq.gz | fastq fastq fastq | 6300899375.0 | 50407195.0 | E MTAB 14075:WT young run2 S10 L001 | 0:8 1:28 2:89 | A:1243074350;C:1030040216;G:1079454879;T:1133663108;N:7802 | 8 | 28 | 89 | 1243074350 | 1030040216 | 1079454879 | 1133663108 | 7802 | ERX12481366 | ERS19896183 | ERA30396266 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | usable mapping rate | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2024-11-05 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||||||||
| 15616 | 15616 | ERR13109733 | ERX12481366 | ERS19896183 | ERP160330 | PRJEB75769 | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E-MTAB-14075 | Transcriptome Analysis | The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | WT young | SAMEA115618603 | Department of Hematology cancer institute ErasmusMC | ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E MTAB 14075:WT young p | WT young p | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP160330 | Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | WT_young_run2_S10_L002_I1_001.fastq.gz WT_young_run2_S10_L002_R1_001.fastq.gz WT_young_run2_S10_L002_R2_001.fastq.gz | fastq fastq fastq | 6323980500.0 | 50591844.0 | E MTAB 14075:WT young run2 S10 L002 | 0:8 1:28 2:89 | A:1248024810;C:1032976792;G:1082805513;T:1138855823;N:11178 | 8 | 28 | 89 | 1248024810 | 1032976792 | 1082805513 | 1138855823 | 11178 | ERX12481366 | ERS19896183 | ERA30396266 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | usable mapping rate | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2024-11-05 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||||||||
| 15617 | 15617 | ERR13109728 | ERX12481366 | ERS19896183 | ERP160330 | PRJEB75769 | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E-MTAB-14075 | Transcriptome Analysis | The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | WT young | SAMEA115618603 | Department of Hematology cancer institute ErasmusMC | ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E MTAB 14075:WT young p | WT young p | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP160330 | Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | WT_young_S16_L001_I1_001.fastq.gz WT_young_S16_L001_R1_001.fastq.gz WT_young_S16_L001_R2_001.fastq.gz | fastq fastq fastq | 9395132467.0 | 73977421.0 | E MTAB 14075:WT young S16 L001 | 0:8 1:28 2:91 | A:1870197969;C:1535772308;G:1609450193;T:1716224344;N:300497 | 8 | 28 | 91 | 1870197969 | 1535772308 | 1609450193 | 1716224344 | 300497 | ERX12481366 | ERS19896183 | ERA30396266 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | usable mapping rate | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2024-11-05 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||||||||
| 15618 | 15618 | ERR13109727 | ERX12481365 | ERS19896182 | ERP160330 | PRJEB75769 | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E-MTAB-14075 | Transcriptome Analysis | The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | WT aged | SAMEA115618602 | Department of Hematology cancer institute ErasmusMC | ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E MTAB 14075:WT aged p | WT aged p | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP160330 | Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | WT_aged_S15_L001_I1_001.fastq.gz WT_aged_S15_L001_R1_001.fastq.gz WT_aged_S15_L001_R2_001.fastq.gz | fastq fastq fastq | 3224055528.0 | 25386264.0 | E MTAB 14075:WT aged S15 L001 | 0:8 1:28 2:91 | A:632762441;C:548488749;G:552881879;T:575917355;N:99600 | 8 | 28 | 91 | 632762441 | 548488749 | 552881879 | 575917355 | 99600 | ERX12481365 | ERS19896182 | ERA30396266 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | usable mapping rate | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2024-11-05 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||||||||
| 15619 | 15619 | ERR13109729 | ERX12481365 | ERS19896182 | ERP160330 | PRJEB75769 | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E-MTAB-14075 | Transcriptome Analysis | The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | WT aged | SAMEA115618602 | Department of Hematology cancer institute ErasmusMC | ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E MTAB 14075:WT aged p | WT aged p | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP160330 | Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | WT_aged_S15_L002_I1_001.fastq.gz WT_aged_S15_L002_R1_001.fastq.gz WT_aged_S15_L002_R2_001.fastq.gz | fastq fastq fastq | 4178136043.0 | 32898709.0 | E MTAB 14075:WT aged S15 L002 | 0:8 1:28 2:91 | A:820476445;C:710661272;G:715891121;T:746611018;N:142663 | 8 | 28 | 91 | 820476445 | 710661272 | 715891121 | 746611018 | 142663 | ERX12481365 | ERS19896182 | ERA30396266 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | usable mapping rate | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2024-11-05 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||||||||
| 15620 | 15620 | ERR13109731 | ERX12481365 | ERS19896182 | ERP160330 | PRJEB75769 | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E-MTAB-14075 | Transcriptome Analysis | The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | WT aged | SAMEA115618602 | Department of Hematology cancer institute ErasmusMC | ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E MTAB 14075:WT aged p | WT aged p | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP160330 | Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | WT_aged_run2_S13_L002_I1_001.fastq.gz WT_aged_run2_S13_L002_R1_001.fastq.gz WT_aged_run2_S13_L002_R2_001.fastq.gz | fastq fastq fastq | 11315635500.0 | 90525084.0 | E MTAB 14075:WT aged run2 S13 L002 | 0:8 1:28 2:89 | A:2205965370;C:1918372621;G:1938090305;T:1994285205;N:18975 | 8 | 28 | 89 | 2205965370 | 1918372621 | 1938090305 | 1994285205 | 18975 | ERX12481365 | ERS19896182 | ERA30396266 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | usable mapping rate | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2024-11-05 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||||||||
| 15621 | 15621 | ERR13109734 | ERX12481365 | ERS19896182 | ERP160330 | PRJEB75769 | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E-MTAB-14075 | Transcriptome Analysis | The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | WT aged | SAMEA115618602 | Department of Hematology cancer institute ErasmusMC | ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:WT aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bWT|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:WT aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed WT | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E MTAB 14075:WT aged p | WT aged p | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP160330 | Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | WT_aged_run2_S13_L001_I1_001.fastq.gz WT_aged_run2_S13_L001_R1_001.fastq.gz WT_aged_run2_S13_L001_R2_001.fastq.gz | fastq fastq fastq | 11297009750.0 | 90376078.0 | E MTAB 14075:WT aged run2 S13 L001 | 0:8 1:28 2:89 | A:2201626807;C:1916371507;G:1936001373;T:1989457619;N:13636 | 8 | 28 | 89 | 2201626807 | 1916371507 | 1936001373 | 1989457619 | 13636 | ERX12481365 | ERS19896182 | ERA30396266 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | usable mapping rate | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2024-11-05 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||||||||
| 15622 | 15622 | ERR13109730 | ERX12481363 | ERS19896180 | ERP160330 | PRJEB75769 | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E-MTAB-14075 | Transcriptome Analysis | The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | Het aged | SAMEA115618600 | Department of Hematology cancer institute ErasmusMC | ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E MTAB 14075:Het aged p | Het aged p | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP160330 | Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Het_aged_run2_S14_L002_I1_001.fastq.gz Het_aged_run2_S14_L002_R1_001.fastq.gz Het_aged_run2_S14_L002_R2_001.fastq.gz | fastq fastq fastq | 4755473375.0 | 38043787.0 | E MTAB 14075:Het aged run2 S14 L002 | 0:8 1:28 2:89 | A:924628155;C:804435427;G:826904786;T:829920091;N:8584 | 8 | 28 | 89 | 924628155 | 804435427 | 826904786 | 829920091 | 8584 | ERX12481363 | ERS19896180 | ERA30396266 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | usable mapping rate | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2024-11-05 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||||||||
| 15623 | 15623 | ERR13109738 | ERX12481363 | ERS19896180 | ERP160330 | PRJEB75769 | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E-MTAB-14075 | Transcriptome Analysis | The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | Het aged | SAMEA115618600 | Department of Hematology cancer institute ErasmusMC | ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E MTAB 14075:Het aged p | Het aged p | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP160330 | Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Het_aged_run2_S14_L001_I1_001.fastq.gz Het_aged_run2_S14_L001_R1_001.fastq.gz Het_aged_run2_S14_L001_R2_001.fastq.gz | fastq fastq fastq | 4757077375.0 | 38056619.0 | E MTAB 14075:Het aged run2 S14 L001 | 0:8 1:28 2:89 | A:924804478;C:805146986;G:827570549;T:829511132;N:5946 | 8 | 28 | 89 | 924804478 | 805146986 | 827570549 | 829511132 | 5946 | ERX12481363 | ERS19896180 | ERA30396266 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | usable mapping rate | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2024-11-05 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||||||||
| 15624 | 15624 | ERR13109725 | ERX12481363 | ERS19896180 | ERP160330 | PRJEB75769 | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E-MTAB-14075 | Transcriptome Analysis | The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | Het aged | SAMEA115618600 | Department of Hematology cancer institute ErasmusMC | ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E MTAB 14075:Het aged p | Het aged p | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP160330 | Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Het_aged_S13_L001_I1_001.fastq.gz Het_aged_S13_L001_R1_001.fastq.gz Het_aged_S13_L001_R2_001.fastq.gz | fastq fastq fastq | 2031302643.0 | 15994509.0 | E MTAB 14075:Het aged S13 L001 | 0:8 1:28 2:91 | A:398278357;C:344264985;G:353424298;T:359473296;N:59383 | 8 | 28 | 91 | 398278357 | 344264985 | 353424298 | 359473296 | 59383 | ERX12481363 | ERS19896180 | ERA30396266 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | usable mapping rate | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2024-11-05 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||||||||
