{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_source = \"TRANSCRIPTOMIC\", technology = \"10x\" and tissue_curation_coarse = \"Digestive System\"", "rows": [[9166, "ERR2788341", "ERX2797590", "ERS2709706", "ERP110806", "PRJEB28589", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E-MTAB-7159", "Transcriptome Analysis", "Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11", null, "Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min 85\u00b0C for 5 min held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min 12 cycles of 90\u00b0C for 15 s 67\u00b0C for 20 s and 72\u00b0C for 1 min 72\u00b0C for 1 min held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly for fragmentation end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min 65\u00b0C for 30 min held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check the libraries were diluted to the concentration required for sequencing.", "5149STDY7292228", "SAMEA4890710", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK", "ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890710|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7292228|age:6|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP|individual:pool 4|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7292228|scientific name:Danio rerio|sex:2 female 1 male|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E MTAB 7159:5149STDY7292228 p", "5149STDY7292228 p", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min 85\u00b0C for 5 min held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min 12 cycles of 90\u00b0C for 15 s 67\u00b0C for 20 s and 72\u00b0C for 1 min 72\u00b0C for 1 min held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly for fragmentation end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min 65\u00b0C for 30 min held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check the libraries were diluted to the concentration required for sequencing.", "Experimental Factor: genotype:Tglck:EGFP|Experimental Factor: infect:n1", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", "8660FApplication ReadForward11RApplication ReadReverse434", "ERP110806", "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options: use QUAL", "5149STDY7292228.bam 5149STDY7292228.bam.bai", "bam bam", 37970494940.0, 387454030.0, "E MTAB 7159:5149STDY7292228", "0:98", "A:11476520187;C:7571635167;G:8189594199;T:10701044279;N:31701108", 98, null, null, null, 11476520187, 7571635167, 8189594199, 10701044279, 31701108, "ERX2797590", "ERS2709706", "ERA1594569", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.87568, null, 0.2122, null, 0.82582, null, 0.5259, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2018-09-11", "Adult", "Adult", "Gut", "Digestive System"], [9167, "ERR2788340", "ERX2797589", "ERS2709705", "ERP110806", "PRJEB28589", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E-MTAB-7159", "Transcriptome Analysis", "Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11", null, "Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min 85\u00b0C for 5 min held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min 12 cycles of 90\u00b0C for 15 s 67\u00b0C for 20 s and 72\u00b0C for 1 min 72\u00b0C for 1 min held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly for fragmentation end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min 65\u00b0C for 30 min held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check the libraries were diluted to the concentration required for sequencing.", "5149STDY7274848", "SAMEA4890709", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK", "ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890709|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274848|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 3|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274848|scientific name:Danio rerio|sex:female|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E MTAB 7159:5149STDY7274848 p", "5149STDY7274848 p", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min 85\u00b0C for 5 min held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min 12 cycles of 90\u00b0C for 15 s 67\u00b0C for 20 s and 72\u00b0C for 1 min 72\u00b0C for 1 min held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly for fragmentation end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min 65\u00b0C for 30 min held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check the libraries were diluted to the concentration required for sequencing.", "Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Vibrio Anguillarum", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", "8660FApplication ReadForward11RApplication ReadReverse434", "ERP110806", "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options: use QUAL", "5149STDY7274848.bam 5149STDY7274848.bam.bai", "bam bam", 34517322840.0, 352217580.0, "E MTAB 7159:5149STDY7274848", "0:98", "A:10635243399;C:6658515314;G:7525079510;T:9695995344;N:2489273", 98, null, null, null, 10635243399, 6658515314, 7525079510, 9695995344, 2489273, "ERX2797589", "ERS2709705", "ERA1594569", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.86206, null, 0.18065, null, 0.83514, null, 0.53609, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2018-09-11", "Adult", "Adult", "Gut", "Digestive System"], [9168, "ERR2788339", "ERX2797588", "ERS2709704", "ERP110806", "PRJEB28589", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E-MTAB-7159", "Transcriptome Analysis", "Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11", null, "Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min 85\u00b0C for 5 min held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min 12 cycles of 90\u00b0C for 15 s 67\u00b0C for 20 s and 72\u00b0C for 1 min 72\u00b0C for 1 min held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly for fragmentation end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min 65\u00b0C for 30 min held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check the libraries were diluted to the concentration required for sequencing.", "5149STDY7274847", "SAMEA4890708", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK", "ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890708|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274847|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 2|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274847|scientific name:Danio rerio|sex:female|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E MTAB 7159:5149STDY7274847 p", "5149STDY7274847 p", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min 85\u00b0C for 5 min held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min 12 cycles of 90\u00b0C for 15 s 67\u00b0C for 20 s and 72\u00b0C for 1 min 72\u00b0C for 1 min held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly for fragmentation end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min 65\u00b0C for 30 min held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check the libraries were diluted to the concentration required for sequencing.", "Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:Anisakis simplex", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", "8660FApplication ReadForward11RApplication ReadReverse434", "ERP110806", "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options: use QUAL", "5149STDY7274847.bam 5149STDY7274847.bam.bai", "bam bam", 34467649678.0, 351710711.0, "E MTAB 7159:5149STDY7274847", "0:98", "A:10609988948;C:6722093635;G:7464497879;T:9667814950;N:3254266", 98, null, null, null, 10609988948, 6722093635, 7464497879, 9667814950, 3254266, "ERX2797588", "ERS2709704", "ERA1594569", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.88751, null, 0.21835, null, 0.83771, null, 0.53927, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2018-09-11", "Adult", "Adult", "Gut", "Digestive System"], [9169, "ERR2788338", "ERX2797587", "ERS2709703", "ERP110806", "PRJEB28589", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E-MTAB-7159", "Transcriptome Analysis", "Transcriptome data from zebrafish single cells from guts from either from Tglck:EGFP rag1 / mutant or wild type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment.", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 09 11", null, "Protocols: The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min 85\u00b0C for 5 min held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min 12 cycles of 90\u00b0C for 15 s 67\u00b0C for 20 s and 72\u00b0C for 1 min 72\u00b0C for 1 min held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly for fragmentation end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min 65\u00b0C for 30 min held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check the libraries were diluted to the concentration required for sequencing.", "5149STDY7274846", "SAMEA4890707", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK", "ENA FIRST PUBLIC:2018 11 16T17:03:30Z|ENA LAST UPDATE:2018 09 11T09:38:07Z|External Id:SAMEA4890707|INSDC center name:Department of Haematology University of Cambridge Cambridge UK Wellcome Trust Sanger Institute Wellcome Trust Genome Campus Cambridge Wellcome Trust Medical Research Council Cambridge Stem Cell Institute Cambridge UK|INSDC first public:2018 11 16T17:03:30Z|INSDC last update:2018 09 11T09:38:07Z|INSDC status:public|Submitter Id:E MTAB 7159:5149STDY7274846|age:4|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:Tglck:EGFP; Rag1 homozygous knockout|individual:pool 1|organism part:intestine|phenotype:lck positive|sample name:E MTAB 7159:5149STDY7274846|scientific name:Danio rerio|sex:female|strain:AB", null, null, null, null, null, null, null, null, "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "E MTAB 7159:5149STDY7274846 p", "5149STDY7274846 p", "Single cell transcriptional analysis reveals ILC like cells in zebrafish", "The guts were dissected and placed in ice cold PBS/5% foetal bovine serum. Single cell suspensions were generated by first passing through a 40 \u00b5m strainer using the plunger of a 1 ml syringe as a pestle. These were then passed through a 20 \u00b5m strainer before adding 4' 6 diamidino 2 phenylindole DAPI Beckman Coulter cat no B30437 to the samples. Three zebrafish per each condition i.e. zebrafish intraperitoneally injected with PBS lyophilised Anisakis simplex or inactivated Vibrio anguillarum were used to collect the total of 12 000 lck+ cells 4000 per zebrafish for 10x experiment. Cell were sorted into 1.5 ml Eppendorf tubes containing 20 \uf06dl 5% FBS in PBS using a BD Influx Index Sorter. Following the sorting cells were spun down and resuspended in ice cold PBS with 0.04% bovine serum albumin at the concentration of 500 cells/\u03bcl. Briefly cellular suspension was added to the master mix containing nuclease free water RT Reagent Mix RT Primer Additive A and RT Enzyme Mix. Master mix with cells was transferred to the wells in the row labelled 1 on the Chromium\u2122 Single Cell A Chip 10x Genomics. Single Cell three prime Gel Beads were transferred