rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
9166,ERR2788341,ERX2797590,ERS2709706,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7292228,SAMEA4890710,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890710|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7292228|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:pool 4|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7292228|scientific name:Danio rerio|sex:2 female  1 male|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7292228 p,5149STDY7292228 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP|Experimental Factor: infect:n1,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7292228.bam 5149STDY7292228.bam.bai,bam bam,37970494940.0,387454030.0,E MTAB 7159:5149STDY7292228,0:98,A:11476520187;C:7571635167;G:8189594199;T:10701044279;N:31701108,98,,,,11476520187,7571635167,8189594199,10701044279,31701108,ERX2797590,ERS2709706,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.87568,,0.2122,,0.82582,,0.5259,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9167,ERR2788340,ERX2797589,ERS2709705,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7274848,SAMEA4890709,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890709|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274848|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 3|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274848|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274848 p,5149STDY7274848 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Vibrio Anguillarum,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7274848.bam 5149STDY7274848.bam.bai,bam bam,34517322840.0,352217580.0,E MTAB 7159:5149STDY7274848,0:98,A:10635243399;C:6658515314;G:7525079510;T:9695995344;N:2489273,98,,,,10635243399,6658515314,7525079510,9695995344,2489273,ERX2797589,ERS2709705,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.86206,,0.18065,,0.83514,,0.53609,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9168,ERR2788339,ERX2797588,ERS2709704,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7274847,SAMEA4890708,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890708|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274847|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 2|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274847|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274847 p,5149STDY7274847 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Anisakis simplex,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7274847.bam 5149STDY7274847.bam.bai,bam bam,34467649678.0,351710711.0,E MTAB 7159:5149STDY7274847,0:98,A:10609988948;C:6722093635;G:7464497879;T:9667814950;N:3254266,98,,,,10609988948,6722093635,7464497879,9667814950,3254266,ERX2797588,ERS2709704,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.88751,,0.21835,,0.83771,,0.53927,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
9169,ERR2788338,ERX2797587,ERS2709703,ERP110806,PRJEB28589,Single cell transcriptional analysis reveals ILC like cells in zebrafish,E-MTAB-7159,Transcriptome Analysis,Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11,,Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,5149STDY7274846,SAMEA4890707,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK",ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890707|INSDC center name:Department of Haematology  University of Cambridge  Cambridge  UK Wellcome Trust Sanger Institute  Wellcome Trust Genome Campus  Cambridge  Wellcome Trust   Medical Research Council Cambridge Stem Cell Institute  Cambridge  UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274846|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 1|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274846|scientific name:Danio rerio|sex:female|strain:AB,,,,,,,,,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,E MTAB 7159:5149STDY7274846 p,5149STDY7274846 p,Single cell transcriptional analysis reveals ILC like cells in zebrafish,The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 µm strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 µm strainer before adding 4' 6 diamidino 2 phenylindole DAPI  Beckman Coulter  cat no B30437 to the samples. Three zebrafish  per each condition i.e. zebrafish intraperitoneally injected with PBS  lyophilised Anisakis simplex or inactivated Vibrio anguillarum  were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 l 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting  cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/μl. Briefly  cellular suspension was added to the master mix containing nuclease free water  RT Reagent Mix  RT Primer  Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium™ Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium™ Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53°C for 45 min  85°C for 5 min  held at 4°C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98°C for 3 min  12 cycles of 90°C for 15 s  67°C for 20 s and 72°C for 1 min  72°C for 1 min  held 4°C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium™ Controller and Chromium™ Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly  for fragmentation  end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32°C for 5 min  65°C for 30 min  held at 4°C. The libraries were then purified using beads. Next adaptor ligation was performed  samples were incubated with Adaptor Ligation Mix at 20°C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check  the libraries were diluted to the concentration required for sequencing.,Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:n1,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>866</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_LABEL>F</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_LABEL>R</READ_LABEL><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>434</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,ERP110806,Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish,ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options:  use QUAL,5149STDY7274846.bam 5149STDY7274846.bam.bai,bam bam,35052538472.0,357678964.0,E MTAB 7159:5149STDY7274846,0:98,A:10698116265;C:6858102477;G:7626019661;T:9866905792;N:3394277,98,,,,10698116265,6858102477,7626019661,9866905792,3394277,ERX2797587,ERS2709703,ERA1594569,"Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive","Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive",1,0.88916,,0.21537,,0.83802,,0.5336,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United Kingdom,2018-09-11,Adult,Adult,Gut,Digestive System
30626,SRR27907720,SRX23567476,SRS20412967,SRP488787,PRJNA1074408,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [scRNA seq],GSE255303,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood  but genetic factors have implicated in genome wide association studies  including CTLA 4  an essential negative regulator of T cell activation. However  establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study  we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 /  zebrafish line. These mutant zebrafish exhibit reduced weight  along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes  disturbing immune system homeostasis. Moreover  single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression  along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally  Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly  supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether  these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: intestine leukocyte WT and KO Ctla 4 deficiency  of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.,,pubmed:40392591,,KO  scRNAseq,GSM8068833,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO|geo loc name:missing|collection date:missing,KO  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 μg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:intestine|cell type:leukocyte|genotype:Ctla 4 KO,GSM8068833,GSM8068833: KO  scRNAseq; Danio rerio; RNA Seq,GSM8068833 r1,GSM8068833,1,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 μg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP488787,,loader:fastq load.py,KO_S1_L001_R2_001.fastq.gz KO_S1_L001_R1_001.fastq.gz,fastq fastq,40958285011.0,344187269.0,GSM8068833 r1,0:28 1:91,A:11614416767;C:9247684357;G:9480911439;T:10614469263;N:803185,28,91,,,11614416767,9247684357,9480911439,10614469263,803185,SRX23567476,SRS20412967,SRA1799569,zhejiang university,zhejiang university,2,0.00982,0.9431,0.00356,0.10625,0.99277,0.8187,0.41297,0.63838,28,91,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30627,SRR27907721,SRX23567475,SRS20412966,SRP488787,PRJNA1074408,Ctla 4 deficiency induces an inflammatory bowel disease like phenotype in a zebrafish model [scRNA seq],GSE255303,Transcriptome Analysis,Inflammatory bowel disease IBD is a chronic and relapsing immune mediated disorder characterized by intestinal inflammation and epithelial injury. The underlying causes of IBD are not fully understood  but genetic factors have implicated in genome wide association studies  including CTLA 4  an essential negative regulator of T cell activation. However  establishing a direct link between CTLA 4 and IBD has been challenging due to the early lethality of CTLA 4 knockout mice. In this study  we identified zebrafish Ctla 4 ortholog and investigated its role in maintaining intestinal immune homeostasis by generating a Ctla 4 deficient ctla 4 /  zebrafish line. These mutant zebrafish exhibit reduced weight  along with impaired epithelial barrier integrity and lymphocytic infiltration in their intestines. Transcriptomics analysis revealed upregulation of inflammation related genes  disturbing immune system homeostasis. Moreover  single cell RNA sequencing analysis indicated increased Th2 cells and interleukin 13 expression  along with decreased innate lymphoid cells and upregulated proinflammatory cytokines. Additionally  Ctla 4 deficient zebrafish exhibited reduced diversity and an altered composition of the intestinal microbiota. All these phenotypes closely resemble those found in mammalian IBD. Lastly  supplementation with Ctla 4 Ig successfully alleviated intestinal inflammation in these mutants. Altogether  these findings offer substantial evidence linking CTLA 4 to IBD and establish a new model for investigating pathogenesis and potential treatments. Overall design: intestine leukocyte WT and KO Ctla 4 deficiency  of the AB zebrafish were isolated by Ficoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.,,pubmed:40392591,,WT  scRNAseq,GSM8068832,,source name:intestine|tissue:intestine|cell type:leukocyte|genotype:Wildtype|geo loc name:missing|collection date:missing,WT  scRNAseq,The demultiplexing  barcoded processing  gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: GRCz11 Supplementary files format and content: Tab separated values files and matrix files,intestine,,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 μg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,tissue:intestine|cell type:leukocyte|genotype:Wildtype,GSM8068832,GSM8068832: WT  scRNAseq; Danio rerio; RNA Seq,GSM8068832 r1,GSM8068832,1,Leukocytes were collected from the intestine samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation. Briefly the intestine was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH  Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15  Gibco supplemented with penicillin 100 U/ml  Sigma Aldrich  streptomycin 100 μg/ml  Sigma Aldrich and heparin sodium 10 U/ml  Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation  centrifuged at 1 200 g for 25 min  and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma  St. Louis  MO  USA  which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol  10x Genomics. Briefly  GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA  which contains an Ilumina R1 primer sequence  Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads  amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence  paired end constructs with P5 and P7 sequences and a sample index were added.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP488787,,loader:fastq load.py,WT_S1_L001_R1_001.fastq.gz WT_S1_L001_R2_001.fastq.gz,fastq fastq,36724066995.0,308605605.0,GSM8068832 r1,0:28 1:91,A:10425178276;C:8399183780;G:8411777361;T:9487202777;N:724801,28,91,,,10425178276,8399183780,8411777361,9487202777,724801,SRX23567475,SRS20412966,SRA1799569,zhejiang university,zhejiang university,2,0.01141,0.94944,0.0039,0.1092,0.99324,0.841,0.43558,0.73314,28,91,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,China,2024-02-07,Undetermined,Undetermined,Gut,Digestive System
30694,SRR28272066,SRX23882001,SRS20705714,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122775  HuNoV infected  replicate 2 scRNAseq,GSM8136771,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing,GC122775  HuNoV infected  replicate 2 scRNAseq,Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 µg/mL proteinase K  0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected,GSM8136771,GSM8136771: GC122775  HuNoV infected  replicate 2 scRNAseq; Danio rerio; RNA Seq,GSM8136771 r1,GSM8136771,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 µg/mL proteinase K  0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122775_SI-GA-D7_S4_L001_R1_001.fastq.gz GC122775_SI-GA-D7_S4_L001_R2_001.fastq.gz,fastq fastq,6487168261.0,54514019.0,GSM8136771 r1,0:28 1:91,A:1754199332;C:1533792234;G:1687916105;T:1511168304;N:92286,28,91,,,1754199332,1533792234,1687916105,1511168304,92286,SRX23882001,SRS20705714,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30695,SRR28272067,SRX23882001,SRS20705714,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122775  HuNoV infected  replicate 2 scRNAseq,GSM8136771,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing,GC122775  HuNoV infected  replicate 2 scRNAseq,Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 µg/mL proteinase K  0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected,GSM8136771,GSM8136771: GC122775  HuNoV infected  replicate 2 scRNAseq; Danio rerio; RNA Seq,GSM8136771 r1,GSM8136771,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 µg/mL proteinase K  0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122775_SI-GA-D7_S4_L002_R1_001.fastq.gz GC122775_SI-GA-D7_S4_L002_R2_001.fastq.gz,fastq fastq,6313572727.0,53055233.0,GSM8136771 r2,0:28 1:91,A:1709609257;C:1491468410;G:1640296277;T:1472111501;N:87282,28,91,,,1709609257,1491468410,1640296277,1472111501,87282,SRX23882001,SRS20705714,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30696,SRR28272068,SRX23882000,SRS20705713,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122774  HuNoV infected  replicate 1  scRNAseq,GSM8136770,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing,GC122774  HuNoV infected  replicate 1  scRNAseq,Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 µg/mL proteinase K  0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected,GSM8136770,GSM8136770: GC122774  HuNoV infected  replicate 1  scRNAseq; Danio rerio; RNA Seq,GSM8136770 r1,GSM8136770,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 µg/mL proteinase K  0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122774_SI-GA-C7_S3_L001_R1_001.fastq.gz GC122774_SI-GA-C7_S3_L001_R2_001.fastq.gz,fastq fastq,15738518978.0,132256462.0,GSM8136770 r1,0:28 1:91,A:4181691582;C:3761213961;G:4083789142;T:3711597081;N:227212,28,91,,,4181691582,3761213961,4083789142,3711597081,227212,SRX23882000,SRS20705713,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30697,SRR28272069,SRX23882000,SRS20705713,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122774  HuNoV infected  replicate 1  scRNAseq,GSM8136770,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected|geo loc name:missing|collection date:missing,GC122774  HuNoV infected  replicate 1  scRNAseq,Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 µg/mL proteinase K  0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:HuNoV infected,GSM8136770,GSM8136770: GC122774  HuNoV infected  replicate 1  scRNAseq; Danio rerio; RNA Seq,GSM8136770 r1,GSM8136770,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 µg/mL proteinase K  0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122774_SI-GA-C7_S3_L002_R1_001.fastq.gz GC122774_SI-GA-C7_S3_L002_R2_001.fastq.gz,fastq fastq,15261653253.0,128249187.0,GSM8136770 r2,0:28 1:91,A:4059552936;C:3644406570;G:3954261902;T:3603216152;N:215693,28,91,,,4059552936,3644406570,3954261902,3603216152,215693,SRX23882000,SRS20705713,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30698,SRR28272070,SRX23881999,SRS20705712,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122773  uninfected  replicate 2  scRNAseq,GSM8136769,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing,GC122773  uninfected  replicate 2  scRNAseq,Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 µg/mL proteinase K  0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected,GSM8136769,GSM8136769: GC122773  uninfected  replicate 2  scRNAseq; Danio rerio; RNA Seq,GSM8136769 r1,GSM8136769,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 µg/mL proteinase K  0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122773_SI-GA-B7_S2_L001_R1_001.fastq.gz GC122773_SI-GA-B7_S2_L001_R2_001.fastq.gz,fastq fastq,15150656598.0,127316442.0,GSM8136769 r1,0:28 1:91,A:4100783574;C:3526779401;G:3845684506;T:3677189004;N:220113,28,91,,,4100783574,3526779401,3845684506,3677189004,220113,SRX23881999,SRS20705712,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30699,SRR28272071,SRX23881999,SRS20705712,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122773  uninfected  replicate 2  scRNAseq,GSM8136769,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing,GC122773  uninfected  replicate 2  scRNAseq,Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 µg/mL proteinase K  0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected,GSM8136769,GSM8136769: GC122773  uninfected  replicate 2  scRNAseq; Danio rerio; RNA Seq,GSM8136769 r1,GSM8136769,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 µg/mL proteinase K  0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122773_SI-GA-B7_S2_L002_R1_001.fastq.gz GC122773_SI-GA-B7_S2_L002_R2_001.fastq.gz,fastq fastq,14942015326.0,125563154.0,GSM8136769 r2,0:28 1:91,A:4048600218;C:3475105088;G:3787275869;T:3630822343;N:211808,28,91,,,4048600218,3475105088,3787275869,3630822343,211808,SRX23881999,SRS20705712,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30700,SRR28272072,SRX23881998,SRS20705711,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122772  uninfected  replicate 1  scRNAseq,GSM8136768,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing,GC122772  uninfected  replicate 1  scRNAseq,Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 µg/mL proteinase K  0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected,GSM8136768,GSM8136768: GC122772  uninfected  replicate 1  scRNAseq; Danio rerio; RNA Seq,GSM8136768 r1,GSM8136768,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 µg/mL proteinase K  0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122772_SI-GA-A7_S1_L001_R1_001.fastq.gz GC122772_SI-GA-A7_S1_L001_R2_001.fastq.gz,fastq fastq,7397061301.0,62160179.0,GSM8136768 r1,0:28 1:91,A:2023651844;C:1711760729;G:1860691426;T:1800850496;N:106806,28,91,,,2023651844,1711760729,1860691426,1800850496,106806,SRX23881998,SRS20705711,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