| 15625 | 15625 | ERR13109739 | ERX12481363 | ERS19896180 | ERP160330 | PRJEB75769 | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E-MTAB-14075 | Transcriptome Analysis | The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | Het aged | SAMEA115618600 | Department of Hematology cancer institute ErasmusMC | ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het aged|age:18|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het aged|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E MTAB 14075:Het aged p | Het aged p | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP160330 | Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Het_aged_S13_L002_I1_001.fastq.gz Het_aged_S13_L002_R1_001.fastq.gz Het_aged_S13_L002_R2_001.fastq.gz | fastq fastq fastq | 2430576292.0 | 19138396.0 | E MTAB 14075:Het aged S13 L002 | 0:8 1:28 2:91 | A:476457271;C:411953563;G:422659830;T:430445714;N:77658 | 8 | 28 | 91 | 476457271 | 411953563 | 422659830 | 430445714 | 77658 | ERX12481363 | ERS19896180 | ERA30396266 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | usable mapping rate | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2024-11-05 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||||||||
| 15626 | 15626 | ERR13109736 | ERX12481364 | ERS19896181 | ERP160330 | PRJEB75769 | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E-MTAB-14075 | Transcriptome Analysis | The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | Het young | SAMEA115618601 | Department of Hematology cancer institute ErasmusMC | ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E MTAB 14075:Het young p | Het young p | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP160330 | Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Het_young_S14_L001_I1_001.fastq.gz Het_young_S14_L001_R1_001.fastq.gz Het_young_S14_L001_R2_001.fastq.gz | fastq fastq fastq | 7202197051.0 | 56710213.0 | E MTAB 14075:Het young S14 L001 | 0:8 1:28 2:91 | A:1452033851;C:1164601809;G:1229900451;T:1313862644;N:230628 | 8 | 28 | 91 | 1452033851 | 1164601809 | 1229900451 | 1313862644 | 230628 | ERX12481364 | ERS19896181 | ERA30396266 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | usable mapping rate | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2024-11-05 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||||||||
| 15627 | 15627 | ERR13109740 | ERX12481364 | ERS19896181 | ERP160330 | PRJEB75769 | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E-MTAB-14075 | Transcriptome Analysis | The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | Het young | SAMEA115618601 | Department of Hematology cancer institute ErasmusMC | ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E MTAB 14075:Het young p | Het young p | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP160330 | Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Het_young_run2_S11_L001_I1_001.fastq.gz Het_young_run2_S11_L001_R1_001.fastq.gz Het_young_run2_S11_L001_R2_001.fastq.gz | fastq fastq fastq | 3012722750.0 | 24101782.0 | E MTAB 14075:Het young run2 S11 L001 | 0:8 1:28 2:89 | A:601664996;C:487380557;G:514748426;T:541261211;N:3408 | 8 | 28 | 89 | 601664996 | 487380557 | 514748426 | 541261211 | 3408 | ERX12481364 | ERS19896181 | ERA30396266 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | usable mapping rate | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2024-11-05 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||||||||
| 15628 | 15628 | ERR13109735 | ERX12481364 | ERS19896181 | ERP160330 | PRJEB75769 | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E-MTAB-14075 | Transcriptome Analysis | The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | Het young | SAMEA115618601 | Department of Hematology cancer institute ErasmusMC | ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E MTAB 14075:Het young p | Het young p | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP160330 | Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Het_young_run2_S11_L002_I1_001.fastq.gz Het_young_run2_S11_L002_R1_001.fastq.gz Het_young_run2_S11_L002_R2_001.fastq.gz | fastq fastq fastq | 3017568125.0 | 24140545.0 | E MTAB 14075:Het young run2 S11 L002 | 0:8 1:28 2:89 | A:602793366;C:487819335;G:515271935;T:542618728;N:5141 | 8 | 28 | 89 | 602793366 | 487819335 | 515271935 | 542618728 | 5141 | ERX12481364 | ERS19896181 | ERA30396266 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | usable mapping rate | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2024-11-05 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||||||||
| 15629 | 15629 | ERR13109726 | ERX12481364 | ERS19896181 | ERP160330 | PRJEB75769 | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E-MTAB-14075 | Transcriptome Analysis | The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans heterozygous germline mutations in GATA2 often lead to a loss of function of one allele causing GATA2 haploinsufficiency. In mice Gata2 has an essential regulatory function in hematopoietic stem cell HSC generation and maintenance. However whereas Gata2 null mice are lethal at embryonic day E 10.53 Gata2 heterozygous Gata2+/ mice survive to maturity with normal blood values. However mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells HSPCs and homozygous deletion gata2b / redirects HSPCs differentiation bias thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro myelodysplasia a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and mutated zebrafish based on the scatter profile of flow cytometry for single cell RNA scRNA sequencing. | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Protocols: Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | Het young | SAMEA115618601 | Department of Hematology cancer institute ErasmusMC | ENA first public:2024 11 05|INSDC center name:Department of Hematology cancer institute ErasmusMC|INSDC status:public|Submitter Id:E MTAB 14075:Het young|age:12|broker name:ArrayExpress|cell type:hematopoietic cell|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:Gata2bHet|geographic location country and/or sea:not collected|individual:pools of 2 fish|isolate:not applicable|organism part:kidney marrow|sample name:E MTAB 14075:Het young|scientific name:Danio rerio|sex:mixed|strain:TgCD41:GFP; runx1:DsRed Gata2b KO | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | E MTAB 14075:Het young p | Het young p | Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | Adult zebrafish were euthanized kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V3. Library was prepared using the manufacturers protocol 10x Chromium V3. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | ERP160330 | Illumina NovaSeq 6000 paired end sequencing; Single cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish | ENA FIRST PUBLIC:2024 11 05|ENA LAST UPDATE:2024 11 05 | Het_young_S14_L002_I1_001.fastq.gz Het_young_S14_L002_R1_001.fastq.gz Het_young_S14_L002_R2_001.fastq.gz | fastq fastq fastq | 8707482077.0 | 68562851.0 | E MTAB 14075:Het young S14 L002 | 0:8 1:28 2:91 | A:1755361511;C:1408255848;G:1486295783;T:1588996810;N:309489 | 8 | 28 | 91 | 1755361511 | 1408255848 | 1486295783 | 1588996810 | 309489 | ERX12481364 | ERS19896181 | ERA30396266 | European Bioinformatics Institute|European Nucleotide Archive | European Bioinformatics Institute|European Nucleotide Archive | B | usable mapping rate | illumina | novaseq_era | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2024-11-05 | Adult | Adult | Multi-tissue | Multi-system | |||||||||||||||||||||||||
| 25302 | 25302 | SRR25793493 | SRX21515745 | SRS18742910 | SRP457465 | PRJNA1010662 | The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. | PRJNA1010662 | Other | Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation. | Single cell Pr1phros ADULT miR 144 mutant Danio rerio | miR 144 | isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:blood|BioSampleModel:Model organism or animal | Single cell Pr1phros ADULT miR 144 mutant Danio rerio | CD 144 1 | CD 144 1 | Single cell library cloning was done with 10X Genomics | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | unspecified | PAIRED | ILLUMINA | NextSeq 2000 | SRP457465 | CD_144_1_S3_R1.fastq CD_144_1_S3_R2.fastq | fastq fastq | 12899093774.0 | 108395746.0 | CD 144 1 S3 R1.fastq | 0:28 1:91 | A:3225260764;C:3211986177;G:3151471558;T:3308055659;N:2319616 | 28 | 91 | 3225260764 | 3211986177 | 3151471558 | 3308055659 | 2319616 | SRX21515745 | SRS18742910 | SRA1701829 | University of East Anglia|Biological Sciences | University of East Anglia | 2 | 0.00483 | 0.97382 | 0.00157 | 0.05913 | 0.99439 | 0.86815 | 0.46634 | 0.45907 | 28 | 91 | T | B | sc-like readlen | illumina | nextseq_v2 | unknown | unknown | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2023-08-30 | Adult | Adult | Blood | Hematopoietic System | ||||||||||||||||||||
| 25303 | 25303 | SRR25793494 | SRX21515744 | SRS18742909 | SRP457465 | PRJNA1010662 | The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. | PRJNA1010662 | Other | Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation. | Single cell Pr1phros ADULT Wild type Danio rerio | WT | isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:blood|BioSampleModel:Model organism or animal | Single cell Pr1phros ADULT Wild type Danio rerio | CD wt 1 | CD wt 1 | Single cell library cloning was done with 10X Genomics | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | unspecified | PAIRED | ILLUMINA | NextSeq 2000 | SRP457465 | CD_wt_1_S2_R1.fastq CD_wt_1_S2_R2.fastq | fastq fastq | 12715533299.0 | 106853221.0 | CD wt 1 S2 R1.fastq | 0:28 1:91 | A:3324705878;C:3042843364;G:3105568183;T:3240105528;N:2310346 | 28 | 91 | 3324705878 | 3042843364 | 3105568183 | 3240105528 | 2310346 | SRX21515744 | SRS18742909 | SRA1701829 | University of East Anglia|Biological Sciences | University of East Anglia | 2 | 0.00593 | 0.93177 | 0.00191 | 0.09596 | 0.99257 | 0.84394 | 0.42447 | 0.4869 | 28 | 91 | T | B | sc-like readlen | illumina | nextseq_v2 | unknown | unknown | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2023-08-30 | Adult | Adult | Blood | Hematopoietic System | ||||||||||||||||||||
| 28589 | 28589 | SRR26491369 | SRX22195232 | SRS19251247 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | KM eos | GSM7854254 | source name:eosinophils|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing | KM eos | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | eosinophils | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP | GSM7854254 | GSM7854254: KM eos; Danio rerio; RNA Seq | GSM7854254 r1 | GSM7854254 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | loader:fastq load.py | LGF-2-LGF-2-1_L1_1.fq.gz LGF-2-LGF-2-1_L1_2.fq.gz | fastq fastq | 25680257100.0 | 85600857.0 | GSM7854254 r1 | 0:150 1:150 | A:8025239149;C:3737115767;G:4237725481;T:9679701617;N:475086 | 150 | 150 | 8025239149 | 3737115767 | 4237725481 | 9679701617 | 475086 | SRX22195232 | SRS19251247 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.21477 | 0.87303 | 0.06136 | 0.18991 | 0.99084 | 0.83187 | 0.58742 | 0.60309 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | ||||||||||