into the row labelled 2 and Partitioning Oil was transferred into the row labelled 3. The chip was loaded on Chromium\u2122 Controller to generate single cell GEMs. GEM RT was performed in a C1000 Touch Thermal cycler Bio Rad at the following conditions: 53\u00b0C for 45 min 85\u00b0C for 5 min held at 4\u00b0C. Post GEM RT cleanup was performed with DynaBeads MyOne Silane Beads Thermo Fisher Scientific. cDNA was amplified using C1000 Touch Thermal cycler at the following conditions: 98\u00b0C for 3 min 12 cycles of 90\u00b0C for 15 s 67\u00b0C for 20 s and 72\u00b0C for 1 min 72\u00b0C for 1 min held 4\u00b0C. Amplified cDNA was cleaned with the SPRIselect Reagent Kit Beckman Coulter and quality was assessed using 2100 Bioanalyser Agilent. Libraries were constructed using Chromium\u2122 Controller and Chromium\u2122 Single Cell three prime Library & Gel Bead Kit v2 10x Genomics according to the manufacturer's protocol. Briefly for fragmentation end repair and A tailing cDNA was incubated with Fragmentation Mix in pre cooled thermocycler at the following conditions: 32\u00b0C for 5 min 65\u00b0C for 30 min held at 4\u00b0C. The libraries were then purified using beads. Next adaptor ligation was performed samples were incubated with Adaptor Ligation Mix at 20\u00b0C for 15 min followed by post ligation clean up with beads and Sample Index PCR. Again libraries were purified using beads. Following a final Bioanalyzer quality check the libraries were diluted to the concentration required for sequencing.", "Experimental Factor: genotype:Tglck:EGFP; Rag1 homozygous knockout|Experimental Factor: infect:n1", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 4000", "8660FApplication ReadForward11RApplication ReadReverse434", "ERP110806", "Illumina HiSeq 4000 sequencing; Single cell transcriptional analysis reveals ILC like cells in zebrafish", "ENA FIRST PUBLIC:2018 11 16|ENA LAST UPDATE:2018 11 16|options: use QUAL", "5149STDY7274846.bam 5149STDY7274846.bam.bai", "bam bam", 35052538472.0, 357678964.0, "E MTAB 7159:5149STDY7274846", "0:98", "A:10698116265;C:6858102477;G:7626019661;T:9866905792;N:3394277", 98, null, null, null, 10698116265, 6858102477, 7626019661, 9866905792, 3394277, "ERX2797587", "ERS2709703", "ERA1594569", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", "Department of Haematology, University of Cambridge, Cambridge, UK Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Wellcome Trust \u00e2\u20ac\u201c Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK|European Nucleotide Archive", 1, 0.88916, null, 0.21537, null, 0.83802, null, 0.5336, null, 98, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2018-09-11", "Adult", "Adult", "Gut", "Digestive System"], [34517, "SRR32044795", "SRX27393953", "SRS23824014", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr+VC 3", "I", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Cr+VC 3", "Cr+VC 3", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, null, "Cr+VC-3.R1.raw.fastq.gz Cr+VC-3.R2.raw.fastq.gz", "fastq fastq", 6773536558.0, 22428929.0, "Cr+VC 3.R1.raw.fastq.gz", "0:151 1:151", "A:1792253952;C:1581454013;G:1629330621;T:1770470694;N:27278", 151, 151, null, null, 1792253952, 1581454013, 1629330621, 1770470694, 27278, "SRX27393953", "SRS23824014", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive System"], [34518, "SRR32044796", "SRX27393952", "SRS23824013", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr+VC 2", "H", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Cr+VC 2", "Cr+VC 2", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, null, "Cr+VC-2.R1.raw.fastq.gz Cr+VC-2.R2.raw.fastq.gz", "fastq fastq", 7449518862.0, 24667281.0, "Cr+VC 2.R1.raw.fastq.gz", "0:151 1:151", "A:1969693675;C:1748150730;G:1771267240;T:1960378098;N:29119", 151, 151, null, null, 1969693675, 1748150730, 1771267240, 1960378098, 29119, "SRX27393952", "SRS23824013", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive System"], [34519, "SRR32044797", "SRX27393951", "SRS23824012", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr+VC 1", "G", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 14|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 14|health state:health|sample type:tissue|replication:Cr+VC 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Cr+VC 1", "Cr+VC 1", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, "loader:fastq load.py|options: doNotUseSharq", "Cr+VC-1.R1.raw.fastq Cr+VC-1.R2.raw.fastq", "fastq fastq", 6865491179.0, 45466829.0, "Cr+VC 1.R1.raw.fastq.gz", "0:151", "A:1830069736;C:1600281531;G:1626303427;T:1808809011;N:27474", 151, null, null, null, 1830069736, 1600281531, 1626303427, 1808809011, 27474, "SRX27393951", "SRS23824012", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive System"], [34520, "SRR32044798", "SRX27393950", "SRS23824011", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr 3", "F", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Cr 3", "Cr 3", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, null, "Cr-3.R1.raw.fastq.gz Cr-3.R2.raw.fastq.gz", "fastq fastq", 6069804078.0, 20098689.0, "Cr 3.R1.raw.fastq.gz", "0:151 1:151", "A:1603886661;C:1431213970;G:1440806224;T:1593873144;N:24079", 151, 151, null, null, 1603886661, 1431213970, 1440806224, 1593873144, 24079, "SRX27393950", "SRS23824011", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive System"], [34521, "SRR32044799", "SRX27393949", "SRS23824010", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr 2", "E", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Cr 2", "Cr 2", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, "loader:fastq load.py|options: doNotUseSharq", "Cr-2.R1.raw.fastq Cr-2.R2.raw.fastq", "fastq fastq", 8327156985.0, 55146735.0, "Cr 2.R1.raw.fastq.gz", "0:151", "A:2181317777;C:1974793526;G:2003240106;T:2167771431;N:34145", 151, null, null, null, 2181317777, 1974793526, 2003240106, 2167771431, 34145, "SRX27393949", "SRS23824010", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive System"], [34522, "SRR32044800", "SRX27393948", "SRS23824009", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Cr 1", "D", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 13|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 13|health state:health|sample type:tissue|replication:Cr 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Cr 1", "Cr 1", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, null, "Cr-1.R1.raw.fastq.gz Cr-1.R2.raw.fastq.gz", "fastq fastq", 7322067614.0, 24245257.0, "Cr 1.R1.raw.fastq.gz", "0:151 1:151", "A:1927213281;C:1727973559;G:1748866497;T:1917985720;N:28557", 151, 151, null, null, 1927213281, 1727973559, 1748866497, 1917985720, 28557, "SRX27393948", "SRS23824009", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive System"], [34523, "SRR32044801", "SRX27393947", "SRS23824008", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Con 3", "C", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Con 3", "Con 3", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, null, "Con-3.R1.raw.fastq.gz Con-3.R2.raw.fastq.gz", "fastq fastq", 10329187314.0, 34202607.0, "Con 3.R1.raw.fastq.gz", "0:151 1:151", "A:2805764955;C:2343400161;G:2421657823;T:2758323021;N:41354", 151, 151, null, null, 2805764955, 2343400161, 2421657823, 2758323021, 41354, "SRX27393947", "SRS23824008", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive System"], [34524, "SRR32044802", "SRX27393946", "SRS23824007", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Con 2", "B", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Con 2", "Con 2", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, null, "Con-2.R1.raw.fastq.gz Con-2.R2.raw.fastq.gz", "fastq fastq", 10789961398.0, 35728349.0, "Con 2.R1.raw.fastq.gz", "0:151 1:151", "A:2983305704;C:2396592872;G:2488165589;T:2921853880;N:43353", 151, 151, null, null, 2983305704, 2396592872, 2488165589, 2921853880, 43353, "SRX27393946", "SRS23824007", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive System"], [34525, "SRR32044803", "SRX27393945", "SRS23824006", "SRP558295", "PRJNA1212482", "vitamin C mitigated hexavalent chromium toxicity by microbiota gut brain axis in zebrafish", "PRJNA1212482", "Other", "Zebrafish is characterized by small size rapid development high fertility short life cycle easy and economical rearing; it has now become one of the model organisms for drug screening disease research and ecological environment evaluation. Therefore this project takes zebrafish as a model organism as the research object and intends to study the role of vitamins in alleviating gut hexavalent chromium toxicity from the perspective of oxidative damage through the application of toxicology transcriptome molecular biology and other techniques.", null, null, null, "Con 1", "A", null, "ecotype:wild type zebrafish|age:6 month|dev stage:adult|collection date:2023 08 12|geo loc name:China: Haikou Hainan Province|sex:pooled male and female|tissue:gut|death date:2023 8 12|health state:health|sample type:tissue|replication:Con 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of brian:Adult female and male zebrafish", "Con 1", "Con 1", "normal", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP558295", null, null, "Con-1.R1.raw.fastq.gz Con-1.R2.raw.fastq.gz", "fastq fastq", 7118179260.0, 23570130.0, "Con 1.R1.raw.fastq.gz", "0:151 1:151", "A:1874284939;C:1673861890;G:1718740497;T:1851263659;N:28275", 151, 151, null, null, 1874284939, 1673861890, 1718740497, 1851263659, 28275, "SRX27393945", "SRS23824006", "SRA2054568", "Hainan University|School of Life and Health Sciences", "Hainan University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2025-01-19", "Adult", "Adult", "Gut", "Digestive System"], [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 5\u00b5m and 200\u00b5m 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 \u00b5m and 200 \u00b5m.", "parent bioproject:PRJNA561326", "pubmed:32092251", null, "MPs200vm", "GSM4029395", null, "source name:intestinal cells|tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:200\u03bcm 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 \u03bcm or 200 \u03bcm PS MPs to culture water with a final concentration of 500\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on an Illumina Hiseq PE150.", null, "tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:200\u03bcm PS MPs", "GSM4029395", "GSM4029395: MPs200vm; Danio rerio; RNA Seq", "GSM4029395", null, "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", null, "SRP218210", null, null, "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, null, null, 27241602982, 19773063887, 28015499540, 30277575281, 1877210, "SRX6707776", "SRS5261677", "SRA938912", "GEO", "Nanjing University", 2, 0.0, 0.87735, 0.0, 0.07963, 1.0, 0.83049, null, 0.55138, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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 5\u00b5m and 200\u00b5m 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 \u00b5m and 200 \u00b5m.", "parent bioproject:PRJNA561326", "pubmed:32092251", null, "MPs5vm", "GSM4029394", null, "source