30701,SRR28272073,SRX23881998,SRS20705711,SRP494129,PRJNA1085664,Human norovirus replicates in macrophages migrating to intestinal tissues and changes their transcriptional profile,GSE261163,Transcriptome Analysis,Human noroviruses HuNoVs are a major cause of diarrheal disease  yet critical aspects of their biology  including cellular tropism  remain unclear. While research traditionally focused on the intestinal epithelium  the hypothesis that HuNoV infects macrophages has been recurrently discussed and is investigated here by a zebrafish larval model. Our study reveals that HuNoV capsid proteins and double stranded RNA colocalize within intestinal macrophages of infected zebrafish larvae  while the negative strand RNA intermediate was detected within FACS sorted macrophages. Flow cytometry confirms viral replication within these macrophages  constituting 9% of HuNoV?s host cells. Single cell RNA sequencing reaffirms their role in viral replication  as all three open reading frames were mapped to individual macrophages. Yet  macrophages were not required for productive infection given the limited changes in viral loads upon their absence. Identifying macrophages as host cells prompts a reevaluation of their role in HuNoV pathogenesis  offering new directions for understanding and controlling this infection. Overall design: Intestines of uninfected and HuNoV infected zebrafish larvae were dissected and subjected to the preparation of a single cell suspension that was analyzed using scRNAseq. Subsequently  an additional sample was analyzed on FACS sorted macrophages of HuNoV infected zebrafish larvae.,,pubmed:39584740,,GC122772  uninfected  replicate 1  scRNAseq,GSM8136768,,source name:Intestines|tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected|geo loc name:missing|collection date:missing,GC122772  uninfected  replicate 1  scRNAseq,Cell Ranger v3.0 10X Genomics  Pleasanton  California  USA was used for single cell analysis to demultiplex raw base call files from Illumina sequencing and to align reads to both the zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1. Cell Ranger output matrices were analyzed using the Seurat R package version 3.1 in RStudio. Assembly: zebrafish reference genome Ensembl GRCz11.106 and the HuNoV reference genome Genbank JX459908.1 Supplementary files format and content: Count Matrix Cell Ranger,Intestines,,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 µg/mL proteinase K  0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell 3’Library & Gel Bead Kit v3 protocol.,,tissue:Intestines|cell line:wildtype AB|cell type:120 hpf|infection:uninfected,GSM8136768,GSM8136768: GC122772  uninfected  replicate 1  scRNAseq; Danio rerio; RNA Seq,GSM8136768 r1,GSM8136768,1,Intestinal tissues were manually dissected and subjected to dissociation using 1mg/mL collagenase  40 µg/mL proteinase K  0.25% trypsin for 40 min at 37°C. Cells were resuspended in 0.04% BSA and live cells were selected via Optiprep density gradient according to the manufacterer's protocol. The single cell suspensions were immediately subjected to the 10X Genomics Chromium Controller with Chromium Single Cell 3′ Library & Gel Bead Kit v3.1. Libraries were constructed according to 10X Genomics Chromium Single Cell three primeLibrary & Gel Bead Kit v3 protocol.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP494129,,,GC122772_SI-GA-A7_S1_L002_R1_001.fastq.gz GC122772_SI-GA-A7_S1_L002_R2_001.fastq.gz,fastq fastq,7290496444.0,61264676.0,GSM8136768 r2,0:28 1:91,A:1996736343;C:1685693360;G:1830823892;T:1777138653;N:104196,28,91,,,1996736343,1685693360,1830823892,1777138653,104196,SRX23881998,SRS20705711,SRA1820104,Genomics Core Leuven,"Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology, and Transplantation, KU Leuven, Rega Institute",,,,,,,,,,,,T,B,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Belgium,2024-03-08,Larval,Larval,Gut,Digestive System
33014,SRR29633212,SRX25139207,SRS21831220,SRP516661,PRJNA1129181,A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing,GSE271002,Transcriptome Analysis,To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish  we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation  and DAPI  live cells were sorted by FACS.,,pubmed:40252728,,Mtz  5dpf,GSM8366963,,source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole|geo loc name:missing|collection date:missing,Mtz  5dpf,Demultiplexing of raw Illumina sequencing files  barcoding processing  gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files,Dissected larval intestines,,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70µm membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole,GSM8366963,GSM8366963: Mtz  5dpf; Danio rerio; RNA Seq,GSM8366963 r1,GSM8366963,1,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70µm membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP516661,,loader:fastq load.py,NTR-Mtz-d5_R1.fastq.gz NTR-Mtz-d5_R2.fastq.gz,fastq fastq,105173263361.0,348971465.0,GSM8366963 r1,0:150.76 1:150.62,A:29260313483;C:18342577741;G:20471735616;T:37097033318;N:1603203,150,150,,,29260313483,18342577741,20471735616,37097033318,1603203,SRX25139207,SRS21831220,SRA1911905,Karolinska Institutet,Karolinska Institutet,2,0.56019,0.89517,0.13273,0.11945,0.9795,0.82258,0.63676,0.6161,151,150,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-06-27,Larval,Larval,Gut,Digestive System
33015,SRR29633213,SRX25139206,SRS21831219,SRP516661,PRJNA1129181,A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing,GSE271002,Transcriptome Analysis,To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish  we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation  and DAPI  live cells were sorted by FACS.,,pubmed:40252728,,Control  5dpf,GSM8366962,,source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control|geo loc name:missing|collection date:missing,Control  5dpf,Demultiplexing of raw Illumina sequencing files  barcoding processing  gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files,Dissected larval intestines,,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70µm membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control,GSM8366962,GSM8366962: Control  5dpf; Danio rerio; RNA Seq,GSM8366962 r1,GSM8366962,1,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70µm membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP516661,,loader:fastq load.py,NTR-Control-d5_R1.fastq.gz NTR-Control-d5_R2.fastq.gz,fastq fastq,139967773505.0,464402100.0,GSM8366962 r1,0:150.76 1:150.63,A:39202616731;C:24289494719;G:27175225437;T:49298534102;N:1902516,150,150,,,39202616731,24289494719,27175225437,49298534102,1902516,SRX25139206,SRS21831219,SRA1911905,Karolinska Institutet,Karolinska Institutet,2,0.54902,0.89315,0.13449,0.13341,0.97954,0.80553,0.69256,0.59244,151,151,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-06-27,Larval,Larval,Gut,Digestive System
33016,SRR29633214,SRX25139205,SRS21831218,SRP516661,PRJNA1129181,A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing,GSE271002,Transcriptome Analysis,To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish  we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation  and DAPI  live cells were sorted by FACS.,,pubmed:40252728,,Mtz  ablation 4dpf,GSM8366961,,source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole|geo loc name:missing|collection date:missing,Mtz  ablation 4dpf,Demultiplexing of raw Illumina sequencing files  barcoding processing  gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files,Dissected larval intestines,,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70µm membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Metronidazole,GSM8366961,GSM8366961: Mtz  ablation 4dpf; Danio rerio; RNA Seq,GSM8366961 r1,GSM8366961,1,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70µm membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP516661,,loader:fastq load.py|options:  readTypes=BBTT   read1PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 R1 001.fastq.gz   read2PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 R2 001.fastq.gz   read3PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 I1 001.fastq.gz   read4PairFiles=Mtz d4 SCI7T062 SCI5T062 H3MGYDSX5 S19 L003 I2 001.fastq.gz,Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_R2_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_R1_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_I2_001.fastq.gz Mtz_d4-SCI7T062-SCI5T062_H3MGYDSX5_S19_L003_I1_001.fastq.gz,fastq fastq fastq fastq,33049837760.0,103280743.0,GSM8366961 r1,0:150 1:150 2:10 3:10,A:9739096160;C:6338831532;G:6106096444;T:8799858219;N:340545,150,150,10,10,9739096160,6338831532,6106096444,8799858219,340545,SRX25139205,SRS21831218,SRA1911905,Karolinska Institutet,Karolinska Institutet,2,0.0,0.91169,0.0,0.19328,1.0,0.81722,,0.64993,150,150,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-06-27,Larval,Larval,Gut,Digestive System
33017,SRR29633215,SRX25139204,SRS21831217,SRP516661,PRJNA1129181,A novel zebrafish model of intestinal epithelial damage reveals macrophages and igfbp1a as major modulators of mucosal healing,GSE271002,Transcriptome Analysis,To elucidate the cellular and molecular mechanisms governing intestinal damage and regeneration in zebrafish  we performed single cell scRNA seq from dissected intestines. Overall design: Intestines from control and Mtz treated zebrafish larvae were dissected at 4 dpf dpf and 5dpf. Single cell suspensions from dissected intestines were prepared througn enzymatic and mechanical disaggregation  and DAPI  live cells were sorted by FACS.,,pubmed:40252728,,Control  ablation 4dpf,GSM8366960,,source name:Dissected larval intestines|tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control|geo loc name:missing|collection date:missing,Control  ablation 4dpf,Demultiplexing of raw Illumina sequencing files  barcoding processing  gene counting and aggregation were performed using the CellRanger v3.0 software Assembly: Ensembl GRCz11.105 Supplementary files format and content: Tab separated values files and matrix files,Dissected larval intestines,,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70µm membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,tissue:Dissected larval intestines|cell type:Mix of intestinal cells|genotype:AB|treatment:Control,GSM8366960,GSM8366960: Control  ablation 4dpf; Danio rerio; RNA Seq,GSM8366960 r1,GSM8366960,1,Larval intestines were manually dissected within an interval of 2 hours and collected in sterile HBSS BSA 0.5%. Single cell preparations were done by incubating dissected intestines in dissaggregation buffer TrypLE supplemented with 0.5mg/mL of Dnase I for 30min at 28°C  with extensive pipetting every 10 minutes. Single cell preparations were washed with HBSS BSA 0.5%  filtered with a 70µm membrane  and stained with DAPI 0.2 mg/mL to exclude dead cells. Live intestinal cells were FACS sorted using a Sony SH800S cell sorter. Library was prepared according to manufacturer's instructions 10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP516661,,loader:fastq load.py|options:  readTypes=BBTT   read1PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 R1 001.fastq.gz   read2PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 R2 001.fastq.gz   read3PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 I1 001.fastq.gz   read4PairFiles=Control d4 SCI7T050 SCI5T050 H5GWKDSX5 S5 L002 I2 001.fastq.gz,Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_R2_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_R1_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_I2_001.fastq.gz Control_d4-SCI7T050-SCI5T050_H5GWKDSX5_S5_L002_I1_001.fastq.gz,fastq fastq fastq fastq,115286504000.0,360270325.0,GSM8366960 r1,0:150 1:150 2:10 3:10,A:32679027944;C:17748865933;G:17885040590;T:39764959491;N:3203542,150,150,10,10,32679027944,17748865933,17885040590,39764959491,3203542,SRX25139204,SRS21831217,SRA1911905,Karolinska Institutet,Karolinska Institutet,2,0.39015,0.90036,0.10989,0.19421,0.97845,0.79401,0.69547,0.6103,150,150,B,B,mate1-mate2 similar by mapping diff,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Sweden,2024-06-27,Larval,Larval,Gut,Digestive System
33417,SRR30186672,SRX25652379,SRS22295184,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS6dpf,GSM8448586,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf|geo loc name:missing|collection date:missing,ENS6dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf,GSM8448586,GSM8448586: ENS6dpf; Danio rerio; RNA Seq,GSM8448586 r1,GSM8448586,1,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26637_S5_L005_I1_001.fastq.gz FT-SA26637_S5_L005_R1_001.fastq.gz FT-SA26637_S5_L005_R2_001.fastq.gz,fastq fastq fastq,40502433410.0,130653011.0,GSM8448586 r1,0:8 1:151 2:151,A:10014178947;C:5704376875;G:6596271508;T:17137143949;N:5238043,8,151,151,,10014178947,5704376875,6596271508,17137143949,5238043,SRX25652379,SRS22295184,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33418,SRR30186673,SRX25652379,SRS22295184,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS6dpf,GSM8448586,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf|geo loc name:missing|collection date:missing,ENS6dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:6dpf,GSM8448586,GSM8448586: ENS6dpf; Danio rerio; RNA Seq,GSM8448586 r1,GSM8448586,1,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26637_S5_L006_I1_001.fastq.gz FT-SA26637_S5_L006_R1_001.fastq.gz FT-SA26637_S5_L006_R2_001.fastq.gz,fastq fastq fastq,41972742020.0,135395942.0,GSM8448586 r2,0:8 1:151 2:151,A:10346550415;C:6105559893;G:6757897068;T:17672755179;N:6811929,8,151,151,,10346550415,6105559893,6757897068,17672755179,6811929,SRX25652379,SRS22295184,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33419,SRR30186674,SRX25652378,SRS22295179,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS5dpf,GSM8448585,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf|geo loc name:missing|collection date:missing,ENS5dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf,GSM8448585,GSM8448585: ENS5dpf; Danio rerio; RNA Seq,GSM8448585 r1,GSM8448585,1,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26636_S4_L005_I1_001.fastq.gz FT-SA26636_S4_L005_R1_001.fastq.gz FT-SA26636_S4_L005_R2_001.fastq.gz,fastq fastq fastq,21590505830.0,69646793.0,GSM8448585 r1,0:8 1:151 2:151,A:5324745627;C:3047288539;G:3517496789;T:9140955618;N:2844913,8,151,151,,5324745627,3047288539,3517496789,9140955618,2844913,SRX25652378,SRS22295179,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33420,SRR30186675,SRX25652378,SRS22295179,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS5dpf,GSM8448585,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf|geo loc name:missing|collection date:missing,ENS5dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:5dpf,GSM8448585,GSM8448585: ENS5dpf; Danio rerio; RNA Seq,GSM8448585 r1,GSM8448585,1,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26636_S4_L006_I1_001.fastq.gz FT-SA26636_S4_L006_R1_001.fastq.gz FT-SA26636_S4_L006_R2_001.fastq.gz,fastq fastq fastq,22493595040.0,72559984.0,GSM8448585 r2,0:8 1:151 2:151,A:5532271824;C:3275587569;G:3623404196;T:9478183540;N:3668039,8,151,151,,5532271824,3275587569,3623404196,9478183540,3668039,SRX25652378,SRS22295179,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33421,SRR30186676,SRX25652377,SRS22295180,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS4dpf,GSM8448584,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:4dpf|geo loc name:missing|collection date:missing,ENS4dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:4dpf,GSM8448584,GSM8448584: ENS4dpf; Danio rerio; RNA Seq,GSM8448584 r1,GSM8448584,1,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26635_S3_L005_I1_001.fastq.gz FT-SA26635_S3_L005_R1_001.fastq.gz FT-SA26635_S3_L005_R2_001.fastq.gz,fastq fastq fastq,29011782450.0,93586395.0,GSM8448584 r1,0:8 1:151 2:151,A:7041483148;C:4220842692;G:4903817651;T:12093250712;N:3697087,8,151,151,,7041483148,4220842692,4903817651,12093250712,3697087,SRX25652377,SRS22295180,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33422,SRR30186677,SRX25652377,SRS22295180,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS4dpf,GSM8448584,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:4dpf|geo loc name:missing|collection date:missing,ENS4dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:4dpf,GSM8448584,GSM8448584: ENS4dpf; Danio rerio; RNA Seq,GSM8448584 r1,GSM8448584,1,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26635_S3_L006_I1_001.fastq.gz FT-SA26635_S3_L006_R1_001.fastq.gz FT-SA26635_S3_L006_R2_001.fastq.gz,fastq fastq fastq,30061975960.0,96974116.0,GSM8448584 r2,0:8 1:151 2:151,A:7272472037;C:4518131790;G:5023942263;T:12466801069;N:4835873,8,151,151,,7272472037,4518131790,5023942263,12466801069,4835873,SRX25652377,SRS22295180,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33423,SRR30186678,SRX25652376,SRS22295175,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS3dpf,GSM8448583,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:3dpf|geo loc name:missing|collection date:missing,ENS3dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:3dpf,GSM8448583,GSM8448583: ENS3dpf; Danio rerio; RNA Seq,GSM8448583 r1,GSM8448583,1,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26634_S2_L005_I1_001.fastq.gz FT-SA26634_S2_L005_R1_001.fastq.gz FT-SA26634_S2_L005_R2_001.fastq.gz,fastq fastq fastq,28701845380.0,92586598.0,GSM8448583 r1,0:8 1:151 2:151,A:6898569356;C:4281479855;G:4993869601;T:11783488306;N:3745478,8,151,151,,6898569356,4281479855,4993869601,11783488306,3745478,SRX25652376,SRS22295175,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33424,SRR30186679,SRX25652376,SRS22295175,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS3dpf,GSM8448583,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:3dpf|geo loc name:missing|collection date:missing,ENS3dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:3dpf,GSM8448583,GSM8448583: ENS3dpf; Danio rerio; RNA Seq,GSM8448583 r1,GSM8448583,1,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26634_S2_L006_I1_001.fastq.gz FT-SA26634_S2_L006_R1_001.fastq.gz FT-SA26634_S2_L006_R2_001.fastq.gz,fastq fastq fastq,29814490250.0,96175775.0,GSM8448583 r2,0:8 1:151 2:151,A:7143218463;C:4592538828;G:5130593993;T:12173956857;N:4775909,8,151,151,,7143218463,4592538828,5130593993,12173956857,4775909,SRX25652376,SRS22295175,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Larval,Larval,Gut,Digestive System