| 28590 | 28590 | SRR26491370 | SRX22195232 | SRS19251247 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | KM eos | GSM7854254 | source name:eosinophils|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing | KM eos | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | eosinophils | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP | GSM7854254 | GSM7854254: KM eos; Danio rerio; RNA Seq | GSM7854254 r1 | GSM7854254 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | loader:fastq load.py | LGF-2-LGF-2-2_L1_1.fq.gz LGF-2-LGF-2-2_L1_2.fq.gz | fastq fastq | 30035236200.0 | 100117454.0 | GSM7854254 r2 | 0:150 1:150 | A:9382913917;C:4364910890;G:4955266285;T:11331735278;N:409830 | 150 | 150 | 9382913917 | 4364910890 | 4955266285 | 11331735278 | 409830 | SRX22195232 | SRS19251247 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.20279 | 0.87187 | 0.05971 | 0.19015 | 0.99068 | 0.83108 | 0.6129 | 0.60029 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | ||||||||||
| 28591 | 28591 | SRR26491371 | SRX22195232 | SRS19251247 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | KM eos | GSM7854254 | source name:eosinophils|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing | KM eos | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | eosinophils | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP | GSM7854254 | GSM7854254: KM eos; Danio rerio; RNA Seq | GSM7854254 r1 | GSM7854254 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | loader:fastq load.py | LGF-2-LGF-2-3_L1_1.fq.gz LGF-2-LGF-2-3_L1_2.fq.gz | fastq fastq | 29383046400.0 | 97943488.0 | GSM7854254 r3 | 0:150 1:150 | A:9183968085;C:4275116661;G:4844377300;T:11079048598;N:535756 | 150 | 150 | 9183968085 | 4275116661 | 4844377300 | 11079048598 | 535756 | SRX22195232 | SRS19251247 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.19524 | 0.87384 | 0.06096 | 0.19095 | 0.99188 | 0.83293 | 0.58701 | 0.58361 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | ||||||||||
| 28592 | 28592 | SRR26491372 | SRX22195232 | SRS19251247 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | KM eos | GSM7854254 | source name:eosinophils|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP|geo loc name:missing|collection date:missing | KM eos | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | eosinophils | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:wild type|transgene:Tgeslec:eGFP | GSM7854254 | GSM7854254: KM eos; Danio rerio; RNA Seq | GSM7854254 r1 | GSM7854254 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | loader:fastq load.py | LGF-2-LGF-2-4_L1_1.fq.gz LGF-2-LGF-2-4_L1_2.fq.gz | fastq fastq | 33167265900.0 | 110557553.0 | GSM7854254 r4 | 0:150 1:150 | A:10380451186;C:4827987987;G:5467300098;T:12490912690;N:613939 | 150 | 150 | 10380451186 | 4827987987 | 5467300098 | 12490912690 | 613939 | SRX22195232 | SRS19251247 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.21222 | 0.87102 | 0.06704 | 0.18877 | 0.99052 | 0.83343 | 0.56053 | 0.58249 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | ||||||||||
| 28593 | 28593 | SRR26491373 | SRX22195231 | SRS19251246 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | cebpb mut KM 3 | GSM7854253 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing | cebpb mut KM 3 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1 | GSM7854253 | GSM7854253: cebpb mut KM 3; Danio rerio; RNA Seq | GSM7854253 r1 | GSM7854253 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | loader:fastq load.py | b3_S0_L003_R2_001.fastq.gz b3_S0_L003_R1_001.fastq.gz | fastq fastq | 112688609700.0 | 375628699.0 | GSM7854253 r1 | 0:150 1:150 | A:38960384866;C:23864873253;G:24209853889;T:25652339570;N:1158122 | 150 | 150 | 38960384866 | 23864873253 | 24209853889 | 25652339570 | 1158122 | SRX22195231 | SRS19251246 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.0 | 0.89036 | 0.0 | 0.11804 | 1.0 | 0.86318 | 0.69315 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | |||||||||||
| 28594 | 28594 | SRR26491374 | SRX22195230 | SRS19251245 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | cebpb mut KM 2 | GSM7854252 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing | cebpb mut KM 2 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1 | GSM7854252 | GSM7854252: cebpb mut KM 2; Danio rerio; RNA Seq | GSM7854252 r1 | GSM7854252 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | loader:fastq load.py | b2_S0_L003_R1_001.fastq.gz b2_S0_L003_R2_001.fastq.gz | fastq fastq | 115982411700.0 | 386608039.0 | GSM7854252 r1 | 0:150 1:150 | A:39966143944;C:23813985234;G:22925287805;T:29275806145;N:1188572 | 150 | 150 | 39966143944 | 23813985234 | 22925287805 | 29275806145 | 1188572 | SRX22195230 | SRS19251245 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.0 | 0.86607 | 0.0 | 0.12954 | 1.0 | 0.83132 | 0.631 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | |||||||||||
| 28595 | 28595 | SRR26491375 | SRX22195229 | SRS19251244 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | cebpb mut KM 1 | GSM7854251 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing | cebpb mut KM 1 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1 | GSM7854251 | GSM7854251: cebpb mut KM 1; Danio rerio; RNA Seq | GSM7854251 r1 | GSM7854251 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | KMB-KMB-1_FKDL210332848-1a-AK4437_1.fq.gz KMB-KMB-1_FKDL210332848-1a-AK4437_2.fq.gz | fastq fastq | 17042007300.0 | 56806691.0 | GSM7854251 r1 | 0:150 1:150 | A:5668533017;C:3385304499;G:3366957982;T:4620992880;N:218922 | 150 | 150 | 5668533017 | 3385304499 | 3366957982 | 4620992880 | 218922 | SRX22195229 | SRS19251244 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.03184 | 0.89149 | 0.00867 | 0.11757 | 0.99758 | 0.82077 | 0.751 | 0.57147 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | |||||||||||
| 28596 | 28596 | SRR26491376 | SRX22195229 | SRS19251244 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | cebpb mut KM 1 | GSM7854251 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing | cebpb mut KM 1 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1 | GSM7854251 | GSM7854251: cebpb mut KM 1; Danio rerio; RNA Seq | GSM7854251 r1 | GSM7854251 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | KMB-KMB-2_FKDL210332848-1a-AK4438_1.fq.gz KMB-KMB-2_FKDL210332848-1a-AK4438_2.fq.gz | fastq fastq | 16343762400.0 | 54479208.0 | GSM7854251 r2 | 0:150 1:150 | A:5450512159;C:3242501005;G:3220219102;T:4430319009;N:211125 | 150 | 150 | 5450512159 | 3242501005 | 3220219102 | 4430319009 | 211125 | SRX22195229 | SRS19251244 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.02568 | 0.8936 | 0.00694 | 0.11929 | 0.99776 | 0.82235 | 0.66666 | 0.57382 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | |||||||||||
| 28597 | 28597 | SRR26491377 | SRX22195229 | SRS19251244 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | cebpb mut KM 1 | GSM7854251 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing | cebpb mut KM 1 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1 | GSM7854251 | GSM7854251: cebpb mut KM 1; Danio rerio; RNA Seq | GSM7854251 r1 | GSM7854251 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | KMB-KMB-3_FKDL210332848-1a-AK4439_1.fq.gz KMB-KMB-3_FKDL210332848-1a-AK4439_2.fq.gz | fastq fastq | 10959163500.0 | 36530545.0 | GSM7854251 r3 | 0:150 1:150 | A:3642539220;C:2179136896;G:2168295053;T:2969053386;N:138945 | 150 | 150 | 3642539220 | 2179136896 | 2168295053 | 2969053386 | 138945 | SRX22195229 | SRS19251244 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.03232 | 0.89137 | 0.00922 | 0.12039 | 0.9974 | 0.82171 | 0.58775 | 0.57177 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | |||||||||||
| 28598 | 28598 | SRR26491378 | SRX22195229 | SRS19251244 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | cebpb mut KM 1 | GSM7854251 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1|geo loc name:missing|collection date:missing | cebpb mut KM 1 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:cebpb / |transgene:n1 | GSM7854251 | GSM7854251: cebpb mut KM 1; Danio rerio; RNA Seq | GSM7854251 r1 | GSM7854251 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | KMB-KMB-4_FKDL210332848-1a-AK4440_1.fq.gz KMB-KMB-4_FKDL210332848-1a-AK4440_2.fq.gz | fastq fastq | 18130067100.0 | 60433557.0 | GSM7854251 r4 | 0:150 1:150 | A:6030347851;C:3607618024;G:3589047945;T:4902820241;N:233039 | 150 | 150 | 6030347851 | 3607618024 | 3589047945 | 4902820241 | 233039 | SRX22195229 | SRS19251244 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.02563 | 0.89333 | 0.00745 | 0.11784 | 0.99805 | 0.82156 | 0.71568 | 0.56377 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | |||||||||||
| 28599 | 28599 | SRR26491379 | SRX22195228 | SRS19251243 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | cebp1 mut KM 3 | GSM7854250 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing | cebp1 mut KM 3 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1 | GSM7854250 | GSM7854250: cebp1 mut KM 3; Danio rerio; RNA Seq | GSM7854250 r1 | GSM7854250 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | loader:fastq load.py | e3_S0_L003_R1_001.fastq.gz e3_S0_L003_R2_001.fastq.gz | fastq fastq | 106692684600.0 | 355642282.0 | GSM7854250 r1 | 0:150 1:150 | A:43760768907;C:19045349028;G:18701042387;T:25183159362;N:2364916 | 150 | 150 | 43760768907 | 19045349028 | 18701042387 | 25183159362 | 2364916 | SRX22195228 | SRS19251243 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.0 | 0.90163 | 0.0 | 0.08054 | 1.0 | 0.7908 | 0.55652 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | |||||||||||
| 28600 | 28600 | SRR26491380 | SRX22195227 | SRS19251242 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | cebp1 mut KM 2 | GSM7854249 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing | cebp1 mut KM 2 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1 | GSM7854249 | GSM7854249: cebp1 mut KM 2; Danio rerio; RNA Seq | GSM7854249 r1 | GSM7854249 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | loader:fastq load.py | e2_S0_L003_R2_001.fastq.gz e2_S0_L003_R1_001.fastq.gz | fastq fastq | 126515726100.0 | 421719087.0 | GSM7854249 r1 | 0:150 1:150 | A:44391473513;C:24602183317;G:23721160983;T:33799587611;N:1320676 | 150 | 150 | 44391473513 | 24602183317 | 23721160983 | 33799587611 | 1320676 | SRX22195227 | SRS19251242 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.0 | 0.90423 | 0.0 | 0.07758 | 1.0 | 0.81509 | 0.5598 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | |||||||||||