name:intestinal cells|tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:5\u03bcm 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 \u03bcm or 200 \u03bcm PS MPs to culture water with a final concentration of 500\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on an Illumina Hiseq PE150.", null, "tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:5\u03bcm PS MPs", "GSM4029394", "GSM4029394: MPs5vm; Danio rerio; RNA Seq", "GSM4029394", null, "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", null, "SRP218210", null, null, "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, null, null, 26023907285, 17974044830, 25736568268, 28827634883, 1748834, "SRX6707775", "SRS5261676", "SRA938912", "GEO", "Nanjing University", 2, 0.0, 0.86592, 0.0, 0.09908, 1.0, 0.81552, null, 0.55476, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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 5\u00b5m and 200\u00b5m 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 \u00b5m and 200 \u00b5m.", "parent bioproject:PRJNA561326", "pubmed:32092251", null, "MPs100nm", "GSM4029393", null, "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 \u03bcm or 200 \u03bcm PS MPs to culture water with a final concentration of 500\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on an Illumina Hiseq PE150.", null, "tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:100nm PS MPs", "GSM4029393", "GSM4029393: MPs100nm; Danio rerio; RNA Seq", "GSM4029393", null, "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", null, "SRP218210", null, null, "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, null, null, 32283417066, 22576112318, 30470461014, 37207888685, 1839317, "SRX6707774", "SRS5261675", "SRA938912", "GEO", "Nanjing University", 2, 0.0, 0.88187, 0.0, 0.09087, 1.0, 0.82428, null, 0.53597, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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 5\u00b5m and 200\u00b5m 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 \u00b5m and 200 \u00b5m.", "parent bioproject:PRJNA561326", "pubmed:32092251", null, "CK", "GSM4029392", null, "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 \u03bcm or 200 \u03bcm PS MPs to culture water with a final concentration of 500\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on an Illumina Hiseq PE150.", null, "tissue:Intestinal single cell suspension|age:16 wpf|exposed pollutants:n1", "GSM4029392", "GSM4029392: CK; Danio rerio; RNA Seq", "GSM4029392", null, "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", null, "SRP218210", null, null, "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, null, null, 29264568248, 21295511514, 29897320083, 31301732224, 2009031, "SRX6707773", "SRS5261674", "SRA938912", "GEO", "Nanjing University", 2, 0.0, 0.88395, 0.0, 0.08593, 1.0, 0.80466, null, 0.46326, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM10", "GSM4878631", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2566209216, 2292038760, 2265576943, 2488871493, 209900, "SRX9426454", "SRS7641325", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.962, null, 0.0608, null, 0.8734, null, 0.67588, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM10", "GSM4878631", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2548745985, 2274433644, 2248703958, 2472613589, 805576, "SRX9426454", "SRS7641325", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.9615, null, 0.06194, null, 0.87247, null, 0.74516, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM09", "GSM4878630", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2545306811, 2315371452, 2200128862, 2489970955, 208553, "SRX9426453", "SRS7641324", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96301, null, 0.05192, null, 0.88743, null, 0.70057, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM09", "GSM4878630", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2528707184, 2298013878, 2184508040, 2474200996, 801751, "SRX9426453", "SRS7641324", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96301, null, 0.05148, null, 0.8846, null, 0.72241, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM08", "GSM4878629", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2870124713, 2509365613, 2345749207, 2681489991, 226784, "SRX9426452", "SRS7641323", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96215, null, 0.03963, null, 0.90057, null, 0.84217, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM08", "GSM4878629", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2855106653, 2493008676, 2331251314, 2666929711, 875090, "SRX9426452", "SRS7641323", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96136, null, 0.03986, null, 0.90021, null, 0.83819, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM07", "GSM4878628", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2569669307, 2214757071, 1969962475, 2368609155, 198576, "SRX9426451", "SRS7641322", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96088, null, 0.05866, null, 0.88708, null, 0.85062, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM07", "GSM4878628", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2551775269, 2196748202, 1954504090, 2351840767, 764965, "SRX9426451", "SRS7641322", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96058, null, 0.05844, null, 0.88939, null, 0.85033, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM06", "GSM4878627", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2473315824, 2129478747, 2022150123, 2331535818, 196503, "SRX9426450", "SRS7641321", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96363, null, 0.04651, null, 0.89988, null, 0.84067, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM06", "GSM4878627", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2456331697, 2112784685, 2006505048, 2315434557, 749808, "SRX9426450", "SRS7641321", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96343, null, 0.04559, null, 0.90165, null, 0.84056, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM05", "GSM4878626", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2554844989, 2175928954, 1956415280, 2377558346, 198930, "SRX9426449", "SRS7641320", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96742, null, 0.0357, null, 0.91737, null, 0.88943, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM05", "GSM4878626", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2536668919, 2157506999, 1940651397, 2360359924, 761258, "SRX9426449", "SRS7641320", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96676, null, 0.03558, null, 0.91666, null, 0.88967, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM04", "GSM4878625", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2687588051, 2283954081, 2107499458, 2521583198, 209845, "SRX9426448", "SRS7641318", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95608, null, 0.06784, null, 0.8538, null, 0.81465, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM04", "GSM4878625", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2673944918, 2269787019, 2095420445, 2508893277, 805880, "SRX9426448", "SRS7641318", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95602, null, 0.06682, null, 0.85433, null, 0.61345, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM03", "GSM4878624", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2627894488, 2152254884, 2064675616, 2312678653, 199291, "SRX9426447", "SRS7641319", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95169, null, 0.08321, null, 0.8802, null, 0.7957, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM03", "GSM4878624", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2607939019, 2133198115, 2047005553, 2295838531, 766469, "SRX9426447", "SRS7641319", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95159, null, 0.08346, null, 0.87799, null, 0.86901, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM02", "GSM4878623", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2568403174, 2203993337, 1949600715, 2418964898, 201316, "SRX9426446", "SRS7641317", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96372, null, 0.04508, null, 0.89416, null, 0.89922, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM02", "GSM4878623", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2556536997, 2191496444, 1938967545, 2407692037, 770496, "SRX9426446", "SRS7641317", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.96463, null, 0.044, null, 0.89286, null, 0.90213, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM01", "GSM4878622", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2742192040, 2208968705, 2007446927, 2400535057, 204849, "SRX9426445", "SRS7641316", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.97296, null, 0.04791, null, 0.91259, null, 0.93709, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJM01", "GSM4878622", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 2721584053, 2190402119, 1990556025, 2383450199, 783655, "SRX9426445", "SRS7641316", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.9733, null, 0.04761, null, 0.91441, null, 0.93019, null, 56, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJC03", "GSM4551420", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 333004523, 277828258, 286036018, 290210763, 270862, "SRX8337992", "SRS6656491", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.94136, null, 0.10077, null, 0.85512, null, 0.75118, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJC03", "GSM4551420", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 366398712, 306757422, 316095972, 319052449, 338896, "SRX8337992", "SRS6656491", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.9424, null, 0.09777, null, 0.85188, null, 0.75485, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJC03", "GSM4551420", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 366013405, 307141773, 319701005, 318562083, 97037, "SRX8337992", "SRS6656491", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.94016, null, 0.09633, null, 0.85291, null, 0.75214, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJC03", "GSM4551420", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 355124126, 298971601, 313182839, 309762369, 128022, "SRX8337992", "SRS6656491", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.93858, null, 0.09543, null, 0.85139, null, 0.75235, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJC02", "GSM4551419", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 317522952, 260688416, 260193778, 267326347, 250681, "SRX8337991", "SRS6656490", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95224, null, 0.05677, null, 0.89012, null, 0.83572, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJC02", "GSM4551419", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 350724821, 288990705, 288572329, 294798443, 318382, "SRX8337991", "SRS6656490", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95282, null, 0.05487, null, 0.88781, null, 0.8357, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJC02", "GSM4551419", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 