33425,SRR30186680,SRX25652375,SRS22295177,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS2dpf,GSM8448582,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:2dpf|geo loc name:missing|collection date:missing,ENS2dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:2dpf,GSM8448582,GSM8448582: ENS2dpf; Danio rerio; RNA Seq,GSM8448582 r1,GSM8448582,1,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26633_S1_L005_I1_001.fastq.gz FT-SA26633_S1_L005_R1_001.fastq.gz FT-SA26633_S1_L005_R2_001.fastq.gz,fastq fastq fastq,16641390240.0,53681904.0,GSM8448582 r1,0:8 1:151 2:151,A:3957785280;C:2573469243;G:2993166279;T:6685407270;N:2106936,8,151,151,,3957785280,2573469243,2993166279,6685407270,2106936,SRX25652375,SRS22295177,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Hatching,Embryo,Gut,Digestive System
33426,SRR30186681,SRX25652375,SRS22295177,SRP525362,PRJNA1146366,Spatiotemporal dynamics of the developing zebrafish enteric nervous system at the whole organ level,GSE274407,Transcriptome Analysis,Neural crest cells give rise to the neurons of the enteric nervous system ENS that innervate the gastrointestinal tract to regulate gut motility. The immense size and distinct subregions of the gut present a challenge to understanding the spatial organization and sequential differentiation of different neuronal subtypes. Here  we profile enteric neurons and progenitors at single cell resolution during zebrafish embryonic and larval development to provide a near complete picture of transcriptional changes that accompany emergence of ENS neurons throughout the gastrointestinal tract. Multiplex spatial RNA transcript analysis reveals the temporal order and distinct localization patterns of neuronal subtypes along the length of the gut. Finally  we show that functional perturbation of select transcription factors Ebf1a  Gata3 and Satb2 alters the cell fate choice  respectively  of inhibitory  excitatory and serotonergic neuronal subtypes in the developing ENS. Overall design: Cells in the developing ENS of the TgPhox2bb:mNeonGreen zebrafish were isolated by Fluorescence activated cell sorting FACS according to the presence of mNeonGreen signal and used for scRNA seq experiment.,,pubmed:39642879,,ENS2dpf,GSM8448582,,source name:intestine|tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:2dpf|geo loc name:missing|collection date:missing,ENS2dpf,The raw data from 5 different time points were preprocessed separately using Kallisto and bustools programs. We constructed a reference transcriptome for pseudoalignment based on zebrafish genome assembly GRCz10. Assembly: GRCz10 Supplementary files format and content: h5ad files,intestine,,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer’s Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,tissue:intestine|cell type:Cells in the ENS|genotype:Phox2bb:mNeonGreen heterozygous|age:2dpf,GSM8448582,GSM8448582: ENS2dpf; Danio rerio; RNA Seq,GSM8448582 r1,GSM8448582,1,To isolate ENS cells  we generated a reporter line by inserting mNeonGreen fluorescent protein post the Phox2bb coding sequence  such that mNeonGreen faithfully recapitulates endogenous Phox2bb expression. Embryos and larvae at 2  3  4  5 dpf and 6 dpf were anesthetized by tricaine Methanesulfonate MS222  followed by deyolking and dissection to remove the head part. The remainder of the embryo/larvae were kept in Ringer's Solution on ice and dissociated with Accumax cell dissociation solution at 30oC for 20  23  28  32 and 36 mins at 1000rpm in the Eppendorf thermomixer R system  with pipetting up and down every 5 minutes. post digestion  Accumax was quenched by ice cold resuspension buffer 1X Hanks' Balanced Salt Solution  no calcium  no magnesium HBSS;10mM HEPES  adjusted to PH 8.0; 2.5 mg/ml BSA  and samples were then passed through a 70um cell strainer into 50ml conical tube  centrifuged at 300g for 10 mins and resuspended in 500ul fresh resuspension buffer for cell sorting. Library was performed following the manufacter's instructions single cell three prime v2 protocol  10x Genomics.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP525362,,loader:fastq load.py,FT-SA26633_S1_L006_I1_001.fastq.gz FT-SA26633_S1_L006_R1_001.fastq.gz FT-SA26633_S1_L006_R2_001.fastq.gz,fastq fastq fastq,17304656010.0,55821471.0,GSM8448582 r2,0:8 1:151 2:151,A:4101777717;C:2763806899;G:3078134302;T:6911601509;N:2763815,8,151,151,,4101777717,2763806899,3078134302,6911601509,2763815,SRX25652375,SRS22295177,SRA1943746,"Bronner lab, Biology and Biological Engineering, Caltech","Bronner lab, Biology and Biological Engineering, Caltech",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,United States,2024-08-09,Hatching,Embryo,Gut,Digestive System
34517,SRR32044795,SRX27393953,SRS23824014,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr+VC 3,I,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr+VC 3,Cr+VC 3,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Cr+VC-3.R1.raw.fastq.gz Cr+VC-3.R2.raw.fastq.gz,fastq fastq,6773536558.0,22428929.0,Cr+VC 3.R1.raw.fastq.gz,0:151 1:151,A:1792253952;C:1581454013;G:1629330621;T:1770470694;N:27278,151,151,,,1792253952,1581454013,1629330621,1770470694,27278,SRX27393953,SRS23824014,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34518,SRR32044796,SRX27393952,SRS23824013,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr+VC 2,H,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr+VC 2,Cr+VC 2,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Cr+VC-2.R1.raw.fastq.gz Cr+VC-2.R2.raw.fastq.gz,fastq fastq,7449518862.0,24667281.0,Cr+VC 2.R1.raw.fastq.gz,0:151 1:151,A:1969693675;C:1748150730;G:1771267240;T:1960378098;N:29119,151,151,,,1969693675,1748150730,1771267240,1960378098,29119,SRX27393952,SRS23824013,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34519,SRR32044797,SRX27393951,SRS23824012,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr+VC 1,G,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr+VC 1,Cr+VC 1,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,loader:fastq load.py|options:  doNotUseSharq,Cr+VC-1.R1.raw.fastq Cr+VC-1.R2.raw.fastq,fastq fastq,6865491179.0,45466829.0,Cr+VC 1.R1.raw.fastq.gz,0:151,A:1830069736;C:1600281531;G:1626303427;T:1808809011;N:27474,151,,,,1830069736,1600281531,1626303427,1808809011,27474,SRX27393951,SRS23824012,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34520,SRR32044798,SRX27393950,SRS23824011,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr 3,F,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr 3,Cr 3,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Cr-3.R1.raw.fastq.gz Cr-3.R2.raw.fastq.gz,fastq fastq,6069804078.0,20098689.0,Cr 3.R1.raw.fastq.gz,0:151 1:151,A:1603886661;C:1431213970;G:1440806224;T:1593873144;N:24079,151,151,,,1603886661,1431213970,1440806224,1593873144,24079,SRX27393950,SRS23824011,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34521,SRR32044799,SRX27393949,SRS23824010,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr 2,E,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr 2,Cr 2,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,loader:fastq load.py|options:  doNotUseSharq,Cr-2.R1.raw.fastq Cr-2.R2.raw.fastq,fastq fastq,8327156985.0,55146735.0,Cr 2.R1.raw.fastq.gz,0:151,A:2181317777;C:1974793526;G:2003240106;T:2167771431;N:34145,151,,,,2181317777,1974793526,2003240106,2167771431,34145,SRX27393949,SRS23824010,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34522,SRR32044800,SRX27393948,SRS23824009,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Cr 1,D,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Cr 1,Cr 1,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Cr-1.R1.raw.fastq.gz Cr-1.R2.raw.fastq.gz,fastq fastq,7322067614.0,24245257.0,Cr 1.R1.raw.fastq.gz,0:151 1:151,A:1927213281;C:1727973559;G:1748866497;T:1917985720;N:28557,151,151,,,1927213281,1727973559,1748866497,1917985720,28557,SRX27393948,SRS23824009,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34523,SRR32044801,SRX27393947,SRS23824008,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Con 3,C,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Con 3,Con 3,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Con-3.R1.raw.fastq.gz Con-3.R2.raw.fastq.gz,fastq fastq,10329187314.0,34202607.0,Con 3.R1.raw.fastq.gz,0:151 1:151,A:2805764955;C:2343400161;G:2421657823;T:2758323021;N:41354,151,151,,,2805764955,2343400161,2421657823,2758323021,41354,SRX27393947,SRS23824008,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34524,SRR32044802,SRX27393946,SRS23824007,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Con 2,B,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Con 2,Con 2,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Con-2.R1.raw.fastq.gz Con-2.R2.raw.fastq.gz,fastq fastq,10789961398.0,35728349.0,Con 2.R1.raw.fastq.gz,0:151 1:151,A:2983305704;C:2396592872;G:2488165589;T:2921853880;N:43353,151,151,,,2983305704,2396592872,2488165589,2921853880,43353,SRX27393946,SRS23824007,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
34525,SRR32044803,SRX27393945,SRS23824006,SRP558295,PRJNA1212482,vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish,PRJNA1212482,Other,Zebrafish is characterized by small size  rapid development  high fertility  short life cycle  easy and economical rearing; it has now become one of the model organisms for drug screening  disease research and ecological environment evaluation. Therefore  this project takes zebrafish as a model organism as the research object  and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology  transcriptome molecular biology and other techniques.,,,,Con 1,A,,ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou  Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of brian:Adult female and male zebrafish,Con 1,Con 1,normal,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,DNBSEQ,DNBSEQ-T7,,SRP558295,,,Con-1.R1.raw.fastq.gz Con-1.R2.raw.fastq.gz,fastq fastq,7118179260.0,23570130.0,Con 1.R1.raw.fastq.gz,0:151 1:151,A:1874284939;C:1673861890;G:1718740497;T:1851263659;N:28275,151,151,,,1874284939,1673861890,1718740497,1851263659,28275,SRX27393945,SRS23824006,SRA2054568,Hainan University|School of Life and Health Sciences,Hainan University,,,,,,,,,,,,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2025-01-19,Adult,Adult,Gut,Digestive System
53594,SRR9960231,SRX6707776,SRS5261677,SRP218210,PRJNA560029,Single Cell RNA Sequencing Analysis of Polystyrene Microplastic Exposed and control Zebrafish Intestine,GSE135767,Transcriptome Analysis,Microplastics MPs as widespread contamination pose high risk for aquatic organisms. However  current understanding of MP toxicities are based on cell population averaged measurements. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafishes exposed to 100nm  5µm and 200µm polystyrene MPs PS MPs for xxx days. Eight intestinal cell populations were identified. We found that all the three sizes of PS MPs induced dysfunction of intestinal immune cells including phagosome and regulation of immune system process. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure MPs with different size 100 nm  5 µm and 200 µm.,parent bioproject:PRJNA561326,pubmed:32092251,,MPs200vm,GSM4029395,,source name:intestinal cells|tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:200μm PS MPs,MPs200vm,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene cell expression matrix,intestinal cells,Exposure solutions were prepared by adding 100 nm  5 μm or 200 μm PS MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles no filtering systems were used in the tanks. post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.,,tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:200μm PS MPs,GSM4029395,GSM4029395: MPs200vm; Danio rerio; RNA Seq,GSM4029395,,1,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.,GEO Accession:GSM4029395,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP218210,,,MPs200vm_1.fq.gz MPs200vm_2.fq.gz,fastq fastq,105309618900.0,351032063.0,GSM4029395 r1,0:150 1:150,A:27241602982;C:19773063887;G:28015499540;T:30277575281;N:1877210,150,150,,,27241602982,19773063887,28015499540,30277575281,1877210,SRX6707776,SRS5261677,SRA938912,GEO,Nanjing University,2,0.0,0.87735,0.0,0.07963,1.0,0.83049,,0.55138,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2019-08-13,Adult,Adult,Gut,Digestive System
53595,SRR9960230,SRX6707775,SRS5261676,SRP218210,PRJNA560029,Single Cell RNA Sequencing Analysis of Polystyrene Microplastic Exposed and control Zebrafish Intestine,GSE135767,Transcriptome Analysis,Microplastics MPs as widespread contamination pose high risk for aquatic organisms. However  current understanding of MP toxicities are based on cell population averaged measurements. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafishes exposed to 100nm  5µm and 200µm polystyrene MPs PS MPs for xxx days. Eight intestinal cell populations were identified. We found that all the three sizes of PS MPs induced dysfunction of intestinal immune cells including phagosome and regulation of immune system process. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure MPs with different size 100 nm  5 µm and 200 µm.,parent bioproject:PRJNA561326,pubmed:32092251,,MPs5vm,GSM4029394,,source name:intestinal cells|tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:5μm PS MPs,MPs5vm,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene cell expression matrix,intestinal cells,Exposure solutions were prepared by adding 100 nm  5 μm or 200 μm PS MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles no filtering systems were used in the tanks. post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.,,tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:5μm PS MPs,GSM4029394,GSM4029394: MPs5vm; Danio rerio; RNA Seq,GSM4029394,,1,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.,GEO Accession:GSM4029394,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP218210,,,MPs5vm_1.fq.gz MPs5vm_2.fq.gz,fastq fastq,98563904100.0,328546347.0,GSM4029394 r1,0:150 1:150,A:26023907285;C:17974044830;G:25736568268;T:28827634883;N:1748834,150,150,,,26023907285,17974044830,25736568268,28827634883,1748834,SRX6707775,SRS5261676,SRA938912,GEO,Nanjing University,2,0.0,0.86592,0.0,0.09908,1.0,0.81552,,0.55476,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2019-08-13,Adult,Adult,Gut,Digestive System
53596,SRR9960229,SRX6707774,SRS5261675,SRP218210,PRJNA560029,Single Cell RNA Sequencing Analysis of Polystyrene Microplastic Exposed and control Zebrafish Intestine,GSE135767,Transcriptome Analysis,Microplastics MPs as widespread contamination pose high risk for aquatic organisms. However  current understanding of MP toxicities are based on cell population averaged measurements. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafishes exposed to 100nm  5µm and 200µm polystyrene MPs PS MPs for xxx days. Eight intestinal cell populations were identified. We found that all the three sizes of PS MPs induced dysfunction of intestinal immune cells including phagosome and regulation of immune system process. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure MPs with different size 100 nm  5 µm and 200 µm.,parent bioproject:PRJNA561326,pubmed:32092251,,MPs100nm,GSM4029393,,source name:intestinal cells|tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:100nm PS MPs,MPs100nm,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene cell expression matrix,intestinal cells,Exposure solutions were prepared by adding 100 nm  5 μm or 200 μm PS MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles no filtering systems were used in the tanks. post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.,,tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:100nm PS MPs,GSM4029393,GSM4029393: MPs100nm; Danio rerio; RNA Seq,GSM4029393,,1,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.,GEO Accession:GSM4029393,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP218210,,,MPs100nm_1.fq.gz MPs100nm_2.fq.gz,fastq fastq,122539718400.0,408465728.0,GSM4029393 r1,0:150 1:150,A:32283417066;C:22576112318;G:30470461014;T:37207888685;N:1839317,150,150,,,32283417066,22576112318,30470461014,37207888685,1839317,SRX6707774,SRS5261675,SRA938912,GEO,Nanjing University,2,0.0,0.88187,0.0,0.09087,1.0,0.82428,,0.53597,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2019-08-13,Adult,Adult,Gut,Digestive System