| 28601 | 28601 | SRR26491381 | SRX22195226 | SRS19251241 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | cebp1 mut KM 1 | GSM7854248 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing | cebp1 mut KM 1 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1 | GSM7854248 | GSM7854248: cebp1 mut KM 1; Danio rerio; RNA Seq | GSM7854248 r1 | GSM7854248 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | KM1-KM1-1_FKDL210332847-1a-AK4772_2.fq.gz KM1-KM1-1_FKDL210332847-1a-AK4772_1.fq.gz | fastq fastq | 18653393400.0 | 62177978.0 | GSM7854248 r1 | 0:150 1:150 | A:6381285195;C:3802506730;G:3637919666;T:4831413881;N:267928 | 150 | 150 | 6381285195 | 3802506730 | 3637919666 | 4831413881 | 267928 | SRX22195226 | SRS19251241 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.0 | 0.86906 | 0.0 | 0.0958 | 1.0 | 0.84423 | 0.5956 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | ||||||||||||
| 28602 | 28602 | SRR26491382 | SRX22195226 | SRS19251241 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | cebp1 mut KM 1 | GSM7854248 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing | cebp1 mut KM 1 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1 | GSM7854248 | GSM7854248: cebp1 mut KM 1; Danio rerio; RNA Seq | GSM7854248 r1 | GSM7854248 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | KM1-KM1-2_FKDL210332847-1a-AK4773_1.fq.gz KM1-KM1-2_FKDL210332847-1a-AK4773_2.fq.gz | fastq fastq | 18326971500.0 | 61089905.0 | GSM7854248 r2 | 0:150 1:150 | A:6267364051;C:3758542961;G:3587627310;T:4713172477;N:264701 | 150 | 150 | 6267364051 | 3758542961 | 3587627310 | 4713172477 | 264701 | SRX22195226 | SRS19251241 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.0 | 0.86638 | 0.0 | 0.09499 | 1.0 | 0.84526 | 0.60651 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | ||||||||||||
| 28603 | 28603 | SRR26491383 | SRX22195226 | SRS19251241 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | cebp1 mut KM 1 | GSM7854248 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing | cebp1 mut KM 1 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1 | GSM7854248 | GSM7854248: cebp1 mut KM 1; Danio rerio; RNA Seq | GSM7854248 r1 | GSM7854248 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | KM1-KM1-3_FKDL210332847-1a-AK4774_1.fq.gz KM1-KM1-3_FKDL210332847-1a-AK4774_2.fq.gz | fastq fastq | 11808660600.0 | 39362202.0 | GSM7854248 r3 | 0:150 1:150 | A:4038900150;C:2417395586;G:2308989220;T:3043205908;N:169736 | 150 | 150 | 4038900150 | 2417395586 | 2308989220 | 3043205908 | 169736 | SRX22195226 | SRS19251241 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.0 | 0.86661 | 0.0 | 0.09574 | 1.0 | 0.84542 | 0.57797 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | ||||||||||||
| 28604 | 28604 | SRR26491384 | SRX22195226 | SRS19251241 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | cebp1 mut KM 1 | GSM7854248 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1|geo loc name:missing|collection date:missing | cebp1 mut KM 1 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:cebp1 / |transgene:n1 | GSM7854248 | GSM7854248: cebp1 mut KM 1; Danio rerio; RNA Seq | GSM7854248 r1 | GSM7854248 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | KM1-KM1-4_FKDL210332847-1a-AK4775_1.fq.gz KM1-KM1-4_FKDL210332847-1a-AK4775_2.fq.gz | fastq fastq | 13766583900.0 | 45888613.0 | GSM7854248 r4 | 0:150 1:150 | A:4706562659;C:2817183636;G:2693650162;T:3548993544;N:193899 | 150 | 150 | 4706562659 | 2817183636 | 2693650162 | 3548993544 | 193899 | SRX22195226 | SRS19251241 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.0 | 0.86464 | 0.0 | 0.09455 | 1.0 | 0.84453 | 0.59712 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | ||||||||||||
| 28605 | 28605 | SRR26491385 | SRX22195225 | SRS19251240 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | WT KM 3 | GSM7854247 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing | WT KM 3 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1 | GSM7854247 | GSM7854247: WT KM 3; Danio rerio; RNA Seq | GSM7854247 r1 | GSM7854247 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | loader:fastq load.py | w3_S0_L003_R1_001.fastq.gz w3_S0_L003_R2_001.fastq.gz | fastq fastq | 142550442300.0 | 475168141.0 | GSM7854247 r1 | 0:150 1:150 | A:56961713939;C:27160797921;G:25876430130;T:32548386896;N:3113414 | 150 | 150 | 56961713939 | 27160797921 | 25876430130 | 32548386896 | 3113414 | SRX22195225 | SRS19251240 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.0 | 0.84672 | 0.0 | 0.09057 | 1.0 | 0.84893 | 0.64916 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | |||||||||||
| 28606 | 28606 | SRR26491386 | SRX22195224 | SRS19251239 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | WT KM 2 | GSM7854246 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing | WT KM 2 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1 | GSM7854246 | GSM7854246: WT KM 2; Danio rerio; RNA Seq | GSM7854246 r1 | GSM7854246 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | loader:fastq load.py | w2_S0_L003_R2_001.fastq.gz w2_S0_L003_R1_001.fastq.gz | fastq fastq | 110520161400.0 | 368400538.0 | GSM7854246 r1 | 0:150 1:150 | A:44333853620;C:20994101993;G:19951597607;T:25238178463;N:2429717 | 150 | 150 | 44333853620 | 20994101993 | 19951597607 | 25238178463 | 2429717 | SRX22195224 | SRS19251239 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.0 | 0.84344 | 0.0 | 0.0961 | 1.0 | 0.83485 | 0.63275 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | |||||||||||
| 28607 | 28607 | SRR26491387 | SRX22195223 | SRS19251238 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | WT KM 1 | GSM7854245 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing | WT KM 1 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1 | GSM7854245 | GSM7854245: WT KM 1; Danio rerio; RNA Seq | GSM7854245 r1 | GSM7854245 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | WKM-WKM-1_BKDL190841222-1a-AK650_1.fq.gz WKM-WKM-1_BKDL190841222-1a-AK650_2.fq.gz | fastq fastq | 20481536700.0 | 68271789.0 | GSM7854245 r1 | 0:150 1:150 | A:4681473958;C:3918612929;G:6623380714;T:5257792172;N:276927 | 150 | 150 | 4681473958 | 3918612929 | 6623380714 | 5257792172 | 276927 | SRX22195223 | SRS19251238 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.0 | 0.91381 | 0.0 | 0.08281 | 1.0 | 0.82386 | 0.55976 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | ||||||||||||
| 28608 | 28608 | SRR26491388 | SRX22195223 | SRS19251238 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | WT KM 1 | GSM7854245 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing | WT KM 1 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1 | GSM7854245 | GSM7854245: WT KM 1; Danio rerio; RNA Seq | GSM7854245 r1 | GSM7854245 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | WKM-WKM-2_BKDL190841222-1a-AK651_2.fq.gz WKM-WKM-2_BKDL190841222-1a-AK651_1.fq.gz | fastq fastq | 24824596500.0 | 82748655.0 | GSM7854245 r2 | 0:150 1:150 | A:5675288010;C:4753602834;G:8033499593;T:6361861422;N:344641 | 150 | 150 | 5675288010 | 4753602834 | 8033499593 | 6361861422 | 344641 | SRX22195223 | SRS19251238 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.0 | 0.9121 | 0.0 | 0.08282 | 1.0 | 0.82613 | 0.56378 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | ||||||||||||
| 28609 | 28609 | SRR26491389 | SRX22195223 | SRS19251238 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | WT KM 1 | GSM7854245 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing | WT KM 1 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1 | GSM7854245 | GSM7854245: WT KM 1; Danio rerio; RNA Seq | GSM7854245 r1 | GSM7854245 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | WKM-WKM-3_BKDL190841222-1a-AK652_1.fq.gz WKM-WKM-3_BKDL190841222-1a-AK652_2.fq.gz | fastq fastq | 20574633600.0 | 68582112.0 | GSM7854245 r3 | 0:150 1:150 | A:4698580031;C:3942306152;G:6657096764;T:5276366726;N:283927 | 150 | 150 | 4698580031 | 3942306152 | 6657096764 | 5276366726 | 283927 | SRX22195223 | SRS19251238 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.0 | 0.9136 | 0.0 | 0.08366 | 1.0 | 0.82373 | 0.55683 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | ||||||||||||
| 28610 | 28610 | SRR26491390 | SRX22195223 | SRS19251238 | SRP468071 | PRJNA1031138 | Cebp1 and Cebpß transcriptional axis controls eosinophilopoiesis in zebrafish [scRNA Seq] | GSE246039 | Transcriptome Analysis | Eosinophils are well known to regulate host protection from parasites and have been reported to paticipate many other physiologic and pathologic processes. Understanding the role of eosinophils in these processes requires a better understanding of eosinophilopoiesis. Using a zebrafish model we have identified an eosinophil lineage specific marker eslec. Using this marker we have established a Tgeslec:eGFP reporter line which specifically labels zebrafish eosinophil lineage cells from early life through maturity. Spatial temporal analysis of eslec+ cells demonstrated organ distribution at the larval stage. By single cell RNA Seq of eslec+ cells tissue distributed eosinophils were found to have similar differentiation paths but different tissue specific expression profiles. Genetic analysis demonstrated a Cebp1 and Cebpß transcriptional axis that regulated eosinophilopoiesis in which Cebp1 directly targeted cebpb to inhibit eosinophil differentiationthe commitment and differentiation of the eosinophil lineage. In summary this study characterized eosinophil development in multiple dimensions including spatial temporal patterns expression profiles and genetic regulators. The results provide for a better understanding of eosinophilopoiesis. Overall design: For scRNA Seq analysis of eosinophils in kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq analysis. The scRNA Seq data of WT cebp1 / and cebpb / KM cells were integrated and analyzed together. | parent bioproject:PRJNA814534 | pubmed:38280871 | WT KM 1 | GSM7854245 | source name:renal cells|strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1|geo loc name:missing|collection date:missing | WT KM 1 | Post basecalling the fastq files were mapped to the zebrafish genome with the CellRanger package. Output files of CellRanger were applied to the R package "Seurat". Samples were filtered to remove low quality or contaminated cells. The renal cells from different genotypes sample 1 9 were integrated with the "IntegrateData" function of Seurat. Further analyses was performed based on the instructions of "Seurat" package. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell cell and gene metadata for integrated KM cells and KM eosinophils and the relevant Seurat objects rds files. | renal cells | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer’s instructions 10x Genomics USA. | strain:AB strain|tissue:Kidney|genotype:wild type|transgene:n1 | GSM7854245 | GSM7854245: WT KM 1; Danio rerio; RNA Seq | GSM7854245 r1 | GSM7854245 | 1 | For scRNA Seq analysis of eosinophils from kidney eosinophils were sorted from adult Tgeslec:eGFP kidneys. For scRNA Seq analysis of renal cells of different genotypes kidneys were collected from WT cebp1 / and cebpb / individuals and prepared into cell suspensions. The cell suspensions were then applied to 10x three prime scRNA Seq GEM generation. Post GEM generation the library construction was performed strictly based on the manufacturer's instructions 10x Genomics USA. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP468071 | WKM-WKM-4_BKDL190841222-1a-AK653_2.fq.gz WKM-WKM-4_BKDL190841222-1a-AK653_1.fq.gz | fastq fastq | 25381641600.0 | 84605472.0 | GSM7854245 r4 | 0:150 1:150 | A:5785664179;C:4874470993;G:8220023956;T:6501127037;N:355435 | 150 | 150 | 5785664179 | 4874470993 | 8220023956 | 6501127037 | 355435 | SRX22195223 | SRS19251238 | SRA1739642 | South China University of Technology | South China University of Technology | 2 | 0.0 | 0.91371 | 0.0 | 0.08381 | 1.0 | 0.8244 | 0.57179 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | novaseq_era | 3prime | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2023-10-23 | Adult | Adult | Kidney | Renal System | ||||||||||||