353256976, 291475235, 293788969, 296442213, 91476, "SRX8337991", "SRS6656490", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95103, null, 0.05401, null, 0.8869, null, 0.81707, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJC02", "GSM4551419", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 343127030, 284042987, 287996072, 288482311, 117629, "SRX8337991", "SRS6656490", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.94817, null, 0.05377, null, 0.88548, null, 0.41506, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNZF2", "GSM4551418", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 325430172, 264437244, 262877435, 287797270, 1890270, "SRX8337990", "SRS6656489", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.9502, null, 0.05655, null, 0.90183, null, 0.88561, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNZF2", "GSM4551418", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 326541749, 265861466, 263268760, 288214490, 2164132, "SRX8337990", "SRS6656489", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95246, null, 0.0553, null, 0.90082, null, 0.88734, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNZF2", "GSM4551418", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 364126807, 297595539, 301588932, 322080166, 2279424, "SRX8337990", "SRS6656489", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.9442, null, 0.05165, null, 0.89414, null, 0.87072, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNZF2", "GSM4551418", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 344940661, 281702462, 282564971, 304818639, 2433811, "SRX8337990", "SRS6656489", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.94948, null, 0.05357, null, 0.894, null, 0.88193, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNZF1", "GSM4551417", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 318266957, 263185714, 261698958, 276036499, 1855516, "SRX8337989", "SRS6656488", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95246, null, 0.04561, null, 0.91131, null, 0.80014, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNZF1", "GSM4551417", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 320336836, 265494414, 262986049, 277346260, 2121659, "SRX8337989", "SRS6656488", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95333, null, 0.04443, null, 0.91072, null, 0.89221, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNZF1", "GSM4551417", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 358320733, 298143124, 302249804, 311018556, 2272782, "SRX8337989", "SRS6656488", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.94848, null, 0.04159, null, 0.90617, null, 0.89091, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNZF1", "GSM4551417", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 339057834, 282010519, 282903285, 294041893, 2388832, "SRX8337989", "SRS6656488", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95017, null, 0.04264, null, 0.90303, null, 0.89249, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJCZ2", "GSM4551416", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 386793838, 328592754, 326298808, 335158719, 315893, "SRX8337988", "SRS6656487", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95832, null, 0.06422, null, 0.87852, null, 0.73546, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJCZ2", "GSM4551416", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 425494105, 363112628, 360572880, 368871810, 400806, "SRX8337988", "SRS6656487", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95946, null, 0.0652, null, 0.87649, null, 0.64868, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJCZ2", "GSM4551416", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 431105301, 369007286, 369511373, 373755247, 111392, "SRX8337988", "SRS6656487", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95749, null, 0.0612, null, 0.87659, null, 0.65691, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJCZ2", "GSM4551416", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 418327578, 359123038, 361317639, 363357288, 149690, "SRX8337988", "SRS6656487", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95529, null, 0.06072, null, 0.87523, null, 0.65804, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJCZ1", "GSM4551415", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 334176306, 267881430, 269991337, 281980065, 260278, "SRX8337987", "SRS6656486", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95462, null, 0.07782, null, 0.87994, null, 0.69253, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJCZ1", "GSM4551415", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 367956165, 296259421, 298606136, 310443339, 328499, "SRX8337987", "SRS6656486", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.9562, null, 0.07523, null, 0.87744, null, 0.71234, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJCZ1", "GSM4551415", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 374341323, 302164288, 307195329, 315582357, 93207, "SRX8337987", "SRS6656486", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95203, null, 0.07407, null, 0.87696, null, 0.70725, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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", null, "pubmed:33789339", null, "SNJCZ1", "GSM4551415", null, "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 \u201cRaw\u201d UMI matrix generated for each sample extracted cell barcodes associated with at least 150 UMIs from the \u201cRaw\u201d 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", null, "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", null, "SRP261473", null, "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, null, 363767572, 294460691, 300901128, 307184946, 125937, "SRX8337987", "SRS6656486", "SRA1075199", "GEO", "Cho lab, Institute of Personalized medicine, Mount Sinai hospital", 1, 0.95089, null, 0.07244, null, 0.87738, null, 0.7883, null, 55, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:35108531", null, "Germ free Sample 4", "GSM5667113", null, "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", null, "Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3", null, "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", null, "1", "Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3", "GEO Accession:GSM5667113", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP293304", null, "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", null, "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.", null, "pubmed:35108531", null, "Conventially reared Sample 3", "GSM5667112", null, "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", null, "Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3", null, "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", null, "1", "Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3", "GEO Accession:GSM5667112", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP293304", null, "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", null, "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.", null, "pubmed:35108531", null, "Germ free Sample 2", "GSM4916094", null, "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", null, "Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3", null, "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", null, "1", "Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3", "GEO Accession:GSM4916094", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP293304", null, "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, null, 16033538561, 12891030760, 13419497134, 25045893164, 16122509, "SRX9535221", "SRS7741720", "SRA1161597", "GEO", "6-59 HMRC, Medical Microbiology and Immunology, University of Alberta", 1, 0.92012, null, 0.08227, null, 0.87988, null, 0.70616, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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.", null, "pubmed:35108531", null, "Conventionally reared Sample 1", "GSM4916093", null, "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", null, "Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3", null, "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", null, "1", "Cellular RNA extracted and barcoded with 10X Genomics Chromium Controller Chromium Single Cell 3\u2032 Library & Gel Bead Kit v3", "GEO Accession:GSM4916093", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP293304", null, "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, null, 18580003391, 14737356417, 15062022999, 28611588832, 18324725, "SRX9535220", "SRS7741719", "SRA1161597", "GEO", "6-59 HMRC, Medical Microbiology and Immunology, University of Alberta", 1, 0.91135, null, 0.09577, null, 0.85512, null, 0.70479, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "PS NPs+Pb scRNA seq", "GSM5057360", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs and 50\u03bcg/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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs and 50\u03bcg/L Pb", "GSM5057360", "GSM5057360: PS NPs+Pb scRNA seq; Danio rerio; RNA Seq", "GSM5057360", null, "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", null, "SRP304100", null, null, "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, null, null, 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, null, 0.54384, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "PS NPs+Pb scRNA seq", "GSM5057360", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs and 50\u03bcg/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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs and 50\u03bcg/L Pb", "GSM5057360", "GSM5057360: PS NPs+Pb scRNA seq; Danio rerio; RNA Seq", "GSM5057360", null, "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", null, "SRP304100", null, null, "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, null, null, 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, null, 0.55615, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "PS NPs+Pb scRNA seq", "GSM5057360", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs and 50\u03bcg/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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs and 50\u03bcg/L Pb", "GSM5057360", "GSM5057360: PS NPs+Pb scRNA seq; Danio rerio; RNA Seq", "GSM5057360", null, "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", null, "SRP304100", null, null, "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, null, null, 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, null, 0.56185, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "PS NPs+Pb scRNA seq", "GSM5057360", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs and 50\u03bcg/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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs and 50\u03bcg/L Pb", "GSM5057360", "GSM5057360: PS NPs+Pb scRNA seq; Danio rerio; RNA Seq", "GSM5057360", null, "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", null, "SRP304100", null, null, "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, null, null, 