53597,SRR9960228,SRX6707773,SRS5261674,SRP218210,PRJNA560029,Single Cell RNA Sequencing Analysis of Polystyrene Microplastic Exposed and control Zebrafish Intestine,GSE135767,Transcriptome Analysis,Microplastics MPs as widespread contamination pose high risk for aquatic organisms. However  current understanding of MP toxicities are based on cell population averaged measurements. Here we used single cell RNA sequencing to provide the transcriptome heterogeneity of 12000 intestinal cells obtained from zebrafishes exposed to 100nm  5µm and 200µm polystyrene MPs PS MPs for xxx days. Eight intestinal cell populations were identified. We found that all the three sizes of PS MPs induced dysfunction of intestinal immune cells including phagosome and regulation of immune system process. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure MPs with different size 100 nm  5 µm and 200 µm.,parent bioproject:PRJNA561326,pubmed:32092251,,CK,GSM4029392,,source name:intestinal cells|tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:n1,CK,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene cell expression matrix,intestinal cells,Exposure solutions were prepared by adding 100 nm  5 μm or 200 μm PS MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles no filtering systems were used in the tanks. post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on an Illumina Hiseq PE150.,,tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:n1,GSM4029392,GSM4029392: CK; Danio rerio; RNA Seq,GSM4029392,,1,The isolated intestinal tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on an Illumina Hiseq PE150.,GEO Accession:GSM4029392,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP218210,,,CK_1.fq.gz CK_2.fq.gz,fastq fastq,111761141100.0,372537137.0,GSM4029392 r1,0:150 1:150,A:29264568248;C:21295511514;G:29897320083;T:31301732224;N:2009031,150,150,,,29264568248,21295511514,29897320083,31301732224,2009031,SRX6707773,SRS5261674,SRA938912,GEO,Nanjing University,2,0.0,0.88395,0.0,0.08593,1.0,0.80466,,0.46326,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2019-08-13,Adult,Adult,Gut,Digestive System
59228,SRR12974176,SRX9426454,SRS7641325,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM10,GSM4878631,,source name:Intestinal dissection|tissue:Intestine|treatment:2X DSS+BZA|genotype/variation:nod2 / |10x chemistry:V3,SNJM10,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:2X DSS+BZA|genotype/variation:nod2 / |10x chemistry:V3,GSM4878631,GSM4878631: SNJM10; Danio rerio; RNA Seq,GSM4878631,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878631,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM10 0 G S10 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM10 0 G S10 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM10 0 G S10 L001 R2 001.fastq.gz,JUCH10_SNJM10_0_G_S10_L001_I1_001.fastq.gz JUCH10_SNJM10_0_G_S10_L001_R1_001.fastq.gz JUCH10_SNJM10_0_G_S10_L001_R2_001.fastq.gz,fastq fastq fastq,9612906312.0,103364584.0,GSM4878631 r1,0:8 1:29 2:56,A:2566209216;C:2292038760;G:2265576943;T:2488871493;N:209900,8,29,56,,2566209216,2292038760,2265576943,2488871493,209900,SRX9426454,SRS7641325,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.962,,0.0608,,0.8734,,0.67588,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59229,SRR12974177,SRX9426454,SRS7641325,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM10,GSM4878631,,source name:Intestinal dissection|tissue:Intestine|treatment:2X DSS+BZA|genotype/variation:nod2 / |10x chemistry:V3,SNJM10,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:2X DSS+BZA|genotype/variation:nod2 / |10x chemistry:V3,GSM4878631,GSM4878631: SNJM10; Danio rerio; RNA Seq,GSM4878631,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878631,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM10 0 G S10 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM10 0 G S10 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM10 0 G S10 L002 R2 001.fastq.gz,JUCH10_SNJM10_0_G_S10_L002_I1_001.fastq.gz JUCH10_SNJM10_0_G_S10_L002_R1_001.fastq.gz JUCH10_SNJM10_0_G_S10_L002_R2_001.fastq.gz,fastq fastq fastq,9545302752.0,102637664.0,GSM4878631 r2,0:8 1:29 2:56,A:2548745985;C:2274433644;G:2248703958;T:2472613589;N:805576,8,29,56,,2548745985,2274433644,2248703958,2472613589,805576,SRX9426454,SRS7641325,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.9615,,0.06194,,0.87247,,0.74516,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59230,SRR12974174,SRX9426453,SRS7641324,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM09,GSM4878630,,source name:Intestinal dissection|tissue:Intestine|treatment:2X DSS|genotype/variation:nod2 / |10x chemistry:V3,SNJM09,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:2X DSS|genotype/variation:nod2 / |10x chemistry:V3,GSM4878630,GSM4878630: SNJM09; Danio rerio; RNA Seq,GSM4878630,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878630,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM9 0 G S9 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM9 0 G S9 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM9 0 G S9 L001 R2 001.fastq.gz,JUCH10_SNJM9_0_G_S9_L001_I1_001.fastq.gz JUCH10_SNJM9_0_G_S9_L001_R1_001.fastq.gz JUCH10_SNJM9_0_G_S9_L001_R2_001.fastq.gz,fastq fastq fastq,9550986633.0,102698781.0,GSM4878630 r1,0:8 1:29 2:56,A:2545306811;C:2315371452;G:2200128862;T:2489970955;N:208553,8,29,56,,2545306811,2315371452,2200128862,2489970955,208553,SRX9426453,SRS7641324,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.96301,,0.05192,,0.88743,,0.70057,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59231,SRR12974175,SRX9426453,SRS7641324,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM09,GSM4878630,,source name:Intestinal dissection|tissue:Intestine|treatment:2X DSS|genotype/variation:nod2 / |10x chemistry:V3,SNJM09,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:2X DSS|genotype/variation:nod2 / |10x chemistry:V3,GSM4878630,GSM4878630: SNJM09; Danio rerio; RNA Seq,GSM4878630,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878630,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM9 0 G S9 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM9 0 G S9 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM9 0 G S9 L002 R2 001.fastq.gz,JUCH10_SNJM9_0_G_S9_L002_I1_001.fastq.gz JUCH10_SNJM9_0_G_S9_L002_R1_001.fastq.gz JUCH10_SNJM9_0_G_S9_L002_R2_001.fastq.gz,fastq fastq fastq,9486231849.0,102002493.0,GSM4878630 r2,0:8 1:29 2:56,A:2528707184;C:2298013878;G:2184508040;T:2474200996;N:801751,8,29,56,,2528707184,2298013878,2184508040,2474200996,801751,SRX9426453,SRS7641324,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.96301,,0.05148,,0.8846,,0.72241,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59232,SRR12974172,SRX9426452,SRS7641323,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM08,GSM4878629,,source name:Intestinal dissection|tissue:Intestine|treatment:untreated|genotype/variation:nod2 /  2X|10x chemistry:V3,SNJM08,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:untreated|genotype/variation:nod2 /  2X|10x chemistry:V3,GSM4878629,GSM4878629: SNJM08; Danio rerio; RNA Seq,GSM4878629,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878629,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM8 0 G S8 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM8 0 G S8 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM8 0 G S8 L001 R2 001.fastq.gz,JUCH10_SNJM8_0_G_S8_L001_I1_001.fastq.gz JUCH10_SNJM8_0_G_S8_L001_R1_001.fastq.gz JUCH10_SNJM8_0_G_S8_L001_R2_001.fastq.gz,fastq fastq fastq,10406956308.0,111902756.0,GSM4878629 r1,0:8 1:29 2:56,A:2870124713;C:2509365613;G:2345749207;T:2681489991;N:226784,8,29,56,,2870124713,2509365613,2345749207,2681489991,226784,SRX9426452,SRS7641323,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.96215,,0.03963,,0.90057,,0.84217,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59233,SRR12974173,SRX9426452,SRS7641323,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM08,GSM4878629,,source name:Intestinal dissection|tissue:Intestine|treatment:untreated|genotype/variation:nod2 /  2X|10x chemistry:V3,SNJM08,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:untreated|genotype/variation:nod2 /  2X|10x chemistry:V3,GSM4878629,GSM4878629: SNJM08; Danio rerio; RNA Seq,GSM4878629,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878629,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM8 0 G S8 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM8 0 G S8 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM8 0 G S8 L002 R2 001.fastq.gz,JUCH10_SNJM8_0_G_S8_L002_I1_001.fastq.gz JUCH10_SNJM8_0_G_S8_L002_R1_001.fastq.gz JUCH10_SNJM8_0_G_S8_L002_R2_001.fastq.gz,fastq fastq fastq,10347171444.0,111259908.0,GSM4878629 r2,0:8 1:29 2:56,A:2855106653;C:2493008676;G:2331251314;T:2666929711;N:875090,8,29,56,,2855106653,2493008676,2331251314,2666929711,875090,SRX9426452,SRS7641323,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.96136,,0.03986,,0.90021,,0.83819,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59234,SRR12974170,SRX9426451,SRS7641322,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM07,GSM4878628,,source name:Intestinal dissection|tissue:Intestine|treatment:2X DSS+BZA|genotype/variation:wildtype|10x chemistry:V3,SNJM07,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:2X DSS+BZA|genotype/variation:wildtype|10x chemistry:V3,GSM4878628,GSM4878628: SNJM07; Danio rerio; RNA Seq,GSM4878628,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878628,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM7 0 G S7 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM7 0 G S7 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM7 0 G S7 L001 R2 001.fastq.gz,JUCH10_SNJM7_0_G_S7_L001_I1_001.fastq.gz JUCH10_SNJM7_0_G_S7_L001_R1_001.fastq.gz JUCH10_SNJM7_0_G_S7_L001_R2_001.fastq.gz,fastq fastq fastq,9123196584.0,98098888.0,GSM4878628 r1,0:8 1:29 2:56,A:2569669307;C:2214757071;G:1969962475;T:2368609155;N:198576,8,29,56,,2569669307,2214757071,1969962475,2368609155,198576,SRX9426451,SRS7641322,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.96088,,0.05866,,0.88708,,0.85062,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59235,SRR12974171,SRX9426451,SRS7641322,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM07,GSM4878628,,source name:Intestinal dissection|tissue:Intestine|treatment:2X DSS+BZA|genotype/variation:wildtype|10x chemistry:V3,SNJM07,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:2X DSS+BZA|genotype/variation:wildtype|10x chemistry:V3,GSM4878628,GSM4878628: SNJM07; Danio rerio; RNA Seq,GSM4878628,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878628,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM7 0 G S7 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM7 0 G S7 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM7 0 G S7 L002 R2 001.fastq.gz,JUCH10_SNJM7_0_G_S7_L002_I1_001.fastq.gz JUCH10_SNJM7_0_G_S7_L002_R1_001.fastq.gz JUCH10_SNJM7_0_G_S7_L002_R2_001.fastq.gz,fastq fastq fastq,9055633293.0,97372401.0,GSM4878628 r2,0:8 1:29 2:56,A:2551775269;C:2196748202;G:1954504090;T:2351840767;N:764965,8,29,56,,2551775269,2196748202,1954504090,2351840767,764965,SRX9426451,SRS7641322,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.96058,,0.05844,,0.88939,,0.85033,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59236,SRR12974168,SRX9426450,SRS7641321,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM06,GSM4878627,,source name:Intestinal dissection|tissue:Intestine|treatment:2X DSS|genotype/variation:wildtype|10x chemistry:V3,SNJM06,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:2X DSS|genotype/variation:wildtype|10x chemistry:V3,GSM4878627,GSM4878627: SNJM06; Danio rerio; RNA Seq,GSM4878627,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878627,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM6 0 G S6 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM6 0 G S6 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM6 0 G S6 L001 R2 001.fastq.gz,JUCH10_SNJM6_0_G_S6_L001_I1_001.fastq.gz JUCH10_SNJM6_0_G_S6_L001_R1_001.fastq.gz JUCH10_SNJM6_0_G_S6_L001_R2_001.fastq.gz,fastq fastq fastq,8956677015.0,96308355.0,GSM4878627 r1,0:8 1:29 2:56,A:2473315824;C:2129478747;G:2022150123;T:2331535818;N:196503,8,29,56,,2473315824,2129478747,2022150123,2331535818,196503,SRX9426450,SRS7641321,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.96363,,0.04651,,0.89988,,0.84067,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59237,SRR12974169,SRX9426450,SRS7641321,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM06,GSM4878627,,source name:Intestinal dissection|tissue:Intestine|treatment:2X DSS|genotype/variation:wildtype|10x chemistry:V3,SNJM06,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:2X DSS|genotype/variation:wildtype|10x chemistry:V3,GSM4878627,GSM4878627: SNJM06; Danio rerio; RNA Seq,GSM4878627,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878627,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM6 0 G S6 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM6 0 G S6 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM6 0 G S6 L002 R2 001.fastq.gz,JUCH10_SNJM6_0_G_S6_L002_I1_001.fastq.gz JUCH10_SNJM6_0_G_S6_L002_R1_001.fastq.gz JUCH10_SNJM6_0_G_S6_L002_R2_001.fastq.gz,fastq fastq fastq,8891805795.0,95610815.0,GSM4878627 r2,0:8 1:29 2:56,A:2456331697;C:2112784685;G:2006505048;T:2315434557;N:749808,8,29,56,,2456331697,2112784685,2006505048,2315434557,749808,SRX9426450,SRS7641321,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.96343,,0.04559,,0.90165,,0.84056,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59238,SRR12974166,SRX9426449,SRS7641320,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM05,GSM4878626,,source name:Intestinal dissection|tissue:Intestine|treatment:untreated|genotype/variation:wildtype 2X|10x chemistry:V3,SNJM05,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:untreated|genotype/variation:wildtype 2X|10x chemistry:V3,GSM4878626,GSM4878626: SNJM05; Danio rerio; RNA Seq,GSM4878626,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878626,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM5 0 G S5 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM5 0 G S5 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM5 0 G S5 L001 R2 001.fastq.gz,JUCH10_SNJM5_0_G_S5_L001_I1_001.fastq.gz JUCH10_SNJM5_0_G_S5_L001_R1_001.fastq.gz JUCH10_SNJM5_0_G_S5_L001_R2_001.fastq.gz,fastq fastq fastq,9064946499.0,97472543.0,GSM4878626 r1,0:8 1:29 2:56,A:2554844989;C:2175928954;G:1956415280;T:2377558346;N:198930,8,29,56,,2554844989,2175928954,1956415280,2377558346,198930,SRX9426449,SRS7641320,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.96742,,0.0357,,0.91737,,0.88943,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59239,SRR12974167,SRX9426449,SRS7641320,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM05,GSM4878626,,source name:Intestinal dissection|tissue:Intestine|treatment:untreated|genotype/variation:wildtype 2X|10x chemistry:V3,SNJM05,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:untreated|genotype/variation:wildtype 2X|10x chemistry:V3,GSM4878626,GSM4878626: SNJM05; Danio rerio; RNA Seq,GSM4878626,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878626,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM5 0 G S5 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM5 0 G S5 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM5 0 G S5 L002 R2 001.fastq.gz,JUCH10_SNJM5_0_G_S5_L002_I1_001.fastq.gz JUCH10_SNJM5_0_G_S5_L002_R1_001.fastq.gz JUCH10_SNJM5_0_G_S5_L002_R2_001.fastq.gz,fastq fastq fastq,8995948497.0,96730629.0,GSM4878626 r2,0:8 1:29 2:56,A:2536668919;C:2157506999;G:1940651397;T:2360359924;N:761258,8,29,56,,2536668919,2157506999,1940651397,2360359924,761258,SRX9426449,SRS7641320,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.96676,,0.03558,,0.91666,,0.88967,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59240,SRR12974164,SRX9426448,SRS7641318,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM04,GSM4878625,,source name:Intestinal dissection|tissue:Intestine|treatment:1X DSS|genotype/variation:nod2 / |10x chemistry:V3,SNJM04,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:1X DSS|genotype/variation:nod2 / |10x chemistry:V3,GSM4878625,GSM4878625: SNJM04; Danio rerio; RNA Seq,GSM4878625,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878625,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM4 0 G S4 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM4 0 G S4 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM4 0 G S4 L001 R2 001.fastq.gz,JUCH10_SNJM4_0_G_S4_L001_I1_001.fastq.gz JUCH10_SNJM4_0_G_S4_L001_R1_001.fastq.gz JUCH10_SNJM4_0_G_S4_L001_R2_001.fastq.gz,fastq fastq fastq,9600834633.0,103234781.0,GSM4878625 r1,0:8 1:29 2:56,A:2687588051;C:2283954081;G:2107499458;T:2521583198;N:209845,8,29,56,,2687588051,2283954081,2107499458,2521583198,209845,SRX9426448,SRS7641318,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95608,,0.06784,,0.8538,,0.81465,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59241,SRR12974165,SRX9426448,SRS7641318,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM04,GSM4878625,,source name:Intestinal dissection|tissue:Intestine|treatment:1X DSS|genotype/variation:nod2 / |10x chemistry:V3,SNJM04,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:1X DSS|genotype/variation:nod2 / |10x chemistry:V3,GSM4878625,GSM4878625: SNJM04; Danio rerio; RNA Seq,GSM4878625,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878625,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM4 0 G S4 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM4 0 G S4 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM4 0 G S4 L002 R2 001.fastq.gz,JUCH10_SNJM4_0_G_S4_L002_I1_001.fastq.gz JUCH10_SNJM4_0_G_S4_L002_R1_001.fastq.gz JUCH10_SNJM4_0_G_S4_L002_R2_001.fastq.gz,fastq fastq fastq,9548851539.0,102675823.0,GSM4878625 r2,0:8 1:29 2:56,A:2673944918;C:2269787019;G:2095420445;T:2508893277;N:805880,8,29,56,,2673944918,2269787019,2095420445,2508893277,805880,SRX9426448,SRS7641318,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95602,,0.06682,,0.85433,,0.61345,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59242,SRR12974162,SRX9426447,SRS7641319,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM03,GSM4878624,,source name:Intestinal dissection|tissue:Intestine|treatment:1X DSS|genotype/variation:wildtype|10x chemistry:V3,SNJM03,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:1X DSS|genotype/variation:wildtype|10x chemistry:V3,GSM4878624,GSM4878624: SNJM03; Danio rerio; RNA Seq,GSM4878624,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878624,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM3 0 G S3 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM3 0 G S3 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM3 0 G S3 L001 R2 001.fastq.gz,JUCH10_SNJM3_0_G_S3_L001_I1_001.fastq.gz JUCH10_SNJM3_0_G_S3_L001_R1_001.fastq.gz JUCH10_SNJM3_0_G_S3_L001_R2_001.fastq.gz,fastq fastq fastq,9157702932.0,98469924.0,GSM4878624 r1,0:8 1:29 2:56,A:2627894488;C:2152254884;G:2064675616;T:2312678653;N:199291,8,29,56,,2627894488,2152254884,2064675616,2312678653,199291,SRX9426447,SRS7641319,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95169,,0.08321,,0.8802,,0.7957,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59243,SRR12974163,SRX9426447,SRS7641319,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM03,GSM4878624,,source name:Intestinal dissection|tissue:Intestine|treatment:1X