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
68149,SRR17630939,SRX13799350,SRS11681639,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 3 compared to intact control testes,GSM5820567,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 3 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820567,GSM5820567: dissociated bulk seq control testes   rep 3 compared to intact control testes; Danio rerio; RNA Seq,GSM5820567 r1,GSM5820567,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C3_S14_L001_R1_001.fastq.gz,fastq,1847371623.0,36222973.0,GSM5820567 r1,0:51 1:0,A:535632392;C:366862698;G:429979337;T:514873991;N:23205,51,0,,,535632392,366862698,429979337,514873991,23205,SRX13799350,SRS11681639,SRA1357269,University of Florida,University of Florida,1,0.87212,,0.1857,,0.69372,,0.56886,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68150,SRR17630940,SRX13799350,SRS11681639,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 3 compared to intact control testes,GSM5820567,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 3 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820567,GSM5820567: dissociated bulk seq control testes   rep 3 compared to intact control testes; Danio rerio; RNA Seq,GSM5820567 r1,GSM5820567,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C3_S14_L002_R1_001.fastq.gz,fastq,1823230824.0,35749624.0,GSM5820567 r2,0:51 1:0,A:529009592;C:361883074;G:424030274;T:508289743;N:18141,51,0,,,529009592,361883074,424030274,508289743,18141,SRX13799350,SRS11681639,SRA1357269,University of Florida,University of Florida,1,0.8708,,0.18714,,0.6955,,0.5716,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68151,SRR17630941,SRX13799349,SRS11681638,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 2 compared to intact control testes,GSM5820566,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 2 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820566,GSM5820566: dissociated bulk seq control testes   rep 2 compared to intact control testes; Danio rerio; RNA Seq,GSM5820566 r1,GSM5820566,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C2_S13_L001_R1_001.fastq.gz,fastq,536561208.0,10520808.0,GSM5820566 r1,0:51 1:0,A:163430759;C:106016694;G:122059136;T:145048023;N:6596,51,0,,,163430759,106016694,122059136,145048023,6596,SRX13799349,SRS11681638,SRA1357269,University of Florida,University of Florida,1,0.83573,,0.2005,,0.71056,,0.52825,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68152,SRR17630942,SRX13799349,SRS11681638,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 2 compared to intact control testes,GSM5820566,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 2 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820566,GSM5820566: dissociated bulk seq control testes   rep 2 compared to intact control testes; Danio rerio; RNA Seq,GSM5820566 r1,GSM5820566,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C2_S13_L002_R1_001.fastq.gz,fastq,530978238.0,10411338.0,GSM5820566 r2,0:51 1:0,A:161875304;C:104815309;G:120705456;T:143576873;N:5296,51,0,,,161875304,104815309,120705456,143576873,5296,SRX13799349,SRS11681638,SRA1357269,University of Florida,University of Florida,1,0.83663,,0.19964,,0.71104,,0.54143,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68153,SRR17630943,SRX13799348,SRS11681637,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 1 compared to intact control testes,GSM5820565,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 1 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820565,GSM5820565: dissociated bulk seq control testes   rep 1 compared to intact control testes; Danio rerio; RNA Seq,GSM5820565 r1,GSM5820565,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C1_S12_L001_R1_001.fastq.gz,fastq,523779282.0,10270182.0,GSM5820565 r1,0:51 1:0,A:155891194;C:103400919;G:120028554;T:144451616;N:6999,51,0,,,155891194,103400919,120028554,144451616,6999,SRX13799348,SRS11681637,SRA1357269,University of Florida,University of Florida,1,0.85957,,0.19557,,0.69501,,0.56637,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68154,SRR17630944,SRX13799348,SRS11681637,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,dissociated bulk seq control testes   rep 1 compared to intact control testes,GSM5820565,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,dissociated