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, null, 0.56254, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "PS NPs+Pb scRNA seq", "GSM5057360", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs and 50\u03bcg/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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs and 50\u03bcg/L Pb", "GSM5057360", "GSM5057360: PS NPs+Pb scRNA seq; Danio rerio; RNA Seq", "GSM5057360", null, "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", null, "SRP304100", null, null, "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, null, null, 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", null, "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "PS NPs+Pb scRNA seq", "GSM5057360", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs and 50\u03bcg/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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs and 50\u03bcg/L Pb", "GSM5057360", "GSM5057360: PS NPs+Pb scRNA seq; Danio rerio; RNA Seq", "GSM5057360", null, "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", null, "SRP304100", null, null, "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, null, null, 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", null, "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "PS NPs+Pb scRNA seq", "GSM5057360", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs and 50\u03bcg/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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs and 50\u03bcg/L Pb", "GSM5057360", "GSM5057360: PS NPs+Pb scRNA seq; Danio rerio; RNA Seq", "GSM5057360", null, "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", null, "SRP304100", null, null, "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, null, null, 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", null, "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "PS NPs+Pb scRNA seq", "GSM5057360", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs and 50\u03bcg/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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs and 50\u03bcg/L Pb", "GSM5057360", "GSM5057360: PS NPs+Pb scRNA seq; Danio rerio; RNA Seq", "GSM5057360", null, "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", null, "SRP304100", null, null, "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, null, null, 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", null, "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "Pb scRNA seq", "GSM5057359", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50\u03bcg/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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50\u03bcg/L Pb", "GSM5057359", "GSM5057359: Pb scRNA seq; Danio rerio; RNA Seq", "GSM5057359", null, "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", null, "SRP304100", null, null, "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, null, null, 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, null, 0.52876, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "Pb scRNA seq", "GSM5057359", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50\u03bcg/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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50\u03bcg/L Pb", "GSM5057359", "GSM5057359: Pb scRNA seq; Danio rerio; RNA Seq", "GSM5057359", null, "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", null, "SRP304100", null, null, "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, null, null, 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, null, 0.54985, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "Pb scRNA seq", "GSM5057359", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50\u03bcg/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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50\u03bcg/L Pb", "GSM5057359", "GSM5057359: Pb scRNA seq; Danio rerio; RNA Seq", "GSM5057359", null, "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", null, "SRP304100", null, null, "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, null, null, 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, null, 0.55535, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63092, "SRR13594972", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "Pb scRNA seq", "GSM5057359", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50\u03bcg/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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50\u03bcg/L Pb", "GSM5057359", "GSM5057359: Pb scRNA seq; Danio rerio; RNA Seq", "GSM5057359", null, "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", null, "SRP304100", null, null, "Pb-4_S1_L002_R1_001.fastq.gz Pb-4_S1_L002_R2_001.fastq.gz", "fastq fastq", 28904617800.0, 96348726.0, "GSM5057359 r4", "0:150 1:150", "A:10921141580;C:5139781240;G:4904879668;T:7938123351;N:691961", 150, 150, null, null, 10921141580, 5139781240, 4904879668, 7938123351, 691961, "SRX9989398", "SRS8160233", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.0, 0.89947, 0.0, 0.09536, 1.0, 0.8255, null, 0.54223, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63093, "SRR13594973", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "Pb scRNA seq", "GSM5057359", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50\u03bcg/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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50\u03bcg/L Pb", "GSM5057359", "GSM5057359: Pb scRNA seq; Danio rerio; RNA Seq", "GSM5057359", null, "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", null, "SRP304100", null, null, "Pb-5_S1_L003_R1_001.fastq.gz Pb-5_S1_L003_R2_001.fastq.gz", "fastq fastq", 4856726400.0, 16189088.0, "GSM5057359 r5", "0:150 1:150", "A:1393259454;C:836723123;G:785636186;T:1840942341;N:165296", 150, 150, null, null, 1393259454, 836723123, 785636186, 1840942341, 165296, "SRX9989398", "SRS8160233", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.01176, 0.89787, 0.00258, 0.09744, 0.99661, 0.8229, 0.515, 0.55288, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63094, "SRR13594974", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "Pb scRNA seq", "GSM5057359", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50\u03bcg/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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50\u03bcg/L Pb", "GSM5057359", "GSM5057359: Pb scRNA seq; Danio rerio; RNA Seq", "GSM5057359", null, "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", null, "SRP304100", null, null, "Pb-6_S1_L003_R1_001.fastq.gz Pb-6_S1_L003_R2_001.fastq.gz", "fastq fastq", 6342755700.0, 21142519.0, "GSM5057359 r6", "0:150 1:150", "A:1826306154;C:1099075312;G:1027909854;T:2389250024;N:214356", 150, 150, null, null, 1826306154, 1099075312, 1027909854, 2389250024, 214356, "SRX9989398", "SRS8160233", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.01186, 0.89905, 0.00221, 0.09495, 0.99671, 0.82315, 0.55913, 0.54098, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63095, "SRR13594975", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "Pb scRNA seq", "GSM5057359", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50\u03bcg/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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50\u03bcg/L Pb", "GSM5057359", "GSM5057359: Pb scRNA seq; Danio rerio; RNA Seq", "GSM5057359", null, "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", null, "SRP304100", null, null, "Pb-7_S1_L003_R1_001.fastq.gz Pb-7_S1_L003_R2_001.fastq.gz", "fastq fastq", 3535414500.0, 11784715.0, "GSM5057359 r7", "0:150 1:150", "A:1018646924;C:603980775;G:566589558;T:1346074263;N:122980", 150, 150, null, null, 1018646924, 603980775, 566589558, 1346074263, 122980, "SRX9989398", "SRS8160233", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.01054, 0.89567, 0.00197, 0.09806, 0.99655, 0.82331, 0.5101, 0.55574, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63096, "SRR13594976", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "Pb scRNA seq", "GSM5057359", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50\u03bcg/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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:50\u03bcg/L Pb", "GSM5057359", "GSM5057359: Pb scRNA seq; Danio rerio; RNA Seq", "GSM5057359", null, "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", null, "SRP304100", null, null, "Pb-8_S1_L003_R1_001.fastq.gz Pb-8_S1_L003_R2_001.fastq.gz", "fastq fastq", 5502346200.0, 18341154.0, "GSM5057359 r8", "0:150 1:150", "A:1578719876;C:949394523;G:890030509;T:2084011618;N:189674", 150, 150, null, null, 1578719876, 949394523, 890030509, 2084011618, 189674, "SRX9989398", "SRS8160233", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.0106, 0.90044, 0.00163, 0.09435, 0.99655, 0.82511, 0.55329, 0.56201, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63097, "SRR13594961", "SRX9989397", "SRS8160232", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "PS NPs scRNA seq", "GSM5057358", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs", "PS NPs 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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs", "GSM5057358", "GSM5057358: PS NPs scRNA seq; Danio rerio; RNA Seq", "GSM5057358", null, "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:GSM5057358", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP304100", null, null, "PS-NPs-1_S1_L002_R1_001.fastq.gz PS-NPs-1_S1_L002_R2_001.fastq.gz", "fastq fastq", 24312795600.0, 81042652.0, "GSM5057358 r1", "0:150 1:150", "A:9146216362;C:4355751443;G:4153351621;T:6656899945;N:576229", 150, 150, null, null, 9146216362, 4355751443, 4153351621, 6656899945, 576229, "SRX9989397", "SRS8160232", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.0, 0.91222, 0.0, 0.11297, 1.0, 0.81964, null, 0.52896, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63098, "SRR13594962", "SRX9989397", "SRS8160232", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "PS NPs scRNA seq", "GSM5057358", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs", "PS NPs 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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs", "GSM5057358", "GSM5057358: PS NPs scRNA seq; Danio rerio; RNA Seq", "GSM5057358", null, "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:GSM5057358", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP304100", null, null, "PS-NPs-2_S1_L002_R1_001.fastq.gz PS-NPs-2_S1_L002_R2_001.fastq.gz", "fastq fastq", 26533956000.0, 88446520.0, "GSM5057358 r2", "0:150 1:150", "A:9982553363;C:4747719874;G:4526017856;T:7277028979;N:635928", 150, 150, null, null, 9982553363, 4747719874, 4526017856, 7277028979, 635928, "SRX9989397", "SRS8160232", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.0, 0.91159, 0.0, 0.11381, 1.0, 0.81962, null, 0.52394, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63099, "SRR13594963", "SRX9989397", "SRS8160232", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "PS NPs scRNA seq", "GSM5057358", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs", "PS