DSS|genotype/variation:wildtype|10x chemistry:V3,SNJM03,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:1X DSS|genotype/variation:wildtype|10x chemistry:V3,GSM4878624,GSM4878624: SNJM03; Danio rerio; RNA Seq,GSM4878624,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878624,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM3 0 G S3 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM3 0 G S3 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM3 0 G S3 L002 R2 001.fastq.gz,JUCH10_SNJM3_0_G_S3_L002_I1_001.fastq.gz JUCH10_SNJM3_0_G_S3_L002_R1_001.fastq.gz JUCH10_SNJM3_0_G_S3_L002_R2_001.fastq.gz,fastq fastq fastq,9084747687.0,97685459.0,GSM4878624 r2,0:8 1:29 2:56,A:2607939019;C:2133198115;G:2047005553;T:2295838531;N:766469,8,29,56,,2607939019,2133198115,2047005553,2295838531,766469,SRX9426447,SRS7641319,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95159,,0.08346,,0.87799,,0.86901,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59244,SRR12974160,SRX9426446,SRS7641317,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM02,GSM4878623,,source name:Intestinal dissection|tissue:Intestine|treatment:untreated|genotype/variation:nod2 / |10x chemistry:V3,SNJM02,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:untreated|genotype/variation:nod2 / |10x chemistry:V3,GSM4878623,GSM4878623: SNJM02; Danio rerio; RNA Seq,GSM4878623,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878623,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM2 0 G S2 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM2 0 G S2 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM2 0 G S2 L001 R2 001.fastq.gz,JUCH10_SNJM2_0_G_S2_L001_I1_001.fastq.gz JUCH10_SNJM2_0_G_S2_L001_R1_001.fastq.gz JUCH10_SNJM2_0_G_S2_L001_R2_001.fastq.gz,fastq fastq fastq,9141163440.0,98292080.0,GSM4878623 r1,0:8 1:29 2:56,A:2568403174;C:2203993337;G:1949600715;T:2418964898;N:201316,8,29,56,,2568403174,2203993337,1949600715,2418964898,201316,SRX9426446,SRS7641317,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.96372,,0.04508,,0.89416,,0.89922,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59245,SRR12974161,SRX9426446,SRS7641317,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM02,GSM4878623,,source name:Intestinal dissection|tissue:Intestine|treatment:untreated|genotype/variation:nod2 / |10x chemistry:V3,SNJM02,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:untreated|genotype/variation:nod2 / |10x chemistry:V3,GSM4878623,GSM4878623: SNJM02; Danio rerio; RNA Seq,GSM4878623,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878623,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM2 0 G S2 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM2 0 G S2 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM2 0 G S2 L002 R2 001.fastq.gz,JUCH10_SNJM2_0_G_S2_L002_I1_001.fastq.gz JUCH10_SNJM2_0_G_S2_L002_R1_001.fastq.gz JUCH10_SNJM2_0_G_S2_L002_R2_001.fastq.gz,fastq fastq fastq,9095463519.0,97800683.0,GSM4878623 r2,0:8 1:29 2:56,A:2556536997;C:2191496444;G:1938967545;T:2407692037;N:770496,8,29,56,,2556536997,2191496444,1938967545,2407692037,770496,SRX9426446,SRS7641317,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.96463,,0.044,,0.89286,,0.90213,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59246,SRR12974158,SRX9426445,SRS7641316,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM01,GSM4878622,,source name:Intestinal dissection|tissue:Intestine|treatment:untreated|genotype/variation:wildtype|10x chemistry:V3,SNJM01,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:untreated|genotype/variation:wildtype|10x chemistry:V3,GSM4878622,GSM4878622: SNJM01; Danio rerio; RNA Seq,GSM4878622,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878622,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM1 0 G S1 L001 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM1 0 G S1 L001 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM1 0 G S1 L001 R2 001.fastq.gz,JUCH10_SNJM1_0_G_S1_L001_I1_001.fastq.gz JUCH10_SNJM1_0_G_S1_L001_R1_001.fastq.gz JUCH10_SNJM1_0_G_S1_L001_R2_001.fastq.gz,fastq fastq fastq,9359347578.0,100638146.0,GSM4878622 r1,0:8 1:29 2:56,A:2742192040;C:2208968705;G:2007446927;T:2400535057;N:204849,8,29,56,,2742192040,2208968705,2007446927,2400535057,204849,SRX9426445,SRS7641316,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.97296,,0.04791,,0.91259,,0.93709,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59247,SRR12974159,SRX9426445,SRS7641316,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJM01,GSM4878622,,source name:Intestinal dissection|tissue:Intestine|treatment:untreated|genotype/variation:wildtype|10x chemistry:V3,SNJM01,FASTQ were demultiplexed using Cell Ranger v2.0/v4.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were single  treated with 0.075% Dextran Sodium Sulphate DSS or co treated with DSS+ 10uM Bazedoxifene BZA in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|treatment:untreated|genotype/variation:wildtype|10x chemistry:V3,GSM4878622,GSM4878622: SNJM01; Danio rerio; RNA Seq,GSM4878622,,1,post 24 hours of DSS/BZA treatment  zebrafish larval intestines were dissected from untreated and treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 and v3 chemistry kits see descriptors for applications.,GEO Accession:GSM4878622,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=JUCH10 SNJM1 0 G S1 L002 I1 001.fastq.gz   read2PairFiles=JUCH10 SNJM1 0 G S1 L002 R1 001.fastq.gz   read3PairFiles=JUCH10 SNJM1 0 G S1 L002 R2 001.fastq.gz,JUCH10_SNJM1_0_G_S1_L002_I1_001.fastq.gz JUCH10_SNJM1_0_G_S1_L002_R1_001.fastq.gz JUCH10_SNJM1_0_G_S1_L002_R2_001.fastq.gz,fastq fastq fastq,9286776051.0,99857807.0,GSM4878622 r2,0:8 1:29 2:56,A:2721584053;C:2190402119;G:1990556025;T:2383450199;N:783655,8,29,56,,2721584053,2190402119,1990556025,2383450199,783655,SRX9426445,SRS7641316,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.9733,,0.04761,,0.91441,,0.93019,,56,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-11-03,Larval,Larval,Gut,Digestive System
59248,SRR11785641,SRX8337992,SRS6656491,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJC03,GSM4551420,,source name:Intestinal dissection|tissue:Intestine|status:DSS treated,SNJC03,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:DSS treated,GSM4551420,GSM4551420: SNJC03; Danio rerio; RNA Seq,GSM4551420,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551420,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJC03 S5 L001 I1 001.fastq.gz   read2PairFiles=SNJC03 S5 L001 R1 001.fastq.gz   read3PairFiles=SNJC03 S5 L001 R2 001.fastq.gz,SNJC03_S5_L001_R2_001.fastq.gz SNJC03_S5_L001_R1_001.fastq.gz SNJC03_S5_L001_I1_001.fastq.gz,fastq fastq fastq,1187350424.0,13341016.0,GSM4551420 r1,0:8 1:26 2:55,A:333004523;C:277828258;G:286036018;T:290210763;N:270862,8,26,55,,333004523,277828258,286036018,290210763,270862,SRX8337992,SRS6656491,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.94136,,0.10077,,0.85512,,0.75118,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59249,SRR11785642,SRX8337992,SRS6656491,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJC03,GSM4551420,,source name:Intestinal dissection|tissue:Intestine|status:DSS treated,SNJC03,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:DSS treated,GSM4551420,GSM4551420: SNJC03; Danio rerio; RNA Seq,GSM4551420,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551420,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJC03 S5 L002 I1 001.fastq.gz   read2PairFiles=SNJC03 S5 L002 R1 001.fastq.gz   read3PairFiles=SNJC03 S5 L002 R2 001.fastq.gz,SNJC03_S5_L002_R2_001.fastq.gz SNJC03_S5_L002_R1_001.fastq.gz SNJC03_S5_L002_I1_001.fastq.gz,fastq fastq fastq,1308643451.0,14703859.0,GSM4551420 r2,0:8 1:26 2:55,A:366398712;C:306757422;G:316095972;T:319052449;N:338896,8,26,55,,366398712,306757422,316095972,319052449,338896,SRX8337992,SRS6656491,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.9424,,0.09777,,0.85188,,0.75485,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59250,SRR11785643,SRX8337992,SRS6656491,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJC03,GSM4551420,,source name:Intestinal dissection|tissue:Intestine|status:DSS treated,SNJC03,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:DSS treated,GSM4551420,GSM4551420: SNJC03; Danio rerio; RNA Seq,GSM4551420,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551420,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJC03 S5 L003 I1 001.fastq.gz   read2PairFiles=SNJC03 S5 L003 R1 001.fastq.gz   read3PairFiles=SNJC03 S5 L003 R2 001.fastq.gz,SNJC03_S5_L003_R2_001.fastq.gz SNJC03_S5_L003_R1_001.fastq.gz SNJC03_S5_L003_I1_001.fastq.gz,fastq fastq fastq,1311515303.0,14736127.0,GSM4551420 r3,0:8 1:26 2:55,A:366013405;C:307141773;G:319701005;T:318562083;N:97037,8,26,55,,366013405,307141773,319701005,318562083,97037,SRX8337992,SRS6656491,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.94016,,0.09633,,0.85291,,0.75214,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59251,SRR11785644,SRX8337992,SRS6656491,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJC03,GSM4551420,,source name:Intestinal dissection|tissue:Intestine|status:DSS treated,SNJC03,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:DSS treated,GSM4551420,GSM4551420: SNJC03; Danio rerio; RNA Seq,GSM4551420,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551420,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJC03 S5 L004 I1 001.fastq.gz   read2PairFiles=SNJC03 S5 L004 R1 001.fastq.gz   read3PairFiles=SNJC03 S5 L004 R2 001.fastq.gz,SNJC03_S5_L004_I1_001.fastq.gz SNJC03_S5_L004_R1_001.fastq.gz SNJC03_S5_L004_R2_001.fastq.gz,fastq fastq fastq,1277168957.0,14350213.0,GSM4551420 r4,0:8 1:26 2:55,A:355124126;C:298971601;G:313182839;T:309762369;N:128022,8,26,55,,355124126,298971601,313182839,309762369,128022,SRX8337992,SRS6656491,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.93858,,0.09543,,0.85139,,0.75235,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59252,SRR11785637,SRX8337991,SRS6656490,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJC02,GSM4551419,,source name:Intestinal dissection|tissue:Intestine|status:untreated ctrl,SNJC02,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:untreated ctrl,GSM4551419,GSM4551419: SNJC02; Danio rerio; RNA Seq,GSM4551419,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551419,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJC02 S4 L001 I1 001.fastq.gz   read2PairFiles=SNJC02 S4 L001 R1 001.fastq.gz   read3PairFiles=SNJC02 S4 L001 R2 001.fastq.gz,SNJC02_S4_L001_I1_001.fastq.gz SNJC02_S4_L001_R1_001.fastq.gz SNJC02_S4_L001_R2_001.fastq.gz,fastq fastq fastq,1105982174.0,12426766.0,GSM4551419 r1,0:8 1:26 2:55,A:317522952;C:260688416;G:260193778;T:267326347;N:250681,8,26,55,,317522952,260688416,260193778,267326347,250681,SRX8337991,SRS6656490,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95224,,0.05677,,0.89012,,0.83572,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59253,SRR11785638,SRX8337991,SRS6656490,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJC02,GSM4551419,,source name:Intestinal dissection|tissue:Intestine|status:untreated ctrl,SNJC02,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:untreated ctrl,GSM4551419,GSM4551419: SNJC02; Danio rerio; RNA Seq,GSM4551419,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551419,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJC02 S4 L002 I1 001.fastq.gz   read2PairFiles=SNJC02 S4 L002 R1 001.fastq.gz   read3PairFiles=SNJC02 S4 L002 R2 001.fastq.gz,SNJC02_S4_L002_I1_001.fastq.gz SNJC02_S4_L002_R1_001.fastq.gz SNJC02_S4_L002_R2_001.fastq.gz,fastq fastq fastq,1223404680.0,13746120.0,GSM4551419 r2,0:8 1:26 2:55,A:350724821;C:288990705;G:288572329;T:294798443;N:318382,8,26,55,,350724821,288990705,288572329,294798443,318382,SRX8337991,SRS6656490,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95282,,0.05487,,0.88781,,0.8357,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59254,SRR11785639,SRX8337991,SRS6656490,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJC02,GSM4551419,,source name:Intestinal dissection|tissue:Intestine|status:untreated ctrl,SNJC02,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:untreated ctrl,GSM4551419,GSM4551419: SNJC02; Danio rerio; RNA Seq,GSM4551419,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551419,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJC02 S4 L003 I1 001.fastq.gz   read2PairFiles=SNJC02 S4 L003 R1 001.fastq.gz   read3PairFiles=SNJC02 S4 L003 R2 001.fastq.gz,SNJC02_S4_L003_I1_001.fastq.gz SNJC02_S4_L003_R1_001.fastq.gz SNJC02_S4_L003_R2_001.fastq.gz,fastq fastq fastq,1235054869.0,13877021.0,GSM4551419 r3,0:8 1:26 2:55,A:353256976;C:291475235;G:293788969;T:296442213;N:91476,8,26,55,,353256976,291475235,293788969,296442213,91476,SRX8337991,SRS6656490,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95103,,0.05401,,0.8869,,0.81707,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59255,SRR11785640,SRX8337991,SRS6656490,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJC02,GSM4551419,,source name:Intestinal dissection|tissue:Intestine|status:untreated ctrl,SNJC02,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:untreated ctrl,GSM4551419,GSM4551419: SNJC02; Danio rerio; RNA Seq,GSM4551419,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551419,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJC02 S4 L004 I1 001.fastq.gz   read2PairFiles=SNJC02 S4 L004 R1 001.fastq.gz   read3PairFiles=SNJC02 S4 L004 R2 001.fastq.gz,SNJC02_S4_L004_I1_001.fastq.gz SNJC02_S4_L004_R1_001.fastq.gz SNJC02_S4_L004_R2_001.fastq.gz,fastq fastq fastq,1203766029.0,13525461.0,GSM4551419 r4,0:8 1:26 2:55,A:343127030;C:284042987;G:287996072;T:288482311;N:117629,8,26,55,,343127030,284042987,287996072,288482311,117629,SRX8337991,SRS6656490,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.94817,,0.05377,,0.88548,,0.41506,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59256,SRR11785633,SRX8337990,SRS6656489,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNZF2,GSM4551418,,source name:Intestinal dissection|tissue:Intestine|status:DSS treated,SNZF2,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:DSS treated,GSM4551418,GSM4551418: SNZF2; Danio rerio; RNA Seq,GSM4551418,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551418,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNZF2 S2 L001 I1 001.fastq.gz   read2PairFiles=SNZF2 S2 L001 R1 001.fastq.gz   read3PairFiles=SNZF2 S2 L001 R2 001.fastq.gz,SNZF2_S2_L001_I1_001.fastq.gz SNZF2_S2_L001_R1_001.fastq.gz SNZF2_S2_L001_R2_001.fastq.gz,fastq fastq fastq,1142432391.0,12836319.0,GSM4551418 r1,0:8 1:26 2:55,A:325430172;C:264437244;G:262877435;T:287797270;N:1890270,8,26,55,,325430172,264437244,262877435,287797270,1890270,SRX8337990,SRS6656489,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.9502,,0.05655,,0.90183,,0.88561,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59257,SRR11785634,SRX8337990,SRS6656489,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNZF2,GSM4551418,,source name:Intestinal dissection|tissue:Intestine|status:DSS treated,SNZF2,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:DSS treated,GSM4551418,GSM4551418: SNZF2; Danio rerio; RNA Seq,GSM4551418,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551418,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNZF2 S2 L002 I1 001.fastq.gz   read2PairFiles=SNZF2 S2 L002 R1 001.fastq.gz   read3PairFiles=SNZF2 S2 L002 R2 001.fastq.gz,SNZF2_S2_L002_I1_001.fastq.gz SNZF2_S2_L002_R1_001.fastq.gz SNZF2_S2_L002_R2_001.fastq.gz,fastq fastq fastq,1146050597.0,12876973.0,GSM4551418 r2,0:8 1:26 2:55,A:326541749;C:265861466;G:263268760;T:288214490;N:2164132,8,26,55,,326541749,265861466,263268760,288214490,2164132,SRX8337990,SRS6656489,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95246,,0.0553,,0.90082,,0.88734,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59258,SRR11785635,SRX8337990,SRS6656489,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNZF2,GSM4551418,,source name:Intestinal dissection|tissue:Intestine|status:DSS treated,SNZF2,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:DSS treated,GSM4551418,GSM4551418: SNZF2; Danio rerio; RNA Seq,GSM4551418,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551418,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNZF2 S2 L003 I1 001.fastq.gz   read2PairFiles=SNZF2 S2 L003 R1 001.fastq.gz   read3PairFiles=SNZF2 S2 L003 R2 001.fastq.gz,SNZF2_S2_L003_I1_001.fastq.gz SNZF2_S2_L003_R1_001.fastq.gz SNZF2_S2_L003_R2_001.fastq.gz,fastq fastq fastq,1287670868.0,14468212.0,GSM4551418 r3,0:8 1:26 2:55,A:364126807;C:297595539;G:301588932;T:322080166;N:2279424,8,26,55,,364126807,297595539,301588932,322080166,2279424,SRX8337990,SRS6656489,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.9442,,0.05165,,0.89414,,0.87072,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59259,SRR11785636,SRX8337990,SRS6656489,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNZF2,GSM4551418,,source name:Intestinal dissection|tissue:Intestine|status:DSS treated,SNZF2,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:DSS treated,GSM4551418,GSM4551418: SNZF2; Danio rerio; RNA Seq,GSM4551418,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551418,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNZF2 S2 L004 I1 001.fastq.gz   read2PairFiles=SNZF2 S2 L004 R1 001.fastq.gz   read3PairFiles=SNZF2 S2 L004 R2 001.fastq.gz,SNZF2_S2_L004_I1_001.fastq.gz SNZF2_S2_L004_R1_001.fastq.gz SNZF2_S2_L004_R2_001.fastq.gz,fastq fastq fastq,1216460544.0,13668096.0,GSM4551418 r4,0:8 1:26 2:55,A:344940661;C:281702462;G:282564971;T:304818639;N:2433811,8,26,55,,344940661,281702462,282564971,304818639,2433811,SRX8337990,SRS6656489,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.94948,,0.05357,,0.894,,0.88193,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59260,SRR11785629,SRX8337989,SRS6656488,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNZF1,GSM4551417,,source name:Intestinal dissection|tissue:Intestine|status:untreated ctrl,SNZF1,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:untreated ctrl,GSM4551417,GSM4551417: SNZF1; Danio rerio; RNA Seq,GSM4551417,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551417,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNZF1 S1 L001 I1 001.fastq.gz   read2PairFiles=SNZF1 S1 L001 R1 001.fastq.gz   read3PairFiles=SNZF1 S1 L001 R2 001.fastq.gz,SNZF1_S1_L001_R2_001.fastq.gz SNZF1_S1_L001_R1_001.fastq.gz