| 28725 | 28725 | SRR26623262 | SRX22323921 | SRS19374450 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Lineage tracing rep1 cirbpb scars | GSM7875190 | source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing | Lineage tracing rep1 cirbpb scars | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M] | GSM7875190 | GSM7875190: Lineage tracing rep1 cirbpb scars; Danio rerio; OTHER | GSM7875190 r1 | GSM7875190 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | lin1_cirbpb_scar_R1.fastq.gz lin1_cirbpb_scar_R2.fastq.gz | fastq fastq | 157576336.0 | 949552.0 | GSM7875190 r1 | SRX22323921 | SRS19374450 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.00141 | 0.78069 | 0.00053 | 0.00877 | 0.99857 | 0.97822 | 0.33536 | 0.05199 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | other | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||
| 28726 | 28726 | SRR26623263 | SRX22323920 | SRS19374449 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Lineage tracing rep1 cfl1 scars | GSM7875189 | source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing | Lineage tracing rep1 cfl1 scars | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M] | GSM7875189 | GSM7875189: Lineage tracing rep1 cfl1 scars; Danio rerio; OTHER | GSM7875189 r1 | GSM7875189 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | lin1_cfl1_scar_R2.fastq.gz lin1_cfl1_scar_R1.fastq.gz | fastq fastq | 381453696.0 | 2184402.0 | GSM7875189 r1 | SRX22323920 | SRS19374449 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.0002 | 0.91626 | 0.00014 | 0.00132 | 0.99987 | 0.99726 | 0.16666 | 0.56363 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | other | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||
| 28727 | 28727 | SRR26623264 | SRX22323919 | SRS19374448 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Lineage tracing rep1 actb2 scars | GSM7875188 | source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing | Lineage tracing rep1 actb2 scars | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M] | GSM7875188 | GSM7875188: Lineage tracing rep1 actb2 scars; Danio rerio; OTHER | GSM7875188 r1 | GSM7875188 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | lin1_actb2_scar_R1.fastq.gz lin1_actb2_scar_R2.fastq.gz | fastq fastq | 491682118.0 | 2851156.0 | GSM7875188 r1 | SRX22323919 | SRS19374448 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.00051 | 0.41901 | 0.00032 | 0.0029 | 0.99945 | 0.99182 | 0.57575 | 0.007 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | other | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||
| 28728 | 28728 | SRR26623265 | SRX22323918 | SRS19374446 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Lineage tracing rep1 actb1 scars | GSM7875187 | source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing | Lineage tracing rep1 actb1 scars | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M] | GSM7875187 | GSM7875187: Lineage tracing rep1 actb1 scars; Danio rerio; OTHER | GSM7875187 r1 | GSM7875187 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | lin1_actb1_scar_R1.fastq.gz lin1_actb1_scar_R2.fastq.gz | fastq fastq | 390405832.0 | 2283319.0 | GSM7875187 r1 | SRX22323918 | SRS19374446 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.00038 | 0.73548 | 0.00017 | 0.00057 | 0.99963 | 0.99571 | 0.29729 | 0.00243 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | other | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||
| 28729 | 28729 | SRR26623266 | SRX22323917 | SRS19374447 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 23 telencephalon Notch inhibition scSLAMseq | GSM7875186 | source name:adult brain|tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|treatment:Notch inhibition DAPT|geo loc name:missing|collection date:missing | Brain 23 telencephalon Notch inhibition scSLAMseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. Library strategy: scSLAM seq | adult brain | Notch inhibiton: zebrafish were incubated in a water bath containing system water with 50 µM DAPT Gamma Secretase Inhibitor Sigma Aldrich for 48 hours. | The samples were prepared according to a scSLAM seq protocol adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts 200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day the reaction was quanched with a quenching buffer containing 100 mM DTT post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions … | tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|treatment:Notch inhibition DAPT | GSM7875186 | GSM7875186: Brain 23 telencephalon Notch inhibition scSLAMseq; Danio rerio; OTHER | GSM7875186 r1 | GSM7875186 | 1 | The samples were prepared according to a scSLAM seq protocol adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts 200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day the reaction was quanched with a quenching buffer containing 100 mM DTT post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions … | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP469552 | loader:fastq load.py | b23_ni_tre_R1.fastq.gz b23_ni_tre_R2.fastq.gz | fastq fastq | 62392458570.0 | 271271559.0 | GSM7875186 r1 | 0:28 1:202 | A:18682905645;C:13783082970;G:14751373116;T:15161083446;N:14013393 | 28 | 202 | 18682905645 | 13783082970 | 14751373116 | 15161083446 | 14013393 | SRX22323917 | SRS19374447 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.01404 | 0.82351 | 0.00466 | 0.1026 | 0.99129 | 0.86774 | 0.36033 | 0.67345 | 28 | 202 | T | B | sc-like readlen | illumina | novaseq_era | unknown | other | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | ||||||||||
| 28730 | 28730 | SRR26623267 | SRX22323916 | SRS19374445 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 22 telencephalon control scSLAMseq | GSM7875185 | source name:adult brain|tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|treatment:Control DMSO|geo loc name:missing|collection date:missing | Brain 22 telencephalon control scSLAMseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. Library strategy: scSLAM seq | adult brain | Control for Notch inhibition: zebrafish were incubated in a water bath containing system water with 1:200 diluted DMSO for 48 hours. | The samples were prepared according to a scSLAM seq protocol adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts 200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day the reaction was quanched with a quenching buffer containing 100 mM DTT post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions … | tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|treatment:Control DMSO | GSM7875185 | GSM7875185: Brain 22 telencephalon control scSLAMseq; Danio rerio; OTHER | GSM7875185 r1 | GSM7875185 | 1 | The samples were prepared according to a scSLAM seq protocol adapted from Neuschulz et al 2023. Briefly: in order to label nascent transcripts 200 mM 4sU was delivered to fish brains by intraventricular injection 6 hours prior to sample collection. The brains were then collected and a single cell suspension was prepared by papain dissociation. The resulting cell suspension was fixed in 80% methanol and a conversion of 4sU using iodoactamide adding 111 µl 100 mM IAA to 800 µl fixed sample was done overnight. The following day the reaction was quanched with a quenching buffer containing 100 mM DTT post which the sample was washed with a wash buffer and filtered though a 35 µm filter. The sample was then loaded on a 10X Chromium Controller and processed according to the standard scRNA seq protocol. Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions … | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP469552 | loader:fastq load.py | b22_ni_con_R1.fastq.gz b22_ni_con_R2.fastq.gz | fastq fastq | 59793114490.0 | 259970063.0 | GSM7875185 r1 | 0:28 1:202 | A:18600519530;C:12714987967;G:14147370465;T:14316863915;N:13372613 | 28 | 202 | 18600519530 | 12714987967 | 14147370465 | 14316863915 | 13372613 | SRX22323916 | SRS19374445 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.01402 | 0.79448 | 0.00498 | 0.11405 | 0.99074 | 0.8518 | 0.39874 | 0.67082 | 28 | 202 | T | B | sc-like readlen | illumina | novaseq_era | unknown | other | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | ||||||||||
| 28731 | 28731 | SRR26623268 | SRX22323915 | SRS19374444 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 20 sorted scRNAseq | GSM7875184 | source name:adult brain|tissue:adult brain|tissue region:sorted|cell type:mixed tissue dissociation|genotype:Tg[gfap:GFP]|geo loc name:missing|collection date:missing | Brain 20 sorted scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:sorted|cell type:mixed tissue dissociation|genotype:Tg[gfap:GFP] | GSM7875184 | GSM7875184: Brain 20 sorted scRNAseq; Danio rerio; RNA Seq | GSM7875184 r1 | GSM7875184 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b20_gfap_R1.fastq.gz b20_gfap_R2.fastq.gz | fastq fastq | 7798133320.0 | 52690090.0 | GSM7875184 r1 | 0:28 1:120 | A:2399592536;C:1516740530;G:1752554415;T:2127715674;N:1530165 | 28 | 120 | 2399592536 | 1516740530 | 1752554415 | 2127715674 | 1530165 | SRX22323915 | SRS19374444 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.0094 | 0.86649 | 0.00431 | 0.28296 | 0.9881 | 0.77607 | 0.40289 | 0.50506 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28732 | 28732 | SRR26623269 | SRX22323914 | SRS19374443 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 19 whole scRNAseq | GSM7875183 | source name:adult brain|tissue:adult brain|tissue region:whole|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing | Brain 19 whole scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:whole|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M] | GSM7875183 | GSM7875183: Brain 19 whole scRNAseq; Danio rerio; RNA Seq | GSM7875183 r1 | GSM7875183 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b19_tdmr_seqrun1_R1.fastq.gz b19_tdmr_seqrun1_R2.fastq.gz | fastq fastq | 17234149570.0 | 96821065.0 | GSM7875183 r1 | 0:28 1:150 | A:5205716192;C:3547964017;G:3688127103;T:4785052541;N:7289717 | 28 | 150 | 5205716192 | 3547964017 | 3688127103 | 4785052541 | 7289717 | SRX22323914 | SRS19374443 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.0063 | 0.8972 | 0.00236 | 0.22454 | 0.99109 | 0.79123 | 0.52086 | 0.54601 | 28 | 150 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28733 | 28733 | SRR26623270 | SRX22323914 | SRS19374443 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 19 whole scRNAseq | GSM7875183 | source name:adult brain|tissue:adult brain|tissue region:whole|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing | Brain 19 whole scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:whole|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M] | GSM7875183 | GSM7875183: Brain 19 whole scRNAseq; Danio rerio; RNA Seq | GSM7875183 r1 | GSM7875183 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b19_tdmr_seqrun2_R1.fastq.gz b19_tdmr_seqrun2_R2.fastq.gz | fastq fastq | 8080308788.0 | 54596681.0 | GSM7875183 r2 | 0:28 1:120 | A:2402417612;C:1698661627;G:1736701450;T:2240964763;N:1563336 | 28 | 120 | 2402417612 | 1698661627 | 1736701450 | 2240964763 | 1563336 | SRX22323914 | SRS19374443 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.00651 | 0.88833 | 0.00255 | 0.2204 | 0.99121 | 0.7865 | 0.532 | 0.57621 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28734 | 28734 | SRR26623271 | SRX22323913 | SRS19374442 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 18 rhombencephalon scRNAseq | GSM7875182 | source name:adult brain|tissue:adult brain|tissue region:rhombencephalon|cell type:mixed tissue dissociation|genotype:wildtype Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing | Brain 18 rhombencephalon scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:rhombencephalon|cell type:mixed tissue dissociation|genotype:wildtype Tg[ubi:zebrabow M] | GSM7875182 | GSM7875182: Brain 18 rhombencephalon scRNAseq; Danio rerio; RNA Seq | GSM7875182 r1 | GSM7875182 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b18_rhom_R1.fastq.gz b18_rhom_R2.fastq.gz | fastq fastq | 18926303344.0 | 127880428.0 | GSM7875182 r1 | 0:28 1:120 | A:5713892455;C:3847687741;G:3928556839;T:5421348321;N:14817988 | 28 | 120 | 5713892455 | 3847687741 | 3928556839 | 5421348321 | 14817988 | SRX22323913 | SRS19374442 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.00496 | 0.88436 | 0.00243 | 0.29801 | 0.99285 | 0.78433 | 0.50833 | 0.63318 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28735 | 28735 | SRR26623272 | SRX22323912 | SRS19374441 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 18 mesencephalon scRNAseq | GSM7875181 | source name:adult brain|tissue:adult brain|tissue region:mesencephalon|cell type:mixed tissue dissociation|genotype:wildtype Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing | Brain 18 mesencephalon scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:mesencephalon|cell type:mixed tissue dissociation|genotype:wildtype Tg[ubi:zebrabow M] | GSM7875181 | GSM7875181: Brain 18 mesencephalon scRNAseq; Danio rerio; RNA Seq | GSM7875181 r1 | GSM7875181 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b18_mes_R1.fastq.gz b18_mes_R2.fastq.gz | fastq fastq | 18106862272.0 | 122343664.0 | GSM7875181 r1 | 0:28 1:120 | A:5459512927;C:3636958859;G:3755613924;T:5240531488;N:14245074 | 28 | 120 | 5459512927 | 3636958859 | 3755613924 | 5240531488 | 14245074 | SRX22323912 | SRS19374441 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.00645 | 0.88033 | 0.00346 | 0.34147 | 0.99127 | 0.76934 | 0.48681 | 0.60464 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28736 | 28736 | SRR26623273 | SRX22323911 | SRS19374440 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 18 diencephalon scRNAseq | GSM7875180 | source name:adult brain|tissue:adult brain|tissue region:diencephalon|cell type:mixed tissue dissociation|genotype:wildtype Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing | Brain 18 diencephalon scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:diencephalon|cell type:mixed tissue dissociation|genotype:wildtype Tg[ubi:zebrabow M] | GSM7875180 | GSM7875180: Brain 18 diencephalon scRNAseq; Danio rerio; RNA Seq | GSM7875180 r1 | GSM7875180 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b18_dien_R1.fastq.gz b18_dien_R2.fastq.gz | fastq fastq | 18653419612.0 | 126036619.0 | GSM7875180 r1 | 0:28 1:120 | A:5614496340;C:3825425595;G:3908771126;T:5290064867;N:14661684 | 28 | 120 | 5614496340 | 3825425595 | 3908771126 | 5290064867 | 14661684 | SRX22323911 | SRS19374440 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.00521 | 0.89782 | 0.00244 | 0.25692 | 0.99302 | 0.77291 | 0.47528 | 0.62168 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28737 | 28737 | SRR26623274 | SRX22323910 | SRS19374439 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 17 whole scRNAseq | GSM7875179 | source name:adult brain|tissue:adult brain|tissue region:whole|cell type:mixed tissue dissociation|genotype:wildtype|geo loc name:missing|collection date:missing | Brain 17 whole scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:whole|cell type:mixed tissue dissociation|genotype:wildtype | GSM7875179 | GSM7875179: Brain 17 whole scRNAseq; Danio rerio; RNA Seq | GSM7875179 r1 | GSM7875179 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b17_tdmr_R1.fastq.gz b17_tdmr_R2.fastq.gz | fastq fastq | 39604379236.0 | 267597157.0 | GSM7875179 r1 | 0:28 1:120 | A:12125317775;C:7792772449;G:8188608274;T:11493334367;N:4346371 | 28 | 120 | 12125317775 | 7792772449 | 8188608274 | 11493334367 | 4346371 | SRX22323910 | SRS19374439 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.00523 | 0.88138 | 0.0024 | 0.31504 | 0.99162 | 0.75895 | 0.40373 | 0.49629 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28738 | 28738 | SRR26623275 | SRX22323909 | SRS19374438 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 16 sorted scRNAseq | GSM7875178 | source name:adult brain|tissue:adult brain|tissue region:sorted|cell type:mixed tissue dissociation|genotype:Tg[gfap:GFP]|geo loc name:missing|collection date:missing | Brain 16 sorted scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:sorted|cell type:mixed tissue dissociation|genotype:Tg[gfap:GFP] | GSM7875178 | GSM7875178: Brain 16 sorted scRNAseq; Danio rerio; RNA Seq | GSM7875178 r1 | GSM7875178 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b16_gfap_R2.fastq.gz b16_gfap_R1.fastq.gz | fastq fastq | 5443014500.0 | 36777125.0 | GSM7875178 r1 | SRX22323909 | SRS19374438 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.00627 | 0.90735 | 0.00227 | 0.18428 | 0.99115 | 0.77242 | 0.4456 | 0.61483 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||
| 28739 | 28739 | SRR26623276 | SRX22323908 | SRS19374437 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 15 whole scRNAseq | GSM7875177 | source name:adult brain|tissue:adult brain|tissue region:whole|cell type:mixed tissue dissociation|genotype:wildtype|geo loc name:missing|collection date:missing | Brain 15 whole scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:whole|cell type:mixed tissue dissociation|genotype:wildtype | GSM7875177 | GSM7875177: Brain 15 whole scRNAseq; Danio rerio; RNA Seq | GSM7875177 r1 | GSM7875177 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b15_mult_R2.fastq.gz b15_mult_R1.fastq.gz | fastq fastq | 11845962180.0 | 80040285.0 | GSM7875177 r1 | 0:28 1:120 | A:2976260508;C:2811030160;G:2912422943;T:3143400974;N:2847595 | 28 | 120 | 2976260508 | 2811030160 | 2912422943 | 3143400974 | 2847595 | SRX22323908 | SRS19374437 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.08396 | 0.93662 | 0.02595 | 0.16615 | 0.93744 | 0.71364 | 0.29067 | 0.56326 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28740 | 28740 | SRR26623277 | SRX22323907 | SRS19374436 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 14 sorted scRNAseq | GSM7875176 | source name:adult brain|tissue:adult brain|tissue region:sorted|cell type:mixed tissue dissociation|genotype:Tg[gfap:GFP]|geo loc name:missing|collection date:missing | Brain 14 sorted scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:sorted|cell type:mixed tissue dissociation|genotype:Tg[gfap:GFP] | GSM7875176 | GSM7875176: Brain 14 sorted scRNAseq; Danio rerio; RNA Seq | GSM7875176 r1 | GSM7875176 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b14_gfap_R2.fastq.gz b14_gfap_R1.fastq.gz | fastq fastq | 17138451800.0 | 115800350.0 | GSM7875176 r1 | 0:28 1:120 | A:4079957203;C:3974923538;G:4289276957;T:4791971757;N:2322345 | 28 | 120 | 4079957203 | 3974923538 | 4289276957 | 4791971757 | 2322345 | SRX22323907 | SRS19374436 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.10093 | 0.95317 | 0.0314 | 0.10551 | 0.97104 | 0.82487 | 0.39909 | 0.4491 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28741 | 28741 | SRR26623278 | SRX22323906 | SRS19374435 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 13 whole scRNAseq | GSM7875175 | source name:adult brain|tissue:adult brain|tissue region:whole|cell type:mixed tissue dissociation|genotype:wildtype|geo loc name:missing|collection date:missing | Brain 13 whole scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:whole|cell type:mixed tissue dissociation|genotype:wildtype | GSM7875175 | GSM7875175: Brain 13 whole scRNAseq; Danio rerio; RNA Seq | GSM7875175 r1 | GSM7875175 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b13_mult_R2.fastq.gz b13_mult_R1.fastq.gz | fastq fastq | 14716484640.0 | 94336440.0 | GSM7875175 r1 | 0:28 1:128 | A:3656679229;C:3244551762;G:3483547888;T:4325660472;N:6045289 | 28 | 128 | 3656679229 | 3244551762 | 3483547888 | 4325660472 | 6045289 | SRX22323906 | SRS19374435 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.0334 | 0.93779 | 0.01344 | 0.20291 | 0.97654 | 0.72991 | 0.35896 | 0.56645 | 28 | 128 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28742 | 28742 | SRR26623279 | SRX22323905 | SRS19374434 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 12 whole scRNAseq | GSM7875174 | source name:adult brain|tissue:adult brain|tissue region:whole|cell type:mixed tissue dissociation|genotype:wildtype|geo loc name:missing|collection date:missing | Brain 12 whole scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:whole|cell type:mixed tissue dissociation|genotype:wildtype | GSM7875174 | GSM7875174: Brain 12 whole scRNAseq; Danio rerio; RNA Seq | GSM7875174 r1 | GSM7875174 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b12_mult_R2.fastq.gz b12_mult_R1.fastq.gz | fastq fastq | 12967118112.0 | 83122552.0 | GSM7875174 r1 | 0:28 1:128 | A:3152750696;C:2922178338;G:3166672580;T:3720207530;N:5308968 | 28 | 128 | 3152750696 | 2922178338 | 3166672580 | 3720207530 | 5308968 | SRX22323905 | SRS19374434 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.06196 | 0.94967 | 0.02426 | 0.19522 | 0.97108 | 0.73886 | 0.33644 | 0.62119 | 28 | 128 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28743 | 28743 | SRR26623280 | SRX22323904 | SRS19374433 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 11 whole scRNAseq | GSM7875173 | source name:adult