NPs 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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs", "GSM5057358", "GSM5057358: PS NPs scRNA seq; Danio rerio; RNA Seq", "GSM5057358", null, "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:GSM5057358", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP304100", null, null, "PS-NPs-3_S1_L002_R1_001.fastq.gz PS-NPs-3_S1_L002_R2_001.fastq.gz", "fastq fastq", 33884397600.0, 112947992.0, "GSM5057358 r3", "0:150 1:150", "A:12738625804;C:6054385952;G:5775879452;T:9314689288;N:817104", 150, 150, null, null, 12738625804, 6054385952, 5775879452, 9314689288, 817104, "SRX9989397", "SRS8160232", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.0, 0.9104, 0.0, 0.11618, 1.0, 0.8196, null, 0.53727, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63100, "SRR13594964", "SRX9989397", "SRS8160232", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "PS NPs scRNA seq", "GSM5057358", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs", "PS NPs 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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs", "GSM5057358", "GSM5057358: PS NPs scRNA seq; Danio rerio; RNA Seq", "GSM5057358", null, "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:GSM5057358", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP304100", null, null, "PS-NPs-4_S1_L002_R1_001.fastq.gz PS-NPs-4_S1_L002_R2_001.fastq.gz", "fastq fastq", 33112751100.0, 110375837.0, "GSM5057358 r4", "0:150 1:150", "A:12453220873;C:5931691053;G:5659942048;T:9067100564;N:796562", 150, 150, null, null, 12453220873, 5931691053, 5659942048, 9067100564, 796562, "SRX9989397", "SRS8160232", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.0, 0.9126, 0.0, 0.11329, 1.0, 0.81953, null, 0.53482, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63101, "SRR13594965", "SRX9989397", "SRS8160232", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "PS NPs scRNA seq", "GSM5057358", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs", "PS NPs 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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs", "GSM5057358", "GSM5057358: PS NPs scRNA seq; Danio rerio; RNA Seq", "GSM5057358", null, "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:GSM5057358", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP304100", null, null, "PS-NPs-5_S1_L003_R1_001.fastq.gz PS-NPs-5_S1_L003_R2_001.fastq.gz", "fastq fastq", 845806200.0, 2819354.0, "GSM5057358 r5", "0:150 1:150", "A:242327209;C:147392555;G:138092223;T:317965045;N:29168", 150, 150, null, null, 242327209, 147392555, 138092223, 317965045, 29168, "SRX9989397", "SRS8160232", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.01535, 0.90964, 0.00306, 0.11468, 0.99547, 0.82067, 0.57518, 0.55153, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63102, "SRR13594966", "SRX9989397", "SRS8160232", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "PS NPs scRNA seq", "GSM5057358", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs", "PS NPs 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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs", "GSM5057358", "GSM5057358: PS NPs scRNA seq; Danio rerio; RNA Seq", "GSM5057358", null, "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:GSM5057358", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP304100", null, null, "PS-NPs-6_S1_L003_R1_001.fastq.gz PS-NPs-6_S1_L003_R2_001.fastq.gz", "fastq fastq", 922363200.0, 3074544.0, "GSM5057358 r6", "0:150 1:150", "A:264546618;C:160415142;G:150151644;T:347217867;N:31929", 150, 150, null, null, 264546618, 160415142, 150151644, 347217867, 31929, "SRX9989397", "SRS8160232", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.01405, 0.90981, 0.00257, 0.11443, 0.99594, 0.81913, 0.54032, 0.55417, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63103, "SRR13594967", "SRX9989397", "SRS8160232", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "PS NPs scRNA seq", "GSM5057358", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs", "PS NPs 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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs", "GSM5057358", "GSM5057358: PS NPs scRNA seq; Danio rerio; RNA Seq", "GSM5057358", null, "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:GSM5057358", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP304100", null, null, "PS-NPs-7_S1_L003_R1_001.fastq.gz PS-NPs-7_S1_L003_R2_001.fastq.gz", "fastq fastq", 1210233000.0, 4034110.0, "GSM5057358 r7", "0:150 1:150", "A:347650558;C:209869126;G:196414628;T:456257230;N:41458", 150, 150, null, null, 347650558, 209869126, 196414628, 456257230, 41458, "SRX9989397", "SRS8160232", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.01473, 0.90816, 0.00268, 0.11594, 0.99543, 0.82059, 0.46096, 0.54812, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63104, "SRR13594968", "SRX9989397", "SRS8160232", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "PS NPs scRNA seq", "GSM5057358", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs", "PS NPs 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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:200\u03bcg/L PS NPs", "GSM5057358", "GSM5057358: PS NPs scRNA seq; Danio rerio; RNA Seq", "GSM5057358", null, "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:GSM5057358", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP304100", null, null, "PS-NPs-8_S1_L003_R1_001.fastq.gz PS-NPs-8_S1_L003_R2_001.fastq.gz", "fastq fastq", 1165587300.0, 3885291.0, "GSM5057358 r8", "0:150 1:150", "A:333885648;C:203083230;G:190335802;T:438240258;N:42362", 150, 150, null, null, 333885648, 203083230, 190335802, 438240258, 42362, "SRX9989397", "SRS8160232", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.01482, 0.90964, 0.00252, 0.11231, 0.99567, 0.82045, 0.52692, 0.54757, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63105, "SRR13594953", "SRX9989396", "SRS8160231", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "CK scRNA seq", "GSM5057357", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:n1", "CK 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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:n1", "GSM5057357", "GSM5057357: CK scRNA seq; Danio rerio; RNA Seq", "GSM5057357", null, "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:GSM5057357", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP304100", null, null, "CK-1_S1_L002_R1_001.fastq.gz CK-1_S1_L002_R2_001.fastq.gz", "fastq fastq", 22687713000.0, 75625710.0, "GSM5057357 r1", "0:150 1:150", "A:8591957358;C:4008066775;G:3799259254;T:6287881304;N:548309", 150, 150, null, null, 8591957358, 4008066775, 3799259254, 6287881304, 548309, "SRX9989396", "SRS8160231", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.0, 0.90572, 0.0, 0.10955, 1.0, 0.81698, null, 0.51358, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63106, "SRR13594954", "SRX9989396", "SRS8160231", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "CK scRNA seq", "GSM5057357", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:n1", "CK 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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:n1", "GSM5057357", "GSM5057357: CK scRNA seq; Danio rerio; RNA Seq", "GSM5057357", null, "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:GSM5057357", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP304100", null, null, "CK-2_S1_L002_R1_001.fastq.gz CK-2_S1_L002_R2_001.fastq.gz", "fastq fastq", 31520716500.0, 105069055.0, "GSM5057357 r2", "0:150 1:150", "A:11911735744;C:5593396462;G:5306773303;T:8708052527;N:758464", 150, 150, null, null, 11911735744, 5593396462, 5306773303, 8708052527, 758464, "SRX9989396", "SRS8160231", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.0, 0.90884, 0.0, 0.10765, 1.0, 0.816, null, 0.52099, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63107, "SRR13594955", "SRX9989396", "SRS8160231", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "CK scRNA seq", "GSM5057357", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:n1", "CK 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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:n1", "GSM5057357", "GSM5057357: CK scRNA seq; Danio rerio; RNA Seq", "GSM5057357", null, "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:GSM5057357", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP304100", null, null, "CK-3_S1_L002_R1_001.fastq.gz CK-3_S1_L002_R2_001.fastq.gz", "fastq fastq", 18557760300.0, 61859201.0, "GSM5057357 r3", "0:150 1:150", "A:6999245780;C:3273750216;G:3112042521;T:5172279555;N:442228", 150, 150, null, null, 6999245780, 3273750216, 3112042521, 5172279555, 442228, "SRX9989396", "SRS8160231", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.0, 0.90374, 0.0, 0.11026, 1.0, 0.81722, null, 0.51518, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63108, "SRR13594956", "SRX9989396", "SRS8160231", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "CK scRNA seq", "GSM5057357", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:n1", "CK 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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:n1", "GSM5057357", "GSM5057357: CK scRNA seq; Danio rerio; RNA Seq", "GSM5057357", null, "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:GSM5057357", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP304100", null, null, "CK-4_S1_L002_R1_001.fastq.gz CK-4_S1_L002_R2_001.fastq.gz", "fastq fastq", 44828189700.0, 149427299.0, "GSM5057357 r4", "0:150 1:150", "A:16912705066;C:7955483510;G:7542979632;T:12415941286;N:1080206", 150, 150, null, null, 16912705066, 7955483510, 7542979632, 12415941286, 1080206, "SRX9989396", "SRS8160231", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.0, 0.90888, 0.0, 0.10772, 1.0, 0.81791, null, 0.51458, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63109, "SRR13594957", "SRX9989396", "SRS8160231", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "CK scRNA seq", "GSM5057357", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:n1", "CK 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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:n1", "GSM5057357", "GSM5057357: CK scRNA seq; Danio rerio; RNA Seq", "GSM5057357", null, "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:GSM5057357", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP304100", null, null, "CK-5_S1_L003_R1_001.fastq.gz CK-5_S1_L003_R2_001.fastq.gz", "fastq fastq", 797925300.0, 2659751.0, "GSM5057357 r5", "0:150 1:150", "A:231261745;C:136517638;G:127031945;T:303086279;N:27693", 150, 150, null, null, 231261745, 136517638, 127031945, 303086279, 27693, "SRX9989396", "SRS8160231", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.01203, 0.9069, 0.0023, 0.11051, 0.99644, 0.81884, 0.53554, 0.51319, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63110, "SRR13594958", "SRX9989396", "SRS8160231", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "CK scRNA seq", "GSM5057357", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:n1", "CK 