SNZF1_S1_L001_I1_001.fastq.gz,fastq fastq fastq,1121043644.0,12595996.0,GSM4551417 r1,0:8 1:26 2:55,A:318266957;C:263185714;G:261698958;T:276036499;N:1855516,8,26,55,,318266957,263185714,261698958,276036499,1855516,SRX8337989,SRS6656488,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95246,,0.04561,,0.91131,,0.80014,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59261,SRR11785630,SRX8337989,SRS6656488,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNZF1,GSM4551417,,source name:Intestinal dissection|tissue:Intestine|status:untreated ctrl,SNZF1,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:untreated ctrl,GSM4551417,GSM4551417: SNZF1; Danio rerio; RNA Seq,GSM4551417,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551417,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNZF1 S1 L002 I1 001.fastq.gz   read2PairFiles=SNZF1 S1 L002 R1 001.fastq.gz   read3PairFiles=SNZF1 S1 L002 R2 001.fastq.gz,SNZF1_S1_L002_R2_001.fastq.gz SNZF1_S1_L002_R1_001.fastq.gz SNZF1_S1_L002_I1_001.fastq.gz,fastq fastq fastq,1128285218.0,12677362.0,GSM4551417 r2,0:8 1:26 2:55,A:320336836;C:265494414;G:262986049;T:277346260;N:2121659,8,26,55,,320336836,265494414,262986049,277346260,2121659,SRX8337989,SRS6656488,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95333,,0.04443,,0.91072,,0.89221,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59262,SRR11785631,SRX8337989,SRS6656488,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNZF1,GSM4551417,,source name:Intestinal dissection|tissue:Intestine|status:untreated ctrl,SNZF1,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:untreated ctrl,GSM4551417,GSM4551417: SNZF1; Danio rerio; RNA Seq,GSM4551417,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551417,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNZF1 S1 L003 I1 001.fastq.gz   read2PairFiles=SNZF1 S1 L003 R1 001.fastq.gz   read3PairFiles=SNZF1 S1 L003 R2 001.fastq.gz,SNZF1_S1_L003_R2_001.fastq.gz SNZF1_S1_L003_R1_001.fastq.gz SNZF1_S1_L003_I1_001.fastq.gz,fastq fastq fastq,1272004999.0,14292191.0,GSM4551417 r3,0:8 1:26 2:55,A:358320733;C:298143124;G:302249804;T:311018556;N:2272782,8,26,55,,358320733,298143124,302249804,311018556,2272782,SRX8337989,SRS6656488,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.94848,,0.04159,,0.90617,,0.89091,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59263,SRR11785632,SRX8337989,SRS6656488,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNZF1,GSM4551417,,source name:Intestinal dissection|tissue:Intestine|status:untreated ctrl,SNZF1,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:untreated ctrl,GSM4551417,GSM4551417: SNZF1; Danio rerio; RNA Seq,GSM4551417,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551417,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNZF1 S1 L004 I1 001.fastq.gz   read2PairFiles=SNZF1 S1 L004 R1 001.fastq.gz   read3PairFiles=SNZF1 S1 L004 R2 001.fastq.gz,SNZF1_S1_L004_R2_001.fastq.gz SNZF1_S1_L004_R1_001.fastq.gz SNZF1_S1_L004_I1_001.fastq.gz,fastq fastq fastq,1200402363.0,13487667.0,GSM4551417 r4,0:8 1:26 2:55,A:339057834;C:282010519;G:282903285;T:294041893;N:2388832,8,26,55,,339057834,282010519,282903285,294041893,2388832,SRX8337989,SRS6656488,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95017,,0.04264,,0.90303,,0.89249,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59264,SRR11785625,SRX8337988,SRS6656487,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJCZ2,GSM4551416,,source name:Intestinal dissection|tissue:Intestine|status:DSS treated,SNJCZ2,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:DSS treated,GSM4551416,GSM4551416: SNJCZ2; Danio rerio; RNA Seq,GSM4551416,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551416,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJCZ2 S2 L001 I1 001.fastq.gz   read2PairFiles=SNJCZ2 S2 L001 R1 001.fastq.gz   read3PairFiles=SNJCZ2 S2 L001 R2 001.fastq.gz,SNJCZ2_S2_L001_I1_001.fastq.gz SNJCZ2_S2_L001_R1_001.fastq.gz SNJCZ2_S2_L001_R2_001.fastq.gz,fastq fastq fastq,1377160012.0,15473708.0,GSM4551416 r1,0:8 1:26 2:55,A:386793838;C:328592754;G:326298808;T:335158719;N:315893,8,26,55,,386793838,328592754,326298808,335158719,315893,SRX8337988,SRS6656487,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95832,,0.06422,,0.87852,,0.73546,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59265,SRR11785626,SRX8337988,SRS6656487,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJCZ2,GSM4551416,,source name:Intestinal dissection|tissue:Intestine|status:DSS treated,SNJCZ2,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:DSS treated,GSM4551416,GSM4551416: SNJCZ2; Danio rerio; RNA Seq,GSM4551416,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551416,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJCZ2 S2 L002 I1 001.fastq.gz   read2PairFiles=SNJCZ2 S2 L002 R1 001.fastq.gz   read3PairFiles=SNJCZ2 S2 L002 R2 001.fastq.gz,SNJCZ2_S2_L002_I1_001.fastq.gz SNJCZ2_S2_L002_R1_001.fastq.gz SNJCZ2_S2_L002_R2_001.fastq.gz,fastq fastq fastq,1518452229.0,17061261.0,GSM4551416 r2,0:8 1:26 2:55,A:425494105;C:363112628;G:360572880;T:368871810;N:400806,8,26,55,,425494105,363112628,360572880,368871810,400806,SRX8337988,SRS6656487,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95946,,0.0652,,0.87649,,0.64868,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59266,SRR11785627,SRX8337988,SRS6656487,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJCZ2,GSM4551416,,source name:Intestinal dissection|tissue:Intestine|status:DSS treated,SNJCZ2,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:DSS treated,GSM4551416,GSM4551416: SNJCZ2; Danio rerio; RNA Seq,GSM4551416,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551416,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJCZ2 S2 L003 I1 001.fastq.gz   read2PairFiles=SNJCZ2 S2 L003 R1 001.fastq.gz   read3PairFiles=SNJCZ2 S2 L003 R2 001.fastq.gz,SNJCZ2_S2_L003_I1_001.fastq.gz SNJCZ2_S2_L003_R1_001.fastq.gz SNJCZ2_S2_L003_R2_001.fastq.gz,fastq fastq fastq,1543490599.0,17342591.0,GSM4551416 r3,0:8 1:26 2:55,A:431105301;C:369007286;G:369511373;T:373755247;N:111392,8,26,55,,431105301,369007286,369511373,373755247,111392,SRX8337988,SRS6656487,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95749,,0.0612,,0.87659,,0.65691,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59267,SRR11785628,SRX8337988,SRS6656487,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJCZ2,GSM4551416,,source name:Intestinal dissection|tissue:Intestine|status:DSS treated,SNJCZ2,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:DSS treated,GSM4551416,GSM4551416: SNJCZ2; Danio rerio; RNA Seq,GSM4551416,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551416,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJCZ2 S2 L004 I1 001.fastq.gz   read2PairFiles=SNJCZ2 S2 L004 R1 001.fastq.gz   read3PairFiles=SNJCZ2 S2 L004 R2 001.fastq.gz,SNJCZ2_S2_L004_R2_001.fastq.gz SNJCZ2_S2_L004_R1_001.fastq.gz SNJCZ2_S2_L004_I1_001.fastq.gz,fastq fastq fastq,1502275233.0,16879497.0,GSM4551416 r4,0:8 1:26 2:55,A:418327578;C:359123038;G:361317639;T:363357288;N:149690,8,26,55,,418327578,359123038,361317639,363357288,149690,SRX8337988,SRS6656487,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95529,,0.06072,,0.87523,,0.65804,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59268,SRR11785621,SRX8337987,SRS6656486,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJCZ1,GSM4551415,,source name:Intestinal dissection|tissue:Intestine|status:untreated ctrl,SNJCZ1,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:untreated ctrl,GSM4551415,GSM4551415: SNJCZ1; Danio rerio; RNA Seq,GSM4551415,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551415,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJCZ1 S1 L001 I1 001.fastq.gz   read2PairFiles=SNJCZ1 S1 L001 R1 001.fastq.gz   read3PairFiles=SNJCZ1 S1 L001 R2 001.fastq.gz,SNJCZ1_S1_L001_I1_001.fastq.gz SNJCZ1_S1_L001_R1_001.fastq.gz SNJCZ1_S1_L001_R2_001.fastq.gz,fastq fastq fastq,1154289416.0,12969544.0,GSM4551415 r1,0:8 1:26 2:55,A:334176306;C:267881430;G:269991337;T:281980065;N:260278,8,26,55,,334176306,267881430,269991337,281980065,260278,SRX8337987,SRS6656486,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95462,,0.07782,,0.87994,,0.69253,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59269,SRR11785622,SRX8337987,SRS6656486,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJCZ1,GSM4551415,,source name:Intestinal dissection|tissue:Intestine|status:untreated ctrl,SNJCZ1,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:untreated ctrl,GSM4551415,GSM4551415: SNJCZ1; Danio rerio; RNA Seq,GSM4551415,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551415,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJCZ1 S1 L002 I1 001.fastq.gz   read2PairFiles=SNJCZ1 S1 L002 R1 001.fastq.gz   read3PairFiles=SNJCZ1 S1 L002 R2 001.fastq.gz,SNJCZ1_S1_L002_I1_001.fastq.gz SNJCZ1_S1_L002_R1_001.fastq.gz SNJCZ1_S1_L002_R2_001.fastq.gz,fastq fastq fastq,1273593560.0,14310040.0,GSM4551415 r2,0:8 1:26 2:55,A:367956165;C:296259421;G:298606136;T:310443339;N:328499,8,26,55,,367956165,296259421,298606136,310443339,328499,SRX8337987,SRS6656486,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.9562,,0.07523,,0.87744,,0.71234,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59270,SRR11785623,SRX8337987,SRS6656486,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJCZ1,GSM4551415,,source name:Intestinal dissection|tissue:Intestine|status:untreated ctrl,SNJCZ1,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:untreated ctrl,GSM4551415,GSM4551415: SNJCZ1; Danio rerio; RNA Seq,GSM4551415,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551415,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJCZ1 S1 L003 I1 001.fastq.gz   read2PairFiles=SNJCZ1 S1 L003 R1 001.fastq.gz   read3PairFiles=SNJCZ1 S1 L003 R2 001.fastq.gz,SNJCZ1_S1_L003_I1_001.fastq.gz SNJCZ1_S1_L003_R1_001.fastq.gz SNJCZ1_S1_L003_R2_001.fastq.gz,fastq fastq fastq,1299376504.0,14599736.0,GSM4551415 r3,0:8 1:26 2:55,A:374341323;C:302164288;G:307195329;T:315582357;N:93207,8,26,55,,374341323,302164288,307195329,315582357,93207,SRX8337987,SRS6656486,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95203,,0.07407,,0.87696,,0.70725,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
59271,SRR11785624,SRX8337987,SRS6656486,SRP261473,PRJNA632595,Myeloid stromal subtypes reveal NOD2 mediated Crohn's and rescue pathways,GSE150498,Transcriptome Analysis,Crohn's disease CD is a chronic inflammatory intestinal disease  often characterized by aberrant healing and stricturing complications. Mechanisms underlying NOD2 pathogenicity and salvage pathways in anti TNF and  refractory patients remain largely uncharacterized. Here we show that loss of NOD2 function leads to aberrant activated fibroblast and macrophage homeostasis through the upregulation of a pathogenic signature  and propose new precision therapeutic approaches involving gp130 blockade for select CD patients  to potentially supplement anti TNF therapy Overall design: Single cell seq analysis of paired zebrafish larval intestine samples from untreated and DSS treated fish,,pubmed:33789339,,SNJCZ1,GSM4551415,,source name:Intestinal dissection|tissue:Intestine|status:untreated ctrl,SNJCZ1,FASTQ were demultiplexed using Cell Ranger v2.0 and aligned to the Grcz11 zebrafish Cell barcodes and unique molecular identifiers UMIs were extracted and “Raw” UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the “Raw” output UMI matrices of CellRanger Genome build: danRer11,Intestinal dissection,6dpf zebrafish larvae were treated with 0.075% Dextran Sodium Sulphate in egg water for 24 hours  in a 37C incubator,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,zebrafish embryos were harvested and grown in standard zebrafish egg water off system in a 37C incubator until dissections were performed,tissue:Intestine|status:untreated ctrl,GSM4551415,GSM4551415: SNJCZ1; Danio rerio; RNA Seq,GSM4551415,,1,post 24 hours of DSS treatment  zebrafish larval intestines were dissected from untreated and DSS treated fish. Single cell suspensions were generated as described in Methods. Briefly  cells were dissociated and digested using standard collagenase and DNAse protocols  and single cell suspensions were filtered through a 70um filter. Live cell % had to exceed 60% to load suspension into 10X Chromium gel beads Library construction was performed as per 10X Genomics v2 chemistry kit. 10X chromium,GEO Accession:GSM4551415,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP261473,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=SNJCZ1 S1 L004 I1 001.fastq.gz   read2PairFiles=SNJCZ1 S1 L004 R1 001.fastq.gz   read3PairFiles=SNJCZ1 S1 L004 R2 001.fastq.gz,SNJCZ1_S1_L004_I1_001.fastq.gz SNJCZ1_S1_L004_R1_001.fastq.gz SNJCZ1_S1_L004_R2_001.fastq.gz,fastq fastq fastq,1266440274.0,14229666.0,GSM4551415 r4,0:8 1:26 2:55,A:363767572;C:294460691;G:300901128;T:307184946;N:125937,8,26,55,,363767572,294460691,300901128,307184946,125937,SRX8337987,SRS6656486,SRA1075199,GEO,"Cho lab, Institute of Personalized medicine, Mount Sinai hospital",1,0.95089,,0.07244,,0.87738,,0.7883,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2020-05-13,Larval,Larval,Gut,Digestive System
61986,SRR16705712,SRX12906194,SRS10848385,SRP293304,PRJNA679624,A Cell Atlas of Microbe Responsive Processes in the Zebrafish Intestine,GSE161855,Transcriptome Analysis,To understand intestinal cell specific responses to host commensal bacteria  we isolated single cells from intestines and associated tissue of zebrafish larvae raised in the presence or absence of a microbiome. We profiled cells with single cell RNA seq. Our analysis revealed extensive heterogeneity among cell populations of the fish intestine and associated tissue  and describe distinct microbial responses in each cell type. Overall design: Zebrafish were raised in the presence of absence of a microbiome for 6 days. Intestines and associated tissue was dissected and dissociated to generate a single cell suspension for sequencing on the 10X Genomics platform.,,pubmed:35108531,,Germ free Sample 4,GSM5667113,,tissue:Dissociated intestines from germ free fish|genotype:TL|cell type:Intestinal and associated tissue|developmental stage:6 dpf larvae|treatment:germ free,Germ free Sample 4,Cell Ranger v3.0 10X Genomics was used to demultiplex raw base call files from Illumina sequencing and to align reads to the Zebrafish reference genome Genome build: Ensembl GRCz11.96 Supplementary files format and content: TSV/MTX files,Dissociated intestines from germ free fish,,Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3′ Library & Gel Bead Kit v3,,genotype:TL|cell type:Intestinal and associated tissue|developmental stage:6 dpf larvae|treatment:germ free,GSM5667113,GSM5667113: Germ free Sample 4; Danio rerio; RNA Seq,GSM5667113,,1,Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3′ Library & Gel Bead Kit v3,GEO Accession:GSM5667113,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP293304,,loader:fastq load.py,GF2_S1_L001_I1_001.fastq.gz GF2_S1_L001_I2_001.fastq.gz GF2_S1_L001_R1_001.fastq.gz GF2_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,59111409280.0,184723154.0,GSM5667113 r1,0:10 1:10 2:150 3:150,A:17648222385;C:8853089309;G:9046869524;T:19868297807;N:467175,10,10,150,150,17648222385,8853089309,9046869524,19868297807,467175,SRX12906194,SRS10848385,SRA1161597,GEO,"6-59 HMRC, Medical Microbiology and Immunology, University of Alberta",2,0.27415,0.90679,0.06832,0.11224,0.98591,0.84762,0.7315,0.6235,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Canada,2021-11-02,Larval,Larval,Gut,Digestive System
61987,SRR16705710,SRX12906193,SRS10848386,SRP293304,PRJNA679624,A Cell Atlas of Microbe Responsive Processes in the Zebrafish Intestine,GSE161855,Transcriptome Analysis,To understand intestinal cell specific responses to host commensal bacteria  we isolated single cells from intestines and associated tissue of zebrafish larvae raised in the presence or absence of a microbiome. We profiled cells with single cell RNA seq. Our analysis revealed extensive heterogeneity among cell populations of the fish intestine and associated tissue  and describe distinct microbial responses in each cell type. Overall design: Zebrafish were raised in the presence of absence of a microbiome for 6 days. Intestines and associated tissue was dissected and dissociated to generate a single cell suspension for sequencing on the 10X Genomics platform.,,pubmed:35108531,,Conventially reared Sample 3,GSM5667112,,tissue:Dissociated intestines from conventionally reared fish|genotype:TL|cell type:Intestinal and associated tissue|developmental stage:6 dpf larvae|treatment:conventionally reared,Conventially reared Sample 3,Cell Ranger v3.0 10X Genomics was used to demultiplex raw base call files from Illumina sequencing and to align reads to the Zebrafish reference genome Genome build: Ensembl GRCz11.96 Supplementary files format and content: TSV/MTX files,Dissociated intestines from conventionally reared fish,,Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3′ Library & Gel Bead Kit v3,,genotype:TL|cell type:Intestinal and associated tissue|developmental stage:6 dpf larvae|treatment:conventionally reared,GSM5667112,GSM5667112: Conventially reared Sample 3; Danio rerio; RNA Seq,GSM5667112,,1,Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3′ Library & Gel Bead Kit v3,GEO Accession:GSM5667112,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP293304,,loader:fastq load.py,CV2_S2_L001_I1_001.fastq.gz CV2_S2_L001_I2_001.fastq.gz CV2_S2_L001_R1_001.fastq.gz CV2_S2_L001_R2_001.fastq.gz,fastq fastq fastq fastq,67735219200.0,211672560.0,GSM5667112 r1,0:10 1:10 2:150 3:150,A:19968346120;C:9956599266;G:10184829576;T:23391452422;N:540616,10,10,150,150,19968346120,9956599266,10184829576,23391452422,540616,SRX12906193,SRS10848386,SRA1161597,GEO,"6-59 HMRC, Medical Microbiology and Immunology, University of Alberta",2,0.19783,0.90538,0.05035,0.10756,0.9875,0.83989,0.71755,0.6162,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Canada,2021-11-02,Larval,Larval,Gut,Digestive System