brain|tissue:adult brain|tissue region:whole|cell type:mixed tissue dissociation|genotype:wildtype|geo loc name:missing|collection date:missing | Brain 11 whole scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:whole|cell type:mixed tissue dissociation|genotype:wildtype | GSM7875173 | GSM7875173: Brain 11 whole scRNAseq; Danio rerio; RNA Seq | GSM7875173 r1 | GSM7875173 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b11_mult_R1.fastq.gz b11_mult_R2.fastq.gz | fastq fastq | 14974963824.0 | 101182188.0 | GSM7875173 r1 | 0:28 1:120 | A:3753936293;C:3687961330;G:3650849763;T:3879258880;N:2957558 | 28 | 120 | 3753936293 | 3687961330 | 3650849763 | 3879258880 | 2957558 | SRX22323904 | SRS19374433 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.16926 | 0.9633 | 0.06452 | 0.20524 | 0.93545 | 0.76274 | 0.26732 | 0.59389 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28744 | 28744 | SRR26623281 | SRX22323903 | SRS19374431 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 10 telencephalon scRNAseq | GSM7875172 | source name:adult brain|tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|geo loc name:missing|collection date:missing | Brain 10 telencephalon scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype | GSM7875172 | GSM7875172: Brain 10 telencephalon scRNAseq; Danio rerio; RNA Seq | GSM7875172 r1 | GSM7875172 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b10_tel_seqrun1_R2.fastq.gz b10_tel_seqrun1_R1.fastq.gz | fastq fastq | 3731199140.0 | 25210805.0 | GSM7875172 r1 | 0:28 1:120 | A:1133663247;C:801786454;G:811411935;T:982912952;N:1424552 | 28 | 120 | 1133663247 | 801786454 | 811411935 | 982912952 | 1424552 | SRX22323903 | SRS19374431 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.01267 | 0.92045 | 0.00689 | 0.20316 | 0.99101 | 0.80876 | 0.4565 | 0.44433 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28745 | 28745 | SRR26623282 | SRX22323903 | SRS19374431 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 10 telencephalon scRNAseq | GSM7875172 | source name:adult brain|tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype|geo loc name:missing|collection date:missing | Brain 10 telencephalon scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:wildtype | GSM7875172 | GSM7875172: Brain 10 telencephalon scRNAseq; Danio rerio; RNA Seq | GSM7875172 r1 | GSM7875172 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b10_tel_seqrun2_R2.fastq.gz b10_tel_seqrun2_R1.fastq.gz | fastq fastq | 506663940.0 | 3423405.0 | GSM7875172 r2 | SRX22323903 | SRS19374431 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.01234 | 0.92119 | 0.00661 | 0.20424 | 0.99176 | 0.81156 | 0.50821 | 0.7283 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||
| 28746 | 28746 | SRR26623283 | SRX22323902 | SRS19374432 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 10 mesencephalon scRNAseq | GSM7875171 | source name:adult brain|tissue:adult brain|tissue region:mesencephalon|cell type:mixed tissue dissociation|genotype:wildtype|geo loc name:missing|collection date:missing | Brain 10 mesencephalon scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:mesencephalon|cell type:mixed tissue dissociation|genotype:wildtype | GSM7875171 | GSM7875171: Brain 10 mesencephalon scRNAseq; Danio rerio; RNA Seq | GSM7875171 r1 | GSM7875171 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b10_ot_seqrun1_R1.fastq.gz b10_ot_seqrun1_R2.fastq.gz | fastq fastq | 13285400412.0 | 89766219.0 | GSM7875171 r1 | 0:28 1:120 | A:4046617952;C:2711660606;G:2795963083;T:3726083915;N:5074856 | 28 | 120 | 4046617952 | 2711660606 | 2795963083 | 3726083915 | 5074856 | SRX22323902 | SRS19374432 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.01072 | 0.91211 | 0.00629 | 0.2341 | 0.99111 | 0.78985 | 0.46996 | 0.63777 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28747 | 28747 | SRR26623284 | SRX22323902 | SRS19374432 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 10 mesencephalon scRNAseq | GSM7875171 | source name:adult brain|tissue:adult brain|tissue region:mesencephalon|cell type:mixed tissue dissociation|genotype:wildtype|geo loc name:missing|collection date:missing | Brain 10 mesencephalon scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:mesencephalon|cell type:mixed tissue dissociation|genotype:wildtype | GSM7875171 | GSM7875171: Brain 10 mesencephalon scRNAseq; Danio rerio; RNA Seq | GSM7875171 r1 | GSM7875171 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b10_ot_seqrun2_R1.fastq.gz b10_ot_seqrun2_R2.fastq.gz | fastq fastq | 1804356800.0 | 12191600.0 | GSM7875171 r2 | 0:28 1:120 | A:547173169;C:367866083;G:382757407;T:506285738;N:274403 | 28 | 120 | 547173169 | 367866083 | 382757407 | 506285738 | 274403 | SRX22323902 | SRS19374432 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.0107 | 0.91103 | 0.00617 | 0.23408 | 0.99058 | 0.79178 | 0.4579 | 0.63098 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28748 | 28748 | SRR26623285 | SRX22323901 | SRS19374430 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 10 diencephalon scRNAseq | GSM7875170 | source name:adult brain|tissue:adult brain|tissue region:diencephalon|cell type:mixed tissue dissociation|genotype:wildtype|geo loc name:missing|collection date:missing | Brain 10 diencephalon scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:diencephalon|cell type:mixed tissue dissociation|genotype:wildtype | GSM7875170 | GSM7875170: Brain 10 diencephalon scRNAseq; Danio rerio; RNA Seq | GSM7875170 r1 | GSM7875170 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b10_dien_seqrun1_R1.fastq.gz b10_dien_seqrun1_R2.fastq.gz | fastq fastq | 16775453532.0 | 113347659.0 | GSM7875170 r1 | 0:28 1:120 | A:5122230488;C:3380526476;G:3500039522;T:4766209405;N:6447641 | 28 | 120 | 5122230488 | 3380526476 | 3500039522 | 4766209405 | 6447641 | SRX22323901 | SRS19374430 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.01031 | 0.90264 | 0.0062 | 0.26938 | 0.99107 | 0.78283 | 0.45373 | 0.61666 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28749 | 28749 | SRR26623286 | SRX22323901 | SRS19374430 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 10 diencephalon scRNAseq | GSM7875170 | source name:adult brain|tissue:adult brain|tissue region:diencephalon|cell type:mixed tissue dissociation|genotype:wildtype|geo loc name:missing|collection date:missing | Brain 10 diencephalon scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:diencephalon|cell type:mixed tissue dissociation|genotype:wildtype | GSM7875170 | GSM7875170: Brain 10 diencephalon scRNAseq; Danio rerio; RNA Seq | GSM7875170 r1 | GSM7875170 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b10_dien_seqrun2_R1.fastq.gz b10_dien_seqrun2_R2.fastq.gz | fastq fastq | 2278985844.0 | 15398553.0 | GSM7875170 r2 | 0:28 1:120 | A:693086062;C:458642995;G:479031763;T:647875888;N:349136 | 28 | 120 | 693086062 | 458642995 | 479031763 | 647875888 | 349136 | SRX22323901 | SRS19374430 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.01062 | 0.90395 | 0.0066 | 0.27264 | 0.99131 | 0.78524 | 0.45789 | 0.61679 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28750 | 28750 | SRR26623287 | SRX22323900 | SRS19374428 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 10 rhombencephalon scRNAseq | GSM7875169 | source name:adult brain|tissue:adult brain|tissue region:rhombencephalon|cell type:mixed tissue dissociation|genotype:wildtype|geo loc name:missing|collection date:missing | Brain 10 rhombencephalon scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:rhombencephalon|cell type:mixed tissue dissociation|genotype:wildtype | GSM7875169 | GSM7875169: Brain 10 rhombencephalon scRNAseq; Danio rerio; RNA Seq | GSM7875169 r1 | GSM7875169 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b10_cer_seqrun1_R1.fastq.gz b10_cer_seqrun1_R2.fastq.gz | fastq fastq | 16240869244.0 | 109735603.0 | GSM7875169 r1 | 0:28 1:120 | A:4994572796;C:3251585988;G:3395902822;T:4592558542;N:6249096 | 28 | 120 | 4994572796 | 3251585988 | 3395902822 | 4592558542 | 6249096 | SRX22323900 | SRS19374428 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.0128 | 0.89159 | 0.00813 | 0.3597 | 0.98991 | 0.82278 | 0.44977 | 0.60211 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28751 | 28751 | SRR26623288 | SRX22323900 | SRS19374428 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 10 rhombencephalon scRNAseq | GSM7875169 | source name:adult brain|tissue:adult brain|tissue region:rhombencephalon|cell type:mixed tissue dissociation|genotype:wildtype|geo loc name:missing|collection date:missing | Brain 10 rhombencephalon scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:rhombencephalon|cell type:mixed tissue dissociation|genotype:wildtype | GSM7875169 | GSM7875169: Brain 10 rhombencephalon scRNAseq; Danio rerio; RNA Seq | GSM7875169 r1 | GSM7875169 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b10_cer_seqrun2_R1.fastq.gz b10_cer_seqrun2_R2.fastq.gz | fastq fastq | 2208762212.0 | 14924069.0 | GSM7875169 r2 | 0:28 1:120 | A:677215802;C:441481145;G:464737322;T:624989898;N:338045 | 28 | 120 | 677215802 | 441481145 | 464737322 | 624989898 | 338045 | SRX22323900 | SRS19374428 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.0127 | 0.89091 | 0.00771 | 0.35998 | 0.9893 | 0.82432 | 0.41448 | 0.59902 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28752 | 28752 | SRR26623289 | SRX22323899 | SRS19374429 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 9 telencephalon scRNAseq | GSM7875168 | source name:adult brain|tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing | Brain 9 telencephalon scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:telencephalon|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M] | GSM7875168 | GSM7875168: Brain 9 telencephalon scRNAseq; Danio rerio; RNA Seq | GSM7875168 r1 | GSM7875168 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP469552 | loader:fastq load.py | b9_tel_R1.fastq.gz b9_tel_R2.fastq.gz | fastq fastq | 15193441000.0 | 122527750.0 | GSM7875168 r1 | 0:26 1:98 | A:4477414579;C:3090884741;G:3307200604;T:4310709839;N:7231237 | 26 | 98 | 4477414579 | 3090884741 | 3307200604 | 4310709839 | 7231237 | SRX22323899 | SRS19374429 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.00277 | 0.88718 | 0.00117 | 0.25579 | 0.99586 | 0.79657 | 0.30868 | 0.52408 | 26 | 98 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28753 | 28753 | SRR26623290 | SRX22323898 | SRS19374427 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Brain 8 whole scRNAseq | GSM7875167 | source name:adult brain|tissue:adult brain|tissue region:whole|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing | Brain 8 whole scRNAseq | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|tissue region:whole|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M] | GSM7875167 | GSM7875167: Brain 8 whole scRNAseq; Danio rerio; RNA Seq | GSM7875167 r1 | GSM7875167 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | b8_mult_R1.fastq.gz b8_mult_R2.fastq.gz | fastq fastq | 16275377550.0 | 108502517.0 | GSM7875167 r1 | 0:26 1:124 | A:5027003801;C:3172670099;G:3435240300;T:4638692244;N:1771106 | 26 | 124 | 5027003801 | 3172670099 | 3435240300 | 4638692244 | 1771106 | SRX22323898 | SRS19374427 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.02156 | 0.88716 | 0.00827 | 0.36741 | 0.97224 | 0.83228 | 0.41427 | 0.52965 | 26 | 124 | T | B | sc-like readlen | illumina | nextseq | unknown | random_priming | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | |||||||||||