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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:n1", "GSM5057357", "GSM5057357: CK scRNA seq; Danio rerio; RNA Seq", "GSM5057357", null, "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:GSM5057357", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP304100", null, null, "CK-6_S1_L003_R1_001.fastq.gz CK-6_S1_L003_R2_001.fastq.gz", "fastq fastq", 1106643000.0, 3688810.0, "GSM5057357 r6", "0:150 1:150", "A:319867556;C:190365426;G:177343708;T:419027852;N:38458", 150, 150, null, null, 319867556, 190365426, 177343708, 419027852, 38458, "SRX9989396", "SRS8160231", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.01248, 0.90755, 0.00231, 0.10893, 0.99616, 0.81949, 0.50943, 0.53149, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63111, "SRR13594959", "SRX9989396", "SRS8160231", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "CK scRNA seq", "GSM5057357", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:n1", "CK 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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:n1", "GSM5057357", "GSM5057357: CK scRNA seq; Danio rerio; RNA Seq", "GSM5057357", null, "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:GSM5057357", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP304100", null, null, "CK-7_S1_L003_R1_001.fastq.gz CK-7_S1_L003_R2_001.fastq.gz", "fastq fastq", 624489900.0, 2081633.0, "GSM5057357 r7", "0:150 1:150", "A:181162125;C:106294375;G:99023461;T:237987570;N:22369", 150, 150, null, null, 181162125, 106294375, 99023461, 237987570, 22369, "SRX9989396", "SRS8160231", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.01103, 0.90522, 0.00235, 0.111, 0.99651, 0.81777, 0.52763, 0.50816, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [63112, "SRR13594960", "SRX9989396", "SRS8160231", "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 \u00b5g/L 100 nm polystyrene nanoplastics PS NPs 50 \u00b5g/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.", null, "pubmed:34861263", null, "CK scRNA seq", "GSM5057357", null, "source name:intestine cells|tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:n1", "CK 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 200\u03bcg/L PS NPs 50\u03bcg/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\u2019 Gel Bead Chip and Library Kits 10x Genomics USA as per the manufacturer\u2019s protocol. Libraries were sequenced on a Nova6000.", null, "tissue:intestine single cell suspension|age:16 wpf|exposed pollutants:n1", "GSM5057357", "GSM5057357: CK scRNA seq; Danio rerio; RNA Seq", "GSM5057357", null, "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:GSM5057357", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP304100", null, null, "CK-8_S1_L003_R1_001.fastq.gz CK-8_S1_L003_R2_001.fastq.gz", "fastq fastq", 1588137000.0, 5293790.0, "GSM5057357 r8", "0:150 1:150", "A:459374512;C:272736999;G:253756415;T:602213797;N:55277", 150, 150, null, null, 459374512, 272736999, 253756415, 602213797, 55277, "SRX9989396", "SRS8160231", "SRA1189975", "GEO", "School of the Environment, Nanjing university", 2, 0.01329, 0.90702, 0.00227, 0.10723, 0.99596, 0.81724, 0.56903, 0.53275, 150, 150, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "China", "2021-02-01", "Adult", "Adult", "Gut", "Digestive System"], [64241, "SRR14367979", "SRX10720521", "SRS8810972", "SRP317951", "PRJNA726184", "Fxr signaling and microbial metabolism of bile salts in the zebrafish intestine", "GSE173570", "Transcriptome Analysis", "The purpose of this study was to elucidate potential effects of fxr mutation on the functional specification of intestinal epithelial cells. To do this we sorted GFP positive cells from TgBACcldn15la:GFP transgenics of either fxr+/+ or fxr / fish larvae and subjected them to 10X Genomics single cell RNA seq. Our results uncovered the requirement of fxr in gene expression and differentiation among multiple intestinal epithelial cell types. Overall design: Analysis of sorted cells from 6 dpf zebrafish larvae that were either fxr+/+ WT or fxr / MUT", null, "pubmed:34301599", null, "fxr / zebrafish intestinal epithelial cells", "GSM5270963", null, "source name:Intestine|transgenic background:TgBACcldn15la:GFP|age:6 dpf|genotype:fxr / |tissue:Intestine|cell type:intestinal epithelial cells|sorting fluorescence:GFP+ 7AAD ", "fxr / zebrafish intestinal epithelial cells", "UMIs were demultiplexed and reads were aligned to the reference genome danRer11 following the CellRanger pipeline In Seurat 3.1.0 https://satijalab.org/seurat/ cell barcodes with <3000 detected genes >30 000 UMIs >25% mitochondrial transcripts were removed. Log normalized and integrated datasets based on WT library Scaled data and performed PCA with 100 priciple components Ran UMAP dimensionality reduction with 54 principle components Used FindNeighbors and FindClusters function at resolution of 0.82 Ran UMAP dimensionality reduction with 54 principle components Genome build: danRer11 Supplementary files format and content: count matrix", "Intestine", null, "Larvae zebrafish were dissociated using standard protocol post which the fxr+/+; TgBACcldn15la GFP and fxr / ; TgBACcldn15la GFP cells were subjected to FACS at the Duke Cancer Institute Flow Cytometry Shared Resource and were sorted side by side with two identical Beckman Coulter Astrios instruments. Non transgenic and single transgenic controls pools of 50 fish/genotype were prepared as above and used for gating and compensation. Approximately 120 k GFP positive 7 AAD negative cells per genotype were collected in 1.5 mL of DMEM/F12 supplemented with 10% heat inactivated FBS and 10 \u03bcM Y 27632 ROCK1 inhibitor and were immediately subjected to the library construction. Each single cell RNA sequencing library was generated from 10 000 FACS sorted TgBACcldn15la GFP IECs of the indicated genotype following the 10x Genomics Single Cell 3\u2019 protocol by the Duke Molecular Genomics Core. The sequencing ready libraries were cleaned with both Silane Dynabeads and SPRI beads and quality controlled for size distribution and yield with the Agilent D5000 screenTape assays using the Agilent 4200 TapeStation system. Illumina P5 and P7 sequences a sample index and TruSeq read 2 primer sequence were ligated for Illumina bridge amplification. Sequence was generated using paired end sequencing on the Novaseq SP flow cell sequencing platform at a minimum of 40 k reads/cell.", "Approximately 600 dpf 700 dpf 6 dpf TgBACcldn15la GFP zebrafish larvae of the fxr+/+ and the fxr / genotypes were collected for the FACS experiment respectively.", "transgenic background:TgBACcldn15la:GFP|age:6 dpf|genotype:fxr / |tissue:Intestine|cell type:intestinal epithelial cells|sorting fluorescence:GFP+ 7AAD ", "GSM5270963", "GSM5270963: fxr / zebrafish intestinal epithelial cells; Danio rerio; RNA Seq", "GSM5270963", null, "1", "Larvae zebrafish were dissociated using standard protocol post which the fxr+/+; TgBACcldn15la GFP and fxr / ; TgBACcldn15la GFP cells were subjected to FACS at the Duke Cancer Institute Flow Cytometry Shared Resource and were sorted side by side with two identical Beckman Coulter Astrios instruments. Non transgenic and single transgenic controls pools of 50 fish/genotype were prepared as above and used for gating and compensation. Approximately 120 k GFP positive 7 AAD negative cells per genotype were collected in 1.5 mL of DMEM/F12 supplemented with 10% heat inactivated FBS and 10 \u03bcM Y 27632 ROCK1 inhibitor and were immediately subjected to the library construction. Each single cell RNA sequencing library was generated from 10 000 FACS sorted TgBACcldn15la GFP IECs of the indicated genotype following the 10x Genomics Single Cell three prime protocol by the Duke Molecular Genomics Core. The sequencing ready libraries were cleaned with both Silane Dynabeads and SPRI beads and quality controlled for size distribution and yield with the Agilent D5000 screenTape assays using the Agilent 4200 TapeStation system. Illumina P5 and P7 sequences a sample index and TruSeq read 2 primer sequence were ligated for Illumina bridge amplification. Sequence was generated using paired end sequencing on the Novaseq SP flow cell sequencing platform at a minimum of 40 k reads/cell.", "GEO Accession:GSM5270963", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP317951", null, "intentional duplicate", "MUT_bam.bam", "10X Genomics bam file", 44735611648.0, 491600128.0, "GSM5270963 r1", "0:91", "A:12721518503;C:9909002158;G:10186048145;T:11874320896;N:44721946", 91, null, null, null, 12721518503, 9909002158, 10186048145, 11874320896, 44721946, "SRX10720521", "SRS8810972", "SRA1225807", "GEO", "John Rawls, Molecular Genetics & Microbiology, Duke University", 1, 0.93486, null, 0.15053, null, 0.83226, null, 0.62985, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "10x", null, "United States", "2021-04-29", "Larval", "Larval", "Gut", "Digestive System"], [64242, "SRR14367978", "SRX10720520", "SRS8810970", "SRP317951", "PRJNA726184", "Fxr signaling and microbial metabolism of bile salts in the zebrafish intestine", "GSE173570", "Transcriptome Analysis", "The purpose of this study was to elucidate potential effects of fxr mutation on the functional specification of intestinal epithelial cells. To do this we sorted GFP positive cells from TgBACcldn15la:GFP transgenics of either fxr+/+ or fxr / fish larvae and subjected them to 10X Genomics single cell RNA seq. Our results uncovered the requirement of fxr in gene expression and differentiation among multiple intestinal epithelial cell types. Overall design: Analysis of sorted cells from 6 dpf zebrafish larvae that were either fxr+/+ WT or fxr / MUT", null, "pubmed:34301599", null, "fxr +/+ zebrafish intestinal epithelial cells", "GSM5270962", null, "source name:Intestine|transgenic background:TgBACcldn15la:GFP|age:6 dpf|genotype:fxr +/+|tissue:Intestine|cell type:intestinal epithelial cells|sorting fluorescence:GFP+ 7AAD ", "fxr +/+ zebrafish intestinal epithelial cells", "UMIs were demultiplexed and reads were aligned to the reference genome danRer11 following the CellRanger pipeline In Seurat 3.1.0 https://satijalab.org/seurat/ cell barcodes with <3000 detected genes >30 000 UMIs >25% mitochondrial transcripts were removed. Log normalized and integrated datasets based on WT library Scaled data and performed PCA with 100 priciple components Ran UMAP dimensionality reduction with 54 principle components Used FindNeighbors and FindClusters function at resolution of 0.82 Ran UMAP dimensionality reduction with 54 principle components Genome build: danRer11 Supplementary files format and content: count matrix", "Intestine", null, "Larvae zebrafish were dissociated using standard protocol post which the fxr+/+; TgBACcldn15la GFP and fxr / ; TgBACcldn15la GFP cells were subjected to FACS at the Duke Cancer Institute Flow Cytometry Shared Resource and were sorted side by side with two identical Beckman Coulter Astrios instruments. Non transgenic and single transgenic controls pools of 