61988,SRR13089283,SRX9535221,SRS7741720,SRP293304,PRJNA679624,A Cell Atlas of Microbe Responsive Processes in the Zebrafish Intestine,GSE161855,Transcriptome Analysis,To understand intestinal cell specific responses to host commensal bacteria  we isolated single cells from intestines and associated tissue of zebrafish larvae raised in the presence or absence of a microbiome. We profiled cells with single cell RNA seq. Our analysis revealed extensive heterogeneity among cell populations of the fish intestine and associated tissue  and describe distinct microbial responses in each cell type. Overall design: Zebrafish were raised in the presence of absence of a microbiome for 6 days. Intestines and associated tissue was dissected and dissociated to generate a single cell suspension for sequencing on the 10X Genomics platform.,,pubmed:35108531,,Germ free Sample 2,GSM4916094,,tissue:Dissociated intestines from germ free fish|genotype:TL|cell type:Intestinal and associated tissue|developmental stage:6 dpf larvae|treatment:germ free,Germ free Sample 2,Cell Ranger v3.0 10X Genomics was used to demultiplex raw base call files from Illumina sequencing and to align reads to the Zebrafish reference genome Genome build: Ensembl GRCz11.96 Supplementary files format and content: TSV/MTX files,Dissociated intestines from germ free fish,,Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3′ Library & Gel Bead Kit v3,,genotype:TL|cell type:Intestinal and associated tissue|developmental stage:6 dpf larvae|treatment:germ free,GSM4916094,GSM4916094: Germ free; Danio rerio; RNA Seq,GSM4916094,,1,Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3′ Library & Gel Bead Kit v3,GEO Accession:GSM4916094,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP293304,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=GF S2 L003 I1 001.fastq.gz   read2PairFiles=GF S2 L003 R1 001.fastq.gz   read3PairFiles=GF S2 L003 R2 001.fastq.gz,GF_S2_L003_I1_001.fastq.gz GF_S2_L003_R1_001.fastq.gz GF_S2_L003_R2_001.fastq.gz,fastq fastq fastq,67406082128.0,218850916.0,GSM4916094 r1,0:8 1:150 2:150,A:16033538561;C:12891030760;G:13419497134;T:25045893164;N:16122509,8,150,150,,16033538561,12891030760,13419497134,25045893164,16122509,SRX9535221,SRS7741720,SRA1161597,GEO,"6-59 HMRC, Medical Microbiology and Immunology, University of Alberta",1,0.92012,,0.08227,,0.87988,,0.70616,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Canada,2020-11-19,Larval,Larval,Gut,Digestive System
61989,SRR13089282,SRX9535220,SRS7741719,SRP293304,PRJNA679624,A Cell Atlas of Microbe Responsive Processes in the Zebrafish Intestine,GSE161855,Transcriptome Analysis,To understand intestinal cell specific responses to host commensal bacteria  we isolated single cells from intestines and associated tissue of zebrafish larvae raised in the presence or absence of a microbiome. We profiled cells with single cell RNA seq. Our analysis revealed extensive heterogeneity among cell populations of the fish intestine and associated tissue  and describe distinct microbial responses in each cell type. Overall design: Zebrafish were raised in the presence of absence of a microbiome for 6 days. Intestines and associated tissue was dissected and dissociated to generate a single cell suspension for sequencing on the 10X Genomics platform.,,pubmed:35108531,,Conventionally reared Sample 1,GSM4916093,,tissue:Dissociated intestines from conventionally reared fish|genotype:TL|cell type:Intestinal and associated tissue|developmental stage:6 dpf larvae|treatment:conventionally reared,Conventionally reared Sample 1,Cell Ranger v3.0 10X Genomics was used to demultiplex raw base call files from Illumina sequencing and to align reads to the Zebrafish reference genome Genome build: Ensembl GRCz11.96 Supplementary files format and content: TSV/MTX files,Dissociated intestines from conventionally reared fish,,Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3′ Library & Gel Bead Kit v3,,genotype:TL|cell type:Intestinal and associated tissue|developmental stage:6 dpf larvae|treatment:conventionally reared,GSM4916093,GSM4916093: Conventially reared; Danio rerio; RNA Seq,GSM4916093,,1,Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3′ Library & Gel Bead Kit v3,GEO Accession:GSM4916093,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP293304,,loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=CV S1 L003 I1 001.fastq.gz   read2PairFiles=CV S1 L003 R1 001.fastq.gz   read3PairFiles=CV S1 L003 R2 001.fastq.gz,CV_S1_L003_I1_001.fastq.gz CV_S1_L003_R1_001.fastq.gz CV_S1_L003_R2_001.fastq.gz,fastq fastq fastq,77009296364.0,250030183.0,GSM4916093 r1,0:8 1:150 2:150,A:18580003391;C:14737356417;G:15062022999;T:28611588832;N:18324725,8,150,150,,18580003391,14737356417,15062022999,28611588832,18324725,SRX9535220,SRS7741719,SRA1161597,GEO,"6-59 HMRC, Medical Microbiology and Immunology, University of Alberta",1,0.91135,,0.09577,,0.85512,,0.70479,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Canada,2020-11-19,Larval,Larval,Gut,Digestive System
63081,SRR13594977,SRX9989399,SRS8160234,SRP304100,PRJNA698538,Heterogeneity effects of nanoplastics and lead on zebrafish intestine identified by single cell sequencing,GSE165888,Transcriptome Analysis,Plastic particles in water environment can adsorb heavy metals  leading to combined toxicity to aquatic organisms. However  current conclusions are mostly obtained based on cell population average responses. Heterogeneity effects among cell populations in aquatic organisms remain unclear. This study analyzed the heterogeneity effects of 200 µg/L 100 nm polystyrene nanoplastics PS NPs  50 µg/L lead Pb  and their combined exposures on zebrafish intestine cells by single cell RNA sequencing.A total of 38640 cells in the zebrafish intestine was obtained and identified as seven cell populations  including enterocytes  macrophages  neutrophils  B cells  T cells  enteroendocrine cells  and goblet cells.Co exposure of PS NPs and Pb caused similar transcriptome profiles with PS NPs exposure in macrophages  which changed immunological recognition processes. The Pb exposure influenced the macrophages by direct cytotoxicity. However  the Pb alone and combined exposures induced similar modes of action in the enterocytes  including the generation of oxidative stress and abnormal lipid metabolism. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure nanoplastics and lead.,,pubmed:34861263,,PS NPs+Pb scRNA seq,GSM5057360,,source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200μg/L PS NPs and 50μg/L Pb,PS NPs+Pb scRNA seq,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene barcode expression matrix,intestine cells,Exposure solutions were prepared by adding 200μg/L PS NPs  50μg/L Pb or both of them to culture water. The exposure solution were was replaced every 2 days.  post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on a Nova6000.,,tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200μg/L PS NPs and 50μg/L Pb,GSM5057360,GSM5057360: PS NPs+Pb scRNA seq; Danio rerio; RNA Seq,GSM5057360,,1,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on a Nova6000.,GEO Accession:GSM5057360,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP304100,,,PS-NPs+Pb-1_S1_L002_R1_001.fastq.gz PS-NPs+Pb-1_S1_L002_R2_001.fastq.gz,fastq fastq,28913858700.0,96379529.0,GSM5057360 r1,0:150 1:150,A:10849569684;C:5242303716;G:4985029201;T:7836260772;N:695327,150,150,,,10849569684,5242303716,4985029201,7836260772,695327,SRX9989399,SRS8160234,SRA1189975,GEO,"School of the Environment, Nanjing university",2,0.0,0.9145,0.0,0.09354,1.0,0.82345,,0.54384,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-02-01,Adult,Adult,Gut,Digestive System
63082,SRR13594978,SRX9989399,SRS8160234,SRP304100,PRJNA698538,Heterogeneity effects of nanoplastics and lead on zebrafish intestine identified by single cell sequencing,GSE165888,Transcriptome Analysis,Plastic particles in water environment can adsorb heavy metals  leading to combined toxicity to aquatic organisms. However  current conclusions are mostly obtained based on cell population average responses. Heterogeneity effects among cell populations in aquatic organisms remain unclear. This study analyzed the heterogeneity effects of 200 µg/L 100 nm polystyrene nanoplastics PS NPs  50 µg/L lead Pb  and their combined exposures on zebrafish intestine cells by single cell RNA sequencing.A total of 38640 cells in the zebrafish intestine was obtained and identified as seven cell populations  including enterocytes  macrophages  neutrophils  B cells  T cells  enteroendocrine cells  and goblet cells.Co exposure of PS NPs and Pb caused similar transcriptome profiles with PS NPs exposure in macrophages  which changed immunological recognition processes. The Pb exposure influenced the macrophages by direct cytotoxicity. However  the Pb alone and combined exposures induced similar modes of action in the enterocytes  including the generation of oxidative stress and abnormal lipid metabolism. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure nanoplastics and lead.,,pubmed:34861263,,PS NPs+Pb scRNA seq,GSM5057360,,source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200μg/L PS NPs and 50μg/L Pb,PS NPs+Pb scRNA seq,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene barcode expression matrix,intestine cells,Exposure solutions were prepared by adding 200μg/L PS NPs  50μg/L Pb or both of them to culture water. The exposure solution were was replaced every 2 days.  post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on a Nova6000.,,tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200μg/L PS NPs and 50μg/L Pb,GSM5057360,GSM5057360: PS NPs+Pb scRNA seq; Danio rerio; RNA Seq,GSM5057360,,1,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on a Nova6000.,GEO Accession:GSM5057360,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP304100,,,PS-NPs+Pb-2_S1_L002_R1_001.fastq.gz PS-NPs+Pb-2_S1_L002_R2_001.fastq.gz,fastq fastq,30693799500.0,102312665.0,GSM5057360 r2,0:150 1:150,A:11517498785;C:5550458870;G:5279663916;T:8345445357;N:732572,150,150,,,11517498785,5550458870,5279663916,8345445357,732572,SRX9989399,SRS8160234,SRA1189975,GEO,"School of the Environment, Nanjing university",2,0.0,0.91302,0.0,0.0942,1.0,0.82258,,0.55615,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-02-01,Adult,Adult,Gut,Digestive System
63083,SRR13594979,SRX9989399,SRS8160234,SRP304100,PRJNA698538,Heterogeneity effects of nanoplastics and lead on zebrafish intestine identified by single cell sequencing,GSE165888,Transcriptome Analysis,Plastic particles in water environment can adsorb heavy metals  leading to combined toxicity to aquatic organisms. However  current conclusions are mostly obtained based on cell population average responses. Heterogeneity effects among cell populations in aquatic organisms remain unclear. This study analyzed the heterogeneity effects of 200 µg/L 100 nm polystyrene nanoplastics PS NPs  50 µg/L lead Pb  and their combined exposures on zebrafish intestine cells by single cell RNA sequencing.A total of 38640 cells in the zebrafish intestine was obtained and identified as seven cell populations  including enterocytes  macrophages  neutrophils  B cells  T cells  enteroendocrine cells  and goblet cells.Co exposure of PS NPs and Pb caused similar transcriptome profiles with PS NPs exposure in macrophages  which changed immunological recognition processes. The Pb exposure influenced the macrophages by direct cytotoxicity. However  the Pb alone and combined exposures induced similar modes of action in the enterocytes  including the generation of oxidative stress and abnormal lipid metabolism. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure nanoplastics and lead.,,pubmed:34861263,,PS NPs+Pb scRNA seq,GSM5057360,,source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200μg/L PS NPs and 50μg/L Pb,PS NPs+Pb scRNA seq,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene barcode expression matrix,intestine cells,Exposure solutions were prepared by adding 200μg/L PS NPs  50μg/L Pb or both of them to culture water. The exposure solution were was replaced every 2 days.  post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on a Nova6000.,,tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200μg/L PS NPs and 50μg/L Pb,GSM5057360,GSM5057360: PS NPs+Pb scRNA seq; Danio rerio; RNA Seq,GSM5057360,,1,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on a Nova6000.,GEO Accession:GSM5057360,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP304100,,,PS-NPs+Pb-3_S1_L002_R1_001.fastq.gz PS-NPs+Pb-3_S1_L002_R2_001.fastq.gz,fastq fastq,20835334200.0,69451114.0,GSM5057360 r3,0:150 1:150,A:7842229934;C:3755450675;G:3565661709;T:5671491296;N:500586,150,150,,,7842229934,3755450675,3565661709,5671491296,500586,SRX9989399,SRS8160234,SRA1189975,GEO,"School of the Environment, Nanjing university",2,0.0,0.9129,0.0,0.09663,1.0,0.82248,,0.56185,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-02-01,Adult,Adult,Gut,Digestive System
63084,SRR13594980,SRX9989399,SRS8160234,SRP304100,PRJNA698538,Heterogeneity effects of nanoplastics and lead on zebrafish intestine identified by single cell sequencing,GSE165888,Transcriptome Analysis,Plastic particles in water environment can adsorb heavy metals  leading to combined toxicity to aquatic organisms. However  current conclusions are mostly obtained based on cell population average responses. Heterogeneity effects among cell populations in aquatic organisms remain unclear. This study analyzed the heterogeneity effects of 200 µg/L 100 nm polystyrene nanoplastics PS NPs  50 µg/L lead Pb  and their combined exposures on zebrafish intestine cells by single cell RNA sequencing.A total of 38640 cells in the zebrafish intestine was obtained and identified as seven cell populations  including enterocytes  macrophages  neutrophils  B cells  T cells  enteroendocrine cells  and goblet cells.Co exposure of PS NPs and Pb caused similar transcriptome profiles with PS NPs exposure in macrophages  which changed immunological recognition processes. The Pb exposure influenced the macrophages by direct cytotoxicity. However  the Pb alone and combined exposures induced similar modes of action in the enterocytes  including the generation of oxidative stress and abnormal lipid metabolism. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure nanoplastics and lead.,,pubmed:34861263,,PS NPs+Pb scRNA seq,GSM5057360,,source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200μg/L PS NPs and 50μg/L Pb,PS NPs+Pb scRNA seq,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene barcode expression matrix,intestine cells,Exposure solutions were prepared by adding 200μg/L PS NPs  50μg/L Pb or both of them to culture water. The exposure solution were was replaced every 2 days.  post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on a Nova6000.,,tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200μg/L PS NPs and 50μg/L Pb,GSM5057360,GSM5057360: PS NPs+Pb scRNA seq; Danio rerio; RNA Seq,GSM5057360,,1,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on a Nova6000.,GEO Accession:GSM5057360,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP304100,,,PS-NPs+Pb-4_S1_L002_R1_001.fastq.gz PS-NPs+Pb-4_S1_L002_R2_001.fastq.gz,fastq fastq,23631366300.0,78771221.0,GSM5057360 r4,0:150 1:150,A:8877517036;C:4268581536;G:4055688376;T:6429008130;N:571222,150,150,,,8877517036,4268581536,4055688376,6429008130,571222,SRX9989399,SRS8160234,SRA1189975,GEO,"School of the Environment, Nanjing university",2,0.0,0.91274,0.0,0.09456,1.0,0.82266,,0.56254,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-02-01,Adult,Adult,Gut,Digestive System
63085,SRR13594981,SRX9989399,SRS8160234,SRP304100,PRJNA698538,Heterogeneity effects of nanoplastics and lead on zebrafish intestine identified by single cell sequencing,GSE165888,Transcriptome Analysis,Plastic particles in water environment can adsorb heavy metals  leading to combined toxicity to aquatic organisms. However  current conclusions are mostly obtained based on cell population average responses. Heterogeneity effects among cell populations in aquatic organisms remain unclear. This study analyzed the heterogeneity effects of 200 µg/L 100 nm polystyrene nanoplastics PS NPs  50 µg/L lead Pb  and their combined exposures on zebrafish intestine cells by single cell RNA sequencing.A total of 38640 cells in the zebrafish intestine was obtained and identified as seven cell populations  including enterocytes  macrophages  neutrophils  B cells  T cells  enteroendocrine cells  and goblet cells.Co exposure of PS NPs and Pb caused similar transcriptome profiles with PS NPs exposure in macrophages  which changed immunological recognition processes. The Pb exposure influenced the macrophages by direct cytotoxicity. However  the Pb alone and combined exposures induced similar modes of action in the enterocytes  including the generation of oxidative stress and abnormal lipid metabolism. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure nanoplastics and lead.,,pubmed:34861263,,PS NPs+Pb scRNA seq,GSM5057360,,source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200μg/L PS NPs and 50μg/L Pb,PS NPs+Pb scRNA seq,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene barcode expression matrix,intestine cells,Exposure solutions were prepared by adding 200μg/L PS NPs  50μg/L Pb or both of them to culture water. The exposure solution were was replaced every 2 days.  post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on a Nova6000.,,tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200μg/L PS NPs and 50μg/L Pb,GSM5057360,GSM5057360: PS NPs+Pb scRNA seq; Danio rerio; RNA Seq,GSM5057360,,1,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on a Nova6000.,GEO Accession:GSM5057360,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP304100,,,PS-NPs+Pb-5_S1_L003_R1_001.fastq.gz PS-NPs+Pb-5_S1_L003_R2_001.fastq.gz,fastq fastq,7898736300.0,26329121.0,GSM5057360 r5,0:150 1:150,A:2254409494;C:1395087363;G:1304008604;T:2944958771;N:272068,150,150,,,2254409494,1395087363,1304008604,2944958771,272068,SRX9989399,SRS8160234,SRA1189975,GEO,"School of the Environment, Nanjing university",2,0.01307,0.91324,0.00237,0.09457,0.99628,0.82361,0.55605,0.56119,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-02-01,Adult,Adult,Gut,Digestive System