bulk seq control testes   rep 1 compared to intact control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820565,GSM5820565: dissociated bulk seq control testes   rep 1 compared to intact control testes; Danio rerio; RNA Seq,GSM5820565 r1,GSM5820565,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,I_C1_S12_L002_R1_001.fastq.gz,fastq,516901983.0,10135333.0,GSM5820565 r2,0:51 1:0,A:153923180;C:101966413;G:118359254;T:142647450;N:5686,51,0,,,153923180,101966413,118359254,142647450,5686,SRX13799348,SRS11681637,SRA1357269,University of Florida,University of Florida,1,0.85795,,0.19403,,0.69627,,0.57159,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68155,SRR17630945,SRX13799347,SRS11681636,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 3,GSM5820564,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 3,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820564,GSM5820564: bulk seq intact control testes   rep 3; Danio rerio; RNA Seq,GSM5820564 r1,GSM5820564,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C3_S16_L001_R1_001.fastq.gz,fastq,1673456880.0,32812880.0,GSM5820564 r1,0:51 1:0,A:496655744;C:334242155;G:387205466;T:455330132;N:23383,51,0,,,496655744,334242155,387205466,455330132,23383,SRX13799347,SRS11681636,SRA1357269,University of Florida,University of Florida,1,0.8707,,0.22045,,0.71078,,0.60605,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68156,SRR17630946,SRX13799347,SRS11681636,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 3,GSM5820564,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 3,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820564,GSM5820564: bulk seq intact control testes   rep 3; Danio rerio; RNA Seq,GSM5820564 r1,GSM5820564,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C3_S16_L002_R1_001.fastq.gz,fastq,1647184587.0,32297737.0,GSM5820564 r2,0:51 1:0,A:489182217;C:328774657;G:380849646;T:448358863;N:19204,51,0,,,489182217,328774657,380849646,448358863,19204,SRX13799347,SRS11681636,SRA1357269,University of Florida,University of Florida,1,0.87032,,0.22081,,0.71261,,0.60917,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68157,SRR17630947,SRX13799346,SRS11681635,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes,GSM5820561,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq TCDD testes rep 2to be compared  to scRNA seq TCDD testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820561,GSM5820561: bulk seq TCDD testes rep 2to be compared  to scRNA seq TCDD testes; Danio rerio; RNA Seq,GSM5820561 r1,GSM5820561,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_T2_S7_L001_R1_001.fastq.gz,fastq,1583815608.0,31055208.0,GSM5820561 r1,0:51 1:0,A:447529477;C:312467507;G:374130013;T:449667219;N:21392,51,0,,,447529477,312467507,374130013,449667219,21392,SRX13799346,SRS11681635,SRA1357269,University of Florida,University of Florida,1,0.86982,,0.25275,,0.70774,,0.5721,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68158,SRR17630948,SRX13799346,SRS11681635,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq TCDD testes rep 2to be compared to scRNA seq TCDD testes,GSM5820561,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq TCDD testes rep 2to be compared  to scRNA seq TCDD testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820561,GSM5820561: bulk seq TCDD testes rep 2to be compared  to scRNA seq TCDD testes; Danio rerio; RNA Seq,GSM5820561 r1,GSM5820561,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_T2_S7_L002_R1_001.fastq.gz,fastq,1564087941.0,30668391.0,GSM5820561 r2,0:51 1:0,A:442209708;C:308400147;G:369229792;T:444230646;N:17648,51,0,,,442209708,308400147,369229792,444230646,17648,SRX13799346,SRS11681635,SRA1357269,University of Florida,University of Florida,1,0.87035,,0.2527,,0.70682,,0.57673,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68159,SRR17630949,SRX13799345,SRS11681634,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 2,GSM5820563,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 2,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820563,GSM5820563: bulk seq intact control testes   rep 2; Danio rerio; RNA Seq,GSM5820563 r1,GSM5820563,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C2_S15_L001_R1_001.fastq.gz,fastq,1493724669.0,29288719.0,GSM5820563 r1,0:51 1:0,A:445588125;C:289131502;G:340459665;T:418525850;N:19527,51,0,,,445588125,289131502,340459665,418525850,19527,SRX13799345,SRS11681634,SRA1357269,University of Florida,University of Florida,1,0.85779,,0.20343,,0.69887,,0.56808,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68160,SRR17630950,SRX13799345,SRS11681634,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 2,GSM5820563,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 2,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820563,GSM5820563: bulk seq intact control testes   rep 2; Danio rerio; RNA Seq,GSM5820563 r1,GSM5820563,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C2_S15_L002_R1_001.fastq.gz,fastq,1475012565.0,28921815.0,GSM5820563 r2,0:51 1:0,A:440339743;C:285301590;G:335922618;T:413432380;N:16234,51,0,,,440339743,285301590,335922618,413432380,16234,SRX13799345,SRS11681634,SRA1357269,University of Florida,University of Florida,1,0.85783,,0.20221,,0.70102,,0.57116,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68161,SRR17630957,SRX13799344,SRS11681633,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 1,GSM5820562,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 1,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820562,GSM5820562: bulk seq intact control testes   rep 1; Danio rerio; RNA Seq,GSM5820562 r1,GSM5820562,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C1_S2_L001_R1_001.fastq.gz,fastq,1783515696.0,34970896.0,GSM5820562 r1,0:51 1:0,A:503613569;C:361648917;G:420357217;T:497872153;N:23840,51,0,,,503613569,361648917,420357217,497872153,23840,SRX13799344,SRS11681633,SRA1357269,University of Florida,University of Florida,1,0.88797,,0.22692,,0.69522,,0.57676,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68162,SRR17630958,SRX13799344,SRS11681633,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq intact control testes   rep 1,GSM5820562,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,bulk seq intact control testes   rep 1,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:non dissociated intact testes,GSM5820562,GSM5820562: bulk seq intact control testes   rep 1; Danio rerio; RNA Seq,GSM5820562 r1,GSM5820562,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,D_C1_S2_L002_R1_001.fastq.gz,fastq,1758067563.0,34471913.0,GSM5820562 r2,0:51 1:0,A:496669418;C:356271536;G:414028881;T:491077933;N:19795,51,0,,,496669418,356271536,414028881,491077933,19795,SRX13799344,SRS11681633,SRA1357269,University of Florida,University of Florida,1,0.88843,,0.22792,,0.69619,,0.57488,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68163,SRR17630951,SRX13799343,SRS11681632,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes,GSM5820560,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820560,GSM5820560: bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes; Danio rerio; RNA Seq,GSM5820560 r1,GSM5820560,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_T1_S6_L001_R1_001.fastq.gz,fastq,3525780042.0,69132942.0,GSM5820560 r1,0:51 1:0,A:1025376436;C:691776192;G:829134506;T:979443851;N:49057,51,0,,,1025376436,691776192,829134506,979443851,49057,SRX13799343,SRS11681632,SRA1357269,University of Florida,University of Florida,1,0.86505,,0.30929,,0.72074,,0.6373,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68164,SRR17630952,SRX13799343,SRS11681632,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes,GSM5820560,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820560,GSM5820560: bulk seq TCDD testes rep 1 to be compared to scRNA seq TCDD testes; Danio rerio; RNA Seq,GSM5820560 r1,GSM5820560,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_T1_S6_L002_R1_001.fastq.gz,fastq,3479799156.0,68231356.0,GSM5820560 r2,0:51 1:0,A:1012622841;C:682305804;G:817948602;T:966881210;N:40699,51,0,,,1012622841,682305804,817948602,966881210,40699,SRX13799343,SRS11681632,SRA1357269,University of Florida,University of Florida,1,0.86392,,0.30933,,0.71863,,0.63706,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68165,SRR17630953,SRX13799342,SRS11681631,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 2  to be compared to scRNA seq control testes,GSM5820558,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 2  to be compared to  scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820558,GSM5820558: bulk seq control testes rep 2  to be compared to  scRNA seq control testes; Danio rerio; RNA Seq,GSM5820558 r1,GSM5820558,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C2_S8_L001_R1_001.fastq.gz,fastq,1264687137.0,24797787.0,GSM5820558 r1,0:51 1:0,A:361072135;C:254984535;G:302043978;T:346569617;N:16872,51,0,,,361072135,254984535,302043978,346569617,16872,SRX13799342,SRS11681631,SRA1357269,University of Florida,University of Florida,1,0.86972,,0.31888,,0.71561,,0.6242,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68166,SRR17630954,SRX13799342,SRS11681631,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 2  to be compared to scRNA seq control testes,GSM5820558,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 2  to be compared to  scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820558,GSM5820558: bulk seq control testes rep 2  to be compared to  scRNA seq control testes; Danio rerio; RNA Seq,GSM5820558 r1,GSM5820558,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C2_S8_L002_R1_001.fastq.gz,fastq,1247134620.0,24453620.0,GSM5820558 r2,0:51 1:0,A:356333809;C:251264657;G:297639103;T:341883185;N:13866,51,0,,,356333809,251264657,297639103,341883185,13866,SRX13799342,SRS11681631,SRA1357269,University of Florida,University of Florida,1,0.8683,,0.31544,,0.71332,,0.62605,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68167,SRR17630955,SRX13799341,SRS11681630,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 3  to be compared to scRNA seq control testes,GSM5820559,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 3  to be compared to  scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820559,GSM5820559: bulk seq control testes rep 3  to be compared to  scRNA seq control testes; Danio rerio; RNA Seq,GSM5820559 r1,GSM5820559,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C3_S5_L001_R1_001.fastq.gz,fastq,1298470557.0,25460207.0,GSM5820559 r1,0:51 1:0,A:370125548;C:258465981;G:307735443;T:362125609;N:17976,51,0,,,370125548,258465981,307735443,362125609,17976,SRX13799341,SRS11681630,SRA1357269,University of Florida,University of Florida,1,0.87017,,0.23168,,0.7049,,0.43404,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68168,SRR17630956,SRX13799341,SRS11681630,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 3  to be compared to scRNA seq control testes,GSM5820559,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 3  to be compared to  scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820559,GSM5820559: bulk seq control testes rep 3  to be compared to  scRNA seq control testes; Danio rerio; RNA Seq,GSM5820559 r1,GSM5820559,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C3_S5_L002_R1_001.fastq.gz,fastq,1282277445.0,25142695.0,GSM5820559 r2,0:51 1:0,A:365706822;C:255117242;G:303741803;T:357696714;N:14864,51,0,,,365706822,255117242,303741803,357696714,14864,SRX13799341,SRS11681630,SRA1357269,University of Florida,University of Florida,1,0.86967,,0.23412,,0.70447,,0.60084,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68169,SRR17630959,SRX13799340,SRS11681629,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 1 to be compared to scRNA seq control testes,GSM5820557,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 1 to be compared to scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820557,GSM5820557: bulk seq control testes rep 1 to be compared to scRNA seq control testes; Danio rerio; RNA Seq,GSM5820557 r1,GSM5820557,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C1_S4_L001_R1_001.fastq.gz,fastq,363711651.0,7131601.0,GSM5820557 r1,0:51 1:0,A:101645255;C:77359657;G:89895787;T:94805817;N:5135,51,0,,,101645255,77359657,89895787,94805817,5135,SRX13799340,SRS11681629,SRA1357269,University of Florida,University of Florida,1,0.86049,,0.29611,,0.72293,,0.54071,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System
68170,SRR17630960,SRX13799340,SRS11681629,SRP355202,PRJNA797655,Toxicotranscriptomics of single cell RNA Seq and conventional RNA Seq in TCDD exposed testicular tissue,GSE193758,Transcriptome Analysis,Spermatogenesis is a dynamic  tightly conserved process that is susceptible to environmental contaminants. Exposure to environmental contaminants such as 2 3 7 8 tetrachlorodibenzo p dioxin TCDD is believed to be a cause of idiopathic male infertility. To understand TCDD induced disruption of spermatogenesis at the single cell level  we profiled adult zebrafish testes with and without xxx life exposure to TCDD. Secondly  to investigate the potential for technical artifacts in scRNA seq  we compared bulk sequenced and scRNA seq paired samples from control and TCDD exposed samples  and included an intact control fish to account for dissociation induced artifacts. We found scRNA seq and bulk seq of dissociated testes produced markedly different profiles both toxicologically and transcriptomically. Through scRNA seq  we found TCDD exposure induces mid late germ cell apoptosis while increasing the population of spermatogonial stem cells. Bulk seq on the same cells returned results of immune dysregulation. The transcriptome was unequally detected by scRNA seq and bulk seq  with scRNA seq biased towards detecting longer and more abundant transcripts  but this was not mediated by TCDD exposure. Overall design: Zebrafish were exposed to 50 pg/mL TCDD or vehicle solution for 1 hour during sexual differentiation and maturation. Adult testes were dissected for toxicotranscriptomic analysis. Samples were prepared by dissociation for scRNA seq  remained intact for bulk seq  or were dissociated for bulk seq.,,pubmed:35615540;pubmed:35799832,,bulk seq control testes rep 1 to be compared to scRNA seq control testes,GSM5820557,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,bulk seq control testes rep 1 to be compared to scRNA seq control testes,"Reads were aligned and tabulated by individual cells in each sample using Cell Ranger 6.01 Count data was imported to Seurat version 4.0.4 for quality control QC filtering  clustering  dimensionality reduction  visualization  and differential gene expression Each sample was filtered to cells containing at least 500 features with clusters requiring a minimum of 30 cells.   Samples were merged prior to normalization and clustering resolution 0.3. Differentially expressed genes between conditions for each cluster were identified using the ""FindMarkers"" function Genome build: Zebrafish May 2017 GRCz11/danRer11 Assembly Supplementary files format and content: xlsx; read counts and DEGs; Cell Ranger output matrices 10X SC TCDD DEG clusters: 10X Single cell cluster DEGs GEO CDxCI read counts DEGs: Control dissociated cells compared to Control intact cells GEO CPxCB read counts DEGs: Control psuedo bulk seq compared to Control dissociated cells for bulk seq GEO TBxCB read counts DEGs: TCDD dissociated cells compared to Control dissociated cells GEO TPxCP read counts DEGs: TCDD psuedo bulk seq compared to Control psuedo bulk seq GEO TPxTB read counts DEGs: TCDD psuedo bulk seq compared to TCDD dissociated cells bulk  seq",testes,Experimental fish Sample 4 and 5 were exposed to 1 hour of TCDD at xxx and 7 wpf  allowed to mature  and testes were harvested as adults.,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,Zebrafish were maintained on a 14:10h light/dark cycle  with temperatures maintained at 27°C– 30°C. Fish were fed twice daily. Fish were raised in beakers with daily water changes. Animal use protocols were approved by the Institutional Animal Care and Use Committees at Wayne State University and the University of Wisconsin Madison  according to the National Institutes of Health Guide to the Care and Use of Laboratory Animals Protocol No. M00489.,strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820557,GSM5820557: bulk seq control testes rep 1 to be compared to scRNA seq control testes; Danio rerio; RNA Seq,GSM5820557 r1,GSM5820557,1,Fish were euthanized in tricaine methanesulfonate; testes were removed and enzymatically dissociated. 5 000 cell suspensions were obtained for each replicate. Cell viability was assessed at 90% or better in each replicate. cDNA libraries of mRNA from 25 000 cells were constructed using the 10x Genomics platform  and sequenced on a NovaSeq.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,,BS_C1_S4_L002_R1_001.fastq.gz,fastq,358349460.0,7026460.0,GSM5820557 r2,0:51 1:0,A:100176173;C:76199709;G:88532838;T:93436578;N:4162,51,0,,,100176173,76199709,88532838,93436578,4162,SRX13799340,SRS11681629,SRA1357269,University of Florida,University of Florida,1,0.86034,,0.29588,,0.72346,,0.54277,,51,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2022-01-15,Juvenile,Juvenile,Gonad,Reproductive System