| 28754 | 28754 | SRR26623291 | SRX22323897 | SRS19374426 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Lineage tracing rep2 ube2e1 scars | GSM7875196 | source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing | Lineage tracing rep2 ube2e1 scars | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M] | GSM7875196 | GSM7875196: Lineage tracing rep2 ube2e1 scars; Danio rerio; OTHER | GSM7875196 r1 | GSM7875196 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP469552 | loader:fastq load.py | lin2_ube2e1_scar_R1.fastq.gz lin2_ube2e1_scar_R2.fastq.gz | fastq fastq | 213092161.0 | 1190459.0 | GSM7875196 r1 | SRX22323897 | SRS19374426 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.00752 | 0.90776 | 0.00286 | 0.01739 | 0.99346 | 0.95444 | 0.46002 | 0.96817 | 28 | 151 | T | B | sc-like readlen | illumina | novaseq_era | unknown | other | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||
| 28755 | 28755 | SRR26623292 | SRX22323896 | SRS19374425 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Lineage tracing rep2 rpl39 scars | GSM7875195 | source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing | Lineage tracing rep2 rpl39 scars | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M] | GSM7875195 | GSM7875195: Lineage tracing rep2 rpl39 scars; Danio rerio; OTHER | GSM7875195 r1 | GSM7875195 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP469552 | loader:fastq load.py | lin2_rpl39_scar_R2.fastq.gz lin2_rpl39_scar_R1.fastq.gz | fastq fastq | 1023403502.0 | 5717338.0 | GSM7875195 r1 | SRX22323896 | SRS19374425 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.00086 | 0.83744 | 0.0003 | 0.00337 | 0.99845 | 0.97057 | 0.26605 | 0.40241 | 28 | 151 | T | B | sc-like readlen | illumina | novaseq_era | unknown | other | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||
| 28756 | 28756 | SRR26623293 | SRX22323895 | SRS19374424 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Lineage tracing rep2 cirbpb scars | GSM7875194 | source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing | Lineage tracing rep2 cirbpb scars | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M] | GSM7875194 | GSM7875194: Lineage tracing rep2 cirbpb scars; Danio rerio; OTHER | GSM7875194 r1 | GSM7875194 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP469552 | loader:fastq load.py | lin2_cirbpb_scar_R1.fastq.gz lin2_cirbpb_scar_R2.fastq.gz | fastq fastq | 276120388.0 | 1542572.0 | GSM7875194 r1 | SRX22323895 | SRS19374424 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.00206 | 0.80328 | 0.00078 | 0.00662 | 0.9975 | 0.98039 | 0.55421 | 0.0258 | 28 | 151 | T | B | sc-like readlen | illumina | novaseq_era | unknown | other | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||
| 28757 | 28757 | SRR26623294 | SRX22323894 | SRS19374423 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Lineage tracing rep2 cfl1 scars | GSM7875193 | source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing | Lineage tracing rep2 cfl1 scars | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M] | GSM7875193 | GSM7875193: Lineage tracing rep2 cfl1 scars; Danio rerio; OTHER | GSM7875193 r1 | GSM7875193 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP469552 | loader:fastq load.py | lin2_cfl1_scar_R1.fastq.gz lin2_cfl1_scar_R2.fastq.gz | fastq fastq | 791318009.0 | 4420771.0 | GSM7875193 r1 | SRX22323894 | SRS19374423 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.00067 | 0.46079 | 0.00055 | 0.16353 | 0.99965 | 0.99332 | 0.52631 | 0.44939 | 28 | 151 | T | B | sc-like readlen | illumina | novaseq_era | unknown | other | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||
| 28758 | 28758 | SRR26623295 | SRX22323893 | SRS19374421 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Lineage tracing rep1 ube2e1 scars | GSM7875192 | source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing | Lineage tracing rep1 ube2e1 scars | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M] | GSM7875192 | GSM7875192: Lineage tracing rep1 ube2e1 scars; Danio rerio; OTHER | GSM7875192 r1 | GSM7875192 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | lin1_ube2e1_scar_R1.fastq.gz lin1_ube2e1_scar_R2.fastq.gz | fastq fastq | 99407618.0 | 601781.0 | GSM7875192 r1 | SRX22323893 | SRS19374421 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.00657 | 0.84532 | 0.00205 | 0.03049 | 0.99537 | 0.95286 | 0.43306 | 0.19203 | 28 | 150 | T | B | sc-like readlen | illumina | nextseq | unknown | other | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System | ||||||||||||||||||||
| 28759 | 28759 | SRR26623296 | SRX22323892 | SRS19374422 | SRP469552 | PRJNA1034159 | Dissecting the spatiotemporal diversity of adult neural stem cells | GSE246714 | Other | Adult stem cells are important for tissue turnover and regeneration. However in most adult systems it remains elusive how stem cells assume different functional states and support spatially patterned tissue architecture. Here we dissected the diversity of neural stem cells in the adult zebrafish brain an organ that is characterized by pronounced zonation and high regenerative capacity. We combined single cell transcriptomics of dissected brain regions with massively parallel lineage tracing and in vivo RNA metabolic labeling to analyze regulation of neural stem cells in space and time. We detected a large diversity of neural stem cells with some subtypes being restricted to a single brain region while others were found globally across the brain. Global stem cell states are linked to neurogenic differentiation with different states being involved in proliferative and non proliferative differentiation. Our work reveals principles of adult stem cell organization and establishes a resource for functional manipulation of neural stem cell subtypes. Overall design: Single cell RNA seq of adult zebrafish brain performed using 10x Genomics Gene Expression protocols to explore transcriptomic diversity of adult cell types. The samples were prepared either from whole brain FACS sorted cells GFP positive cells from gfap:GFP line or a dissected single brain region as indicated in the sample title. CRISPR based lineage tracing was performed for a subset of samples to dissect developmental lineage relationships between cells. ScSLAM seq was performed in combination with Notch pathway inhibition to assess response of stem cells to perturbation. | pubmed:38365956 | Lineage tracing rep1 rpl39 scars | GSM7875191 | source name:adult brain|tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M]|geo loc name:missing|collection date:missing | Lineage tracing rep1 rpl39 scars | The transcriptome libraries were demultiplexed and mapped with CellRanger 6.1.1. In order to reduce batch effect the gene expression matrices were processed with the SoupX tool Young & Behjati 2020 for removing ambient RNA contamination. A subset of libraries was also mapped with Velocyto v0.17.17 La Manno et al 2018 to create count matrices for unspliced and spliced molecules. The targeted lineage tracing libraries were aligned using bwa mem3 v.0.7.12 to individual references of endogenous genes used in the lineage tracing experiment actb1 actb2 cfl1 cirbpb rpl39 and ube2e1. The scars were filtered with a custom pipeline to eliminate sequences that originate from PCR or sequencing errors. For custom code and further downstream analysis see: https://github.com/nimitic/radial glia. Assembly: GRCz11 Supplementary files format and content: Tab separated barcode files and matrix files along with the tab separated gene file supplementary file are the output of CellRanger mapping further processed by the SoupX package for ambient RNA removal. Supplementary files format and content: Loom files are the output of velocyto mapping distinguishing spliced and unspliced mRNAs. Supplementary files format and content: filtered scars.csv files contain the output of a custom scar filtering pipeline. | adult brain | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | tissue:adult brain|cell type:mixed tissue dissociation|genotype:Tg[ubi:zebrabow M] | GSM7875191 | GSM7875191: Lineage tracing rep1 rpl39 scars; Danio rerio; OTHER | GSM7875191 r1 | GSM7875191 | 1 | Adult zebrafish brain tissue was extracted optionally dissected to select a specific region of interest telencephalon diencephalon mesencephalon or rhombencephalon and then dissociated with a trypsin protocol. Briefly the samples were incubated in 750 µl of HBSS glucose solution and dissocated with 15 µl of 0.05% trypsin EDTA Gibco for 30 minutes at 37°C with intermittent mixing. The disociation was stopped by addition of 750 µl of a BSA EBSS HEPES solution. Further sample handling steps were carried out on ice and for centrifugation at 4°C. The sample was filtered through a 100 µm filter washed with cold HBSS and resuspended in 100 200 µl HBSS with 0.05% BSA then filtered through a 35 µm filter and loaded on the 10x Chromium Controller. For the scSLAM seq samples a papain dissociation protocol Worthington kit according to manufecturer's instructions was used followed by an adapted scSLAM seq protocol for labeling nascent transcripts see sample specific entry. The standard transcriptome libraries were constructed according to the manufacturer's protocol 10X Genomics. For targeted libraries of scars used for lineage tracing the cDNA obtained during the 10x protocol was used to set up individual PCR reactions for each target specifically amplifying the sgRNA target site. The libraries for targeted PCR were constructed with primers compatible with the 10X Genomics kit so they could be sequenced on the same platform. | OTHER | TRANSCRIPTOMIC | other | PAIRED | ILLUMINA | NextSeq 500 | SRP469552 | loader:fastq load.py | lin1_rpl39_scar_R1.fastq.gz lin1_rpl39_scar_R2.fastq.gz | fastq fastq | 401898718.0 | 2276836.0 | GSM7875191 r1 | SRX22323892 | SRS19374422 | SRA1743007 | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | Junker Lab, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine | 2 | 0.00037 | 0.2642 | 0.00015 | 0.00086 | 0.99922 | 0.99026 | 0.23076 | 0.42455 | 28 | 120 | T | B | sc-like readlen | illumina | nextseq | unknown | other | unknown | sc | single_cell_droplet | 10x | Germany | 2023-10-31 | Adult | Adult | Brain | Nervous System |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;