63086,SRR13594982,SRX9989399,SRS8160234,SRP304100,PRJNA698538,Heterogeneity effects of nanoplastics and lead on zebrafish intestine identified by single cell sequencing,GSE165888,Transcriptome Analysis,Plastic particles in water environment can adsorb heavy metals  leading to combined toxicity to aquatic organisms. However  current conclusions are mostly obtained based on cell population average responses. Heterogeneity effects among cell populations in aquatic organisms remain unclear. This study analyzed the heterogeneity effects of 200 µg/L 100 nm polystyrene nanoplastics PS NPs  50 µg/L lead Pb  and their combined exposures on zebrafish intestine cells by single cell RNA sequencing.A total of 38640 cells in the zebrafish intestine was obtained and identified as seven cell populations  including enterocytes  macrophages  neutrophils  B cells  T cells  enteroendocrine cells  and goblet cells.Co exposure of PS NPs and Pb caused similar transcriptome profiles with PS NPs exposure in macrophages  which changed immunological recognition processes. The Pb exposure influenced the macrophages by direct cytotoxicity. However  the Pb alone and combined exposures induced similar modes of action in the enterocytes  including the generation of oxidative stress and abnormal lipid metabolism. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure nanoplastics and lead.,,pubmed:34861263,,PS NPs+Pb scRNA seq,GSM5057360,,source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200μg/L PS NPs and 50μg/L Pb,PS NPs+Pb scRNA seq,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene barcode expression matrix,intestine cells,Exposure solutions were prepared by adding 200μg/L PS NPs  50μg/L Pb or both of them to culture water. The exposure solution were was replaced every 2 days.  post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on a Nova6000.,,tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200μg/L PS NPs and 50μg/L Pb,GSM5057360,GSM5057360: PS NPs+Pb scRNA seq; Danio rerio; RNA Seq,GSM5057360,,1,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on a Nova6000.,GEO Accession:GSM5057360,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP304100,,,PS-NPs+Pb-6_S1_L003_R1_001.fastq.gz PS-NPs+Pb-6_S1_L003_R2_001.fastq.gz,fastq fastq,8424616800.0,28082056.0,GSM5057360 r6,0:150 1:150,A:2406028290;C:1483325372;G:1386742830;T:3148232701;N:287607,150,150,,,2406028290,1483325372,1386742830,3148232701,287607,SRX9989399,SRS8160234,SRA1189975,GEO,"School of the Environment, Nanjing university",2,0.0145,0.9122,0.0024,0.0949,0.99569,0.82221,0.53435,0.55806,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-02-01,Adult,Adult,Gut,Digestive System
63087,SRR13594983,SRX9989399,SRS8160234,SRP304100,PRJNA698538,Heterogeneity effects of nanoplastics and lead on zebrafish intestine identified by single cell sequencing,GSE165888,Transcriptome Analysis,Plastic particles in water environment can adsorb heavy metals  leading to combined toxicity to aquatic organisms. However  current conclusions are mostly obtained based on cell population average responses. Heterogeneity effects among cell populations in aquatic organisms remain unclear. This study analyzed the heterogeneity effects of 200 µg/L 100 nm polystyrene nanoplastics PS NPs  50 µg/L lead Pb  and their combined exposures on zebrafish intestine cells by single cell RNA sequencing.A total of 38640 cells in the zebrafish intestine was obtained and identified as seven cell populations  including enterocytes  macrophages  neutrophils  B cells  T cells  enteroendocrine cells  and goblet cells.Co exposure of PS NPs and Pb caused similar transcriptome profiles with PS NPs exposure in macrophages  which changed immunological recognition processes. The Pb exposure influenced the macrophages by direct cytotoxicity. However  the Pb alone and combined exposures induced similar modes of action in the enterocytes  including the generation of oxidative stress and abnormal lipid metabolism. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure nanoplastics and lead.,,pubmed:34861263,,PS NPs+Pb scRNA seq,GSM5057360,,source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200μg/L PS NPs and 50μg/L Pb,PS NPs+Pb scRNA seq,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene barcode expression matrix,intestine cells,Exposure solutions were prepared by adding 200μg/L PS NPs  50μg/L Pb or both of them to culture water. The exposure solution were was replaced every 2 days.  post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on a Nova6000.,,tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200μg/L PS NPs and 50μg/L Pb,GSM5057360,GSM5057360: PS NPs+Pb scRNA seq; Danio rerio; RNA Seq,GSM5057360,,1,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on a Nova6000.,GEO Accession:GSM5057360,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP304100,,,PS-NPs+Pb-7_S1_L003_R1_001.fastq.gz PS-NPs+Pb-7_S1_L003_R2_001.fastq.gz,fastq fastq,5721987300.0,19073291.0,GSM5057360 r7,0:150 1:150,A:1639437382;C:1003646832;G:936562303;T:2142146368;N:194415,150,150,,,1639437382,1003646832,936562303,2142146368,194415,SRX9989399,SRS8160234,SRA1189975,GEO,"School of the Environment, Nanjing university",2,0.01382,0.91046,0.00308,0.09808,0.99598,0.82195,0.51541,0.55631,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-02-01,Adult,Adult,Gut,Digestive System
63088,SRR13594984,SRX9989399,SRS8160234,SRP304100,PRJNA698538,Heterogeneity effects of nanoplastics and lead on zebrafish intestine identified by single cell sequencing,GSE165888,Transcriptome Analysis,Plastic particles in water environment can adsorb heavy metals  leading to combined toxicity to aquatic organisms. However  current conclusions are mostly obtained based on cell population average responses. Heterogeneity effects among cell populations in aquatic organisms remain unclear. This study analyzed the heterogeneity effects of 200 µg/L 100 nm polystyrene nanoplastics PS NPs  50 µg/L lead Pb  and their combined exposures on zebrafish intestine cells by single cell RNA sequencing.A total of 38640 cells in the zebrafish intestine was obtained and identified as seven cell populations  including enterocytes  macrophages  neutrophils  B cells  T cells  enteroendocrine cells  and goblet cells.Co exposure of PS NPs and Pb caused similar transcriptome profiles with PS NPs exposure in macrophages  which changed immunological recognition processes. The Pb exposure influenced the macrophages by direct cytotoxicity. However  the Pb alone and combined exposures induced similar modes of action in the enterocytes  including the generation of oxidative stress and abnormal lipid metabolism. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure nanoplastics and lead.,,pubmed:34861263,,PS NPs+Pb scRNA seq,GSM5057360,,source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200μg/L PS NPs and 50μg/L Pb,PS NPs+Pb scRNA seq,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene barcode expression matrix,intestine cells,Exposure solutions were prepared by adding 200μg/L PS NPs  50μg/L Pb or both of them to culture water. The exposure solution were was replaced every 2 days.  post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on a Nova6000.,,tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200μg/L PS NPs and 50μg/L Pb,GSM5057360,GSM5057360: PS NPs+Pb scRNA seq; Danio rerio; RNA Seq,GSM5057360,,1,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on a Nova6000.,GEO Accession:GSM5057360,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP304100,,,PS-NPs+Pb-8_S1_L003_R1_001.fastq.gz PS-NPs+Pb-8_S1_L003_R2_001.fastq.gz,fastq fastq,6480721200.0,21602404.0,GSM5057360 r8,0:150 1:150,A:1852646540;C:1139449660;G:1063640686;T:2424762670;N:221644,150,150,,,1852646540,1139449660,1063640686,2424762670,221644,SRX9989399,SRS8160234,SRA1189975,GEO,"School of the Environment, Nanjing university",2,0.01391,0.91265,0.00221,0.09687,0.99579,0.82317,0.53571,0.55537,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-02-01,Adult,Adult,Gut,Digestive System
63089,SRR13594969,SRX9989398,SRS8160233,SRP304100,PRJNA698538,Heterogeneity effects of nanoplastics and lead on zebrafish intestine identified by single cell sequencing,GSE165888,Transcriptome Analysis,Plastic particles in water environment can adsorb heavy metals  leading to combined toxicity to aquatic organisms. However  current conclusions are mostly obtained based on cell population average responses. Heterogeneity effects among cell populations in aquatic organisms remain unclear. This study analyzed the heterogeneity effects of 200 µg/L 100 nm polystyrene nanoplastics PS NPs  50 µg/L lead Pb  and their combined exposures on zebrafish intestine cells by single cell RNA sequencing.A total of 38640 cells in the zebrafish intestine was obtained and identified as seven cell populations  including enterocytes  macrophages  neutrophils  B cells  T cells  enteroendocrine cells  and goblet cells.Co exposure of PS NPs and Pb caused similar transcriptome profiles with PS NPs exposure in macrophages  which changed immunological recognition processes. The Pb exposure influenced the macrophages by direct cytotoxicity. However  the Pb alone and combined exposures induced similar modes of action in the enterocytes  including the generation of oxidative stress and abnormal lipid metabolism. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure nanoplastics and lead.,,pubmed:34861263,,Pb scRNA seq,GSM5057359,,source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50μg/L Pb,Pb scRNA seq,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene barcode expression matrix,intestine cells,Exposure solutions were prepared by adding 200μg/L PS NPs  50μg/L Pb or both of them to culture water. The exposure solution were was replaced every 2 days.  post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on a Nova6000.,,tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50μg/L Pb,GSM5057359,GSM5057359: Pb scRNA seq; Danio rerio; RNA Seq,GSM5057359,,1,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on a Nova6000.,GEO Accession:GSM5057359,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP304100,,,Pb-1_S1_L002_R1_001.fastq.gz Pb-1_S1_L002_R2_001.fastq.gz,fastq fastq,25835822700.0,86119409.0,GSM5057359 r1,0:150 1:150,A:9755231798;C:4594114561;G:4385069464;T:7100782044;N:624833,150,150,,,9755231798,4594114561,4385069464,7100782044,624833,SRX9989398,SRS8160233,SRA1189975,GEO,"School of the Environment, Nanjing university",2,0.0,0.89877,0.0,0.09567,1.0,0.82203,,0.52876,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-02-01,Adult,Adult,Gut,Digestive System
63090,SRR13594970,SRX9989398,SRS8160233,SRP304100,PRJNA698538,Heterogeneity effects of nanoplastics and lead on zebrafish intestine identified by single cell sequencing,GSE165888,Transcriptome Analysis,Plastic particles in water environment can adsorb heavy metals  leading to combined toxicity to aquatic organisms. However  current conclusions are mostly obtained based on cell population average responses. Heterogeneity effects among cell populations in aquatic organisms remain unclear. This study analyzed the heterogeneity effects of 200 µg/L 100 nm polystyrene nanoplastics PS NPs  50 µg/L lead Pb  and their combined exposures on zebrafish intestine cells by single cell RNA sequencing.A total of 38640 cells in the zebrafish intestine was obtained and identified as seven cell populations  including enterocytes  macrophages  neutrophils  B cells  T cells  enteroendocrine cells  and goblet cells.Co exposure of PS NPs and Pb caused similar transcriptome profiles with PS NPs exposure in macrophages  which changed immunological recognition processes. The Pb exposure influenced the macrophages by direct cytotoxicity. However  the Pb alone and combined exposures induced similar modes of action in the enterocytes  including the generation of oxidative stress and abnormal lipid metabolism. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure nanoplastics and lead.,,pubmed:34861263,,Pb scRNA seq,GSM5057359,,source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50μg/L Pb,Pb scRNA seq,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene barcode expression matrix,intestine cells,Exposure solutions were prepared by adding 200μg/L PS NPs  50μg/L Pb or both of them to culture water. The exposure solution were was replaced every 2 days.  post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on a Nova6000.,,tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50μg/L Pb,GSM5057359,GSM5057359: Pb scRNA seq; Danio rerio; RNA Seq,GSM5057359,,1,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on a Nova6000.,GEO Accession:GSM5057359,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP304100,,,Pb-2_S1_L002_R2_001.fastq.gz Pb-2_S1_L002_R1_001.fastq.gz,fastq fastq,33815040900.0,112716803.0,GSM5057359 r2,0:150 1:150,A:13026671769;C:6021504758;G:5670052854;T:9096003398;N:808121,150,150,,,13026671769,6021504758,5670052854,9096003398,808121,SRX9989398,SRS8160233,SRA1189975,GEO,"School of the Environment, Nanjing university",2,0.0,0.89971,0.0,0.09369,1.0,0.82276,,0.54985,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-02-01,Adult,Adult,Gut,Digestive System
63091,SRR13594971,SRX9989398,SRS8160233,SRP304100,PRJNA698538,Heterogeneity effects of nanoplastics and lead on zebrafish intestine identified by single cell sequencing,GSE165888,Transcriptome Analysis,Plastic particles in water environment can adsorb heavy metals  leading to combined toxicity to aquatic organisms. However  current conclusions are mostly obtained based on cell population average responses. Heterogeneity effects among cell populations in aquatic organisms remain unclear. This study analyzed the heterogeneity effects of 200 µg/L 100 nm polystyrene nanoplastics PS NPs  50 µg/L lead Pb  and their combined exposures on zebrafish intestine cells by single cell RNA sequencing.A total of 38640 cells in the zebrafish intestine was obtained and identified as seven cell populations  including enterocytes  macrophages  neutrophils  B cells  T cells  enteroendocrine cells  and goblet cells.Co exposure of PS NPs and Pb caused similar transcriptome profiles with PS NPs exposure in macrophages  which changed immunological recognition processes. The Pb exposure influenced the macrophages by direct cytotoxicity. However  the Pb alone and combined exposures induced similar modes of action in the enterocytes  including the generation of oxidative stress and abnormal lipid metabolism. Overall design: Single cell RNA sequencing were adopted to learn the transcriptional variation in zebrafish intestine followed exposure nanoplastics and lead.,,pubmed:34861263,,Pb scRNA seq,GSM5057359,,source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50μg/L Pb,Pb scRNA seq,We use FastQC to perform basic statistics on the quality of the raw reads. Then  those read sequences produced by the Illumina pipeline in FASTQ format were pre processed through Trimmomatic software which can be summarized as below:1 Remove low quality reads: scan the read with a 4 base wide sliding window  cutting when the average quality per base drops below 10 SLIDINGWINDOW:  4:10 2 Remove trailing low quality or N bases below quality 3 TRAILING:3 3 Remove adapters : there are two modes to remove the adapter sequence: a.  alignment with the adapter sequence  the number of matching bases were greater than 7 and mismatch=2; b.when read1 and read2 overlapping base scoring  greater than 30  removed non overlapping portions ILLUMINACLIP: adapter.fa:  2: 30: 7 4 Drop reads below the 26 bases long 5 Discard those reads that can not form paired The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last  we use FastQC to perform basic statistics on the quality of the clean reads. Cell Ranger uses an aligner called STAR  which peforms splicing aware alignment of reads to the genome. Cell Ranger then uses the transcript annotation GTF to bucket the reads into exonic  intronic  and intergenic  and by whether the reads align confidently to the genome. A read is exonic if at least 50% of it intersects an exon  intronic if it is non exonic and intersects an intron  and intergenic otherwise. For reads that align to a single exonic locus but also align to 1 or more non exonic loci  the exonic locus is prioritized and the read is considered to be confidently mapped to the exonic locus with MAPQ 255. Cell Ranger further aligns exonic reads to annotated transcripts  looking for compatibility. A read that is compatible with the exons of an annotated transcript  and aligned to the same strand  is considered mapped to the transcriptome. If the read is compatible with a single gene annotation  it is considered uniquely confidently mapped to the transcriptome. Only reads that  are confidently mapped to the transcriptome are used for UMI counting. Cell Ranger takes as input the expected number of recovered cells  N see    expect cells. Let m be a robust estimate of the maximum total UMI counts  taken as the 99th percentile of the top N barcodes by total UMI counts. All barcodes whose total UMI counts exceed m/10 are called as cells. This is performed separately for each GEM group library and  if the reference contains multiple genomes  for each genome. Genome build: Danio rerio Ensemble 91 Supplementary files format and content: gene barcode expression matrix,intestine cells,Exposure solutions were prepared by adding 200μg/L PS NPs  50μg/L Pb or both of them to culture water. The exposure solution were was replaced every 2 days.  post 21 d exposure  zebrafish were collected and intestine were rapidly extracted on ice.,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell 3’ Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer’s protocol. Libraries were sequenced on a Nova6000.,,tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50μg/L Pb,GSM5057359,GSM5057359: Pb scRNA seq; Danio rerio; RNA Seq,GSM5057359,,1,The isolated intestine tissue was digested into  cell suspension with dispase. Cells were loaded on a GemCode Single Cell Instrument10x Genomics  USA to generate single cell Gel bead in Emulsion GEMs. ScRNA seq libraries were prepared using the GemCode Single Cell three prime Gel Bead  Chip and Library Kits 10x Genomics  USA as per the manufacturer's protocol. Libraries were sequenced on a Nova6000.,GEO Accession:GSM5057359,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP304100,,,Pb-3_S1_L002_R1_001.fastq.gz Pb-3_S1_L002_R2_001.fastq.gz,fastq fastq,20016441600.0,66721472.0,GSM5057359 r3,0:150 1:150,A:7552609483;C:3548581370;G:3386994715;T:5527787801;N:468231,150,150,,,7552609483,3548581370,3386994715,5527787801,468231,SRX9989398,SRS8160233,SRA1189975,GEO,"School of the Environment, Nanjing university",2,0.0,0.89853,0.0,0.09849,1.0,0.8213,,0.55535,150,150,T,B,mate1 technical by mapping diff,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2021-02-01,Adult,Adult,Gut,Digestive System