50 fish/genotype were prepared as above and used for gating and compensation. Approximately 120 k GFP positive 7 AAD negative cells per genotype were collected in 1.5 mL of DMEM/F12 supplemented with 10% heat inactivated FBS and 10 \u03bcM Y 27632 ROCK1 inhibitor and were immediately subjected to the library construction. Each single cell RNA sequencing library was generated from 10 000 FACS sorted TgBACcldn15la GFP IECs of the indicated genotype following the 10x Genomics Single Cell 3\u2019 protocol by the Duke Molecular Genomics Core. The sequencing ready libraries were cleaned with both Silane Dynabeads and SPRI beads and quality controlled for size distribution and yield with the Agilent D5000 screenTape assays using the Agilent 4200 TapeStation system. Illumina P5 and P7 sequences a sample index and TruSeq read 2 primer sequence were ligated for Illumina bridge amplification. Sequence was generated using paired end sequencing on the Novaseq SP flow cell sequencing platform at a minimum of 40 k reads/cell.", "Approximately 600 dpf 700 dpf 6 dpf TgBACcldn15la GFP zebrafish larvae of the fxr+/+ and the fxr / genotypes were collected for the FACS experiment respectively.", "transgenic background:TgBACcldn15la:GFP|age:6 dpf|genotype:fxr +/+|tissue:Intestine|cell type:intestinal epithelial cells|sorting fluorescence:GFP+ 7AAD ", "GSM5270962", "GSM5270962: fxr +/+ zebrafish intestinal epithelial cells; Danio rerio; RNA Seq", "GSM5270962", null, "1", "Larvae zebrafish were dissociated using standard protocol post which the fxr+/+; TgBACcldn15la GFP and fxr / ; TgBACcldn15la GFP cells were subjected to FACS at the Duke Cancer Institute Flow Cytometry Shared Resource and were sorted side by side with two identical Beckman Coulter Astrios instruments. Non transgenic and single transgenic controls pools of 50 fish/genotype were prepared as above and used for gating and compensation. Approximately 120 k GFP positive 7 AAD negative cells per genotype were collected in 1.5 mL of DMEM/F12 supplemented with 10% heat inactivated FBS and 10 \u03bcM Y 27632 ROCK1 inhibitor and were immediately subjected to the library construction. Each single cell RNA sequencing library was generated from 10 000 FACS sorted TgBACcldn15la GFP IECs of the indicated genotype following the 10x Genomics Single Cell three prime protocol by the Duke Molecular Genomics Core. The sequencing ready libraries were cleaned with both Silane Dynabeads and SPRI beads and quality controlled for size distribution and yield with the Agilent D5000 screenTape assays using the Agilent 4200 TapeStation system. Illumina P5 and P7 sequences a sample index and TruSeq read 2 primer sequence were ligated for Illumina bridge amplification. Sequence was generated using paired end sequencing on the Novaseq SP flow cell sequencing platform at a minimum of 40 k reads/cell.", "GEO Accession:GSM5270962", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP317951", null, "intentional duplicate", "WT_bam.bam", "10X Genomics bam file", 41992986763.0, 461461393.0, "GSM5270962 r1", "0:91", "A:12152716332;C:8974304021;G:9433492952;T:11389979720;N:42493738", 91, null, null, null, 12152716332, 8974304021, 9433492952, 11389979720, 42493738, "SRX10720520", "SRS8810970", "SRA1225807", "GEO", "John Rawls, Molecular Genetics & Microbiology, Duke University", 1, 0.92473, null, 0.17567, null, 0.81688, null, 0.59128, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "sc", "single_cell_droplet", "10x", null, "United States", "2021-04-29", "Larval", "Larval", "Gut", "Digestive System"], [66176, "SRR15931549", "SRX12221647", "SRS10197714", "SRP337628", "PRJNA764222", "Loss of autism candidate CHD8 perturbs neural crest development and intestinal homeostatic balance [scRNA seq]", "GSE184363", "Transcriptome Analysis", "Individuals with mutations in CHD8 present with gastrointestinal complaints yet the underlying mechanisms are understudied. Here utilizing a stable constitutive chd8 mutant zebrafish model we found that the loss of chd8 leads to reduced number of vagal neural crest cells NCCs enteric neural and glial progenitors emigrating from the neural tube and that their early migration capability was altered. At later stages although the intestinal colonization by the NCCs was complete we found decreased numbers of both serotonin producing enterochromaffin cells and NCC derived serotonergic neurons suggesting an intestinal hyposerotonemia in absence of chd8. Further transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Tissue examination of chd8 mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last single cell sequencing of whole intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8 NCC development intestinal homeostasis and autism associated gastrointestinal complaints. Overall design: 2 samples were analyzed: 1 chd8+/+ wild type and 1 chd8sa19827/sa19827 homogous mutants. Each sample is comprised of dissociated cells from the mid and posterior intestine of 3 adult zebrafish.", "parent bioproject:PRJNA764218", "pubmed:36375841", null, "chd8 KO", "GSM5585126", null, "tissue:Intestinal cells|genotype:chd8 / ", "chd8 KO", "Alignment barcode and UMI filtering and counting were performed with Cell Ranger 3.1.0 count using GRCz11 assembly and Ensembl release 98 annotations. Genome build: GRCz11 Supplementary files format and content: Filtered contains only detected cellular barcodes feature barcode matrix each element of the matrix is the number of UMIs associated with a feature row and a barcode column in Market Exchange Format MEX and gzipped. Supplementary files format and content: Gzipped tsv files with feature and barcode sequences corresponding respectively to row and column indices from the matrix.", "Intestinal cells", null, "chd8+/+ and homozygous chd8 sa19827/sa19827 male adult zebrafish were euthanized in 800 \u00b5g/ml tricaine solution. The fish were dissected their guts were harvested and placed in RPMI at room temperature. The guts were rolled on paper moistened with RPMI to remove the fat residue then placed in RPMI with 10% fetal calf serum and cut into small pieces that were placed in 1 ml of digestion medium 1 ml of RPMI 12 \u00b5l of activated fetal calf serum 10 mg of dispase collagenase for 15 minutes at 37 \u00b0C under agitation at 500 rpm. The cells were then filtered on a cell filter diameter 40 \u00b5m Dutscher ref 141378C using the plunger of 1 ml syringe. Cell number and viability were determined by a Trypan Blue exclusion assay on a Neubauer Chamber. Samples consisted of > 90 % viable cells were processed on the Chromium Controller from 10X Genomics Leiden The Netherlands. 10 000 total cells were loaded per well to yield approximately 6 500 captured cells into nanoliter scale Gel Beads in Emulsion GEMs. Single cell 3\u2019 mRNA seq library were generated according to 10X Genomics User Guide for Chromium Single Cell 3\u2019 Reagent Kits v3 Chemistry. Briefly GEMs were generated by combining barcoded gel beads a RT master mix containing cells and partitioning oil onto Chromium Chip B. Following full length cDNA synthesis and barcoding from poly adenylated mRNA GEMs were broken and pooled before cDNA amplification by PCR using 11 cycles. post enzymatic fragmentation and size selection sequencing library were constructed by adding Illumina Paris France P5 and P7 primers as well as sample index via end repair A tailing adaptor ligation and PCR with 14 cycles. Library quantification and quality control was performed using Bioanalyzer 2100 Agilent Technologies Santa Clara CA.", null, "genotype:chd8 / ", "GSM5585126", "GSM5585126: chd8 KO; Danio rerio; RNA Seq", "GSM5585126", null, "1", "chd8+/+ and homozygous chd8 sa19827/sa19827 male adult zebrafish were euthanized in 800 \u00b5g/ml tricaine solution. The fish were dissected their guts were harvested and placed in RPMI at room temperature. The guts were rolled on paper moistened with RPMI to remove the fat residue then placed in RPMI with 10% fetal calf serum and cut into small pieces that were placed in 1 ml of digestion medium 1 ml of RPMI 12 \u00b5l of activated fetal calf serum 10 mg of dispase collagenase for 15 minutes at 37 \u00b0C under agitation at 500 rpm. The cells were then filtered on a cell filter diameter 40 \u00b5m Dutscher ref 141378C using the plunger of 1 ml syringe. Cell number and viability were determined by a Trypan Blue exclusion assay on a Neubauer Chamber. Samples consisted of > 90 % viable cells were processed on the Chromium Controller from 10X Genomics Leiden The Netherlands. 10 000 total cells were loaded per well to yield approximately 6 500 captured cells into nanoliter scale Gel Beads in Emulsion GEMs. Single cell three prime mRNA seq library were generated according to 10X Genomics User Guide for Chromium Single Cell three prime Reagent Kits v3 Chemistry. Briefly GEMs were generated by combining barcoded gel beads a RT master mix containing cells and partitioning oil onto Chromium Chip B. Following full length cDNA synthesis and barcoding from poly adenylated mRNA GEMs were broken and pooled before cDNA amplification by PCR using 11 cycles. post enzymatic fragmentation and size selection sequencing library were constructed by adding Illumina Paris France P5 and P7 primers as well as sample index via end repair A tailing adaptor ligation and PCR with 14 cycles. Library quantification and quality control was performed using Bioanalyzer 2100 Agilent Technologies Santa Clara CA.", "GEO Accession:GSM5585126", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "SRP337628", null, null, "GLHT10.R1.fastq.gz GLHT10.R2.fastq.gz", "fastq fastq", 64945652822.0, 391218083.0, "GSM5585126 r1", "0:67.32 1:98.69", "A:18328460514;C:11753978727;G:12225228372;T:22573401879;N:64583330", 67, 98, null, null, 18328460514, 11753978727, 12225228372, 22573401879, 64583330, "SRX12221647", "SRS10197714", "SRA1296109", "GEO", "IGBMC", 2, 0.00942, 0.92207, 0.00301, 0.14877, 0.99324, 0.82416, 0.42574, 0.69119, 28, 96, "T", "B", "sc-like readlen", "illumina", "nextseq", "3prime", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "France", "2021-09-17", "Adult", "Adult", "Gut", "Digestive System"]], "truncated": false, "filtered_table_rows_count": 101, "expanded_columns": [], "expandable_columns": [], "columns": ["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"], "primary_keys": [], "units": {}, "query": {"sql": "select 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 from run_metadata where \"experiment.library_source\" = :p0 and \"technology\" = :p1 and \"tissue_curation_coarse\" = :p2 order by rowid limit 101", "params": {"p0": "TRANSCRIPTOMIC", "p1": "10x", "p2": "Digestive System"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=10x&tissue_curation_coarse=Digestive+System", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 101, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_source=TRANSCRIPTOMIC&technology=10x&tissue_curation_coarse=Digestive+System&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": 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