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
29187,SRR8176747,SRX4996876,SRS4031879,SRP480945,PRJNA1055160,Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain,PRJNA1055160,Other,We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf,,pubmed:38529407,,Nadia 19dpf ZZ Gonad Single Cell RNA Seq,Nadia 19dpf ZZ Gonad Single Cell RNA Seq,,strain:Nadia|age:19 dpf provider:John H. Postlethwait  University of Oregon|genotype:ZZ|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: Nadia 19dpf ZZ gonad,Nadia 19dpf ZZ gonad,Nadia 19dpf ZZ gonad,A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP480945,,loader:fastq load.py,,,15090036999.0,107021539.0,zz 19NAmale I1 001.fastq.gz,0:8 1:133,A:4154103253;C:3402890354;G:3765557416;T:3755723849;N:11762127,8,133,,,4154103253,3402890354,3765557416,3755723849,11762127,SRX4996876,SRS4031879,SRA807619,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2018-11-08,Larval,Larval,Gonad,Reproductive System
29188,SRR8176753,SRX4996870,SRS4031878,SRP480945,PRJNA1055160,Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain,PRJNA1055160,Other,We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf,,pubmed:38529407,,Nadia 30dpf ZZ Gonad Single Cell RNA Seq,Nadia 30dpf ZZ Gonad Single Cell RNA Seq,,strain:Nadia|age:30 dpf provider:John H. Postlethwait  University of Oregon|genotype:ZZ|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: Nadia 30dpf ZZ gonad,Nadia 30dpf ZZ gonad,Nadia 30dpf ZZ gonad,A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP480945,,loader:fastq load.py,,,23587173438.0,167284918.0,1 I1 001.fastq.gz,0:8 1:133,A:6732844252;C:4934497997;G:5685086026;T:6219863789;N:14881374,8,133,,,6732844252,4934497997,5685086026,6219863789,14881374,SRX4996870,SRS4031878,SRA807619,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2018-11-08,Juvenile,Juvenile,Gonad,Reproductive System
29189,SRR8176754,SRX4996869,SRS4031877,SRP480945,PRJNA1055160,Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain,PRJNA1055160,Other,We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf,,pubmed:38529407,,Nadia 30dpf ZW Gonad Single Cell RNA Seq,Nadia 30dpf ZW Gonad Single Cell RNA Seq,,strain:Nadia|age:30 dpf provider:John H. Postlethwait  University of Oregon|genotype:ZW|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: Nadia 30dpf ZW gonad,Nadia 30dpf ZW gonad,Nadia 30dpf ZW gonad,A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP480945,,loader:fastq load.py,,,43358808480.0,307509280.0,2 I1 001.fastq.gz,0:8 1:133,A:12290612367;C:8880655083;G:10261318751;T:11898771792;N:27450487,8,133,,,12290612367,8880655083,10261318751,11898771792,27450487,SRX4996869,SRS4031877,SRA807619,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2018-11-08,Juvenile,Juvenile,Gonad,Reproductive System
29190,SRR8176756,SRX4996867,SRS4031876,SRP480945,PRJNA1055160,Single cell RNA seq of Juvenile Zebrafish Gonads from the Nadia Strain,PRJNA1055160,Other,We used single cell RNA Seq 10x Genomics Chromium to profile the transcriptomes of undifferentiated ZZ and ZW gonads at 19 dpf and immature ZZ and ZW gonads at 30 dpf,,pubmed:38529407,,Nadia 19dpf ZW Gonad Single Cell RNA Seq,Nadia 19dpf ZW Gonad Single Cell RNA Seq,,strain:Nadia|age:19 dpf provider:John H. Postlethwait  University of Oregon|genotype:ZW|BioSampleModel:Model organism or animal,,,,,,,,,scRNA Seq of Danio rerio: Nadia 19dpf ZW gonad,Nadia 19dpf ZW gonad,Nadia 19dpf ZW gonad,A single cell suspension was prepared from the pooled gonads of five individuals. The sequencing library was prepared with the Chromium Single Cell 3 Library & Gel Bead Kit v2 10x Genomics.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,NextSeq 500,,SRP480945,,loader:fastq load.py,,,17141425554.0,121570394.0,zw 19NAfem I1 001.fastq.gz,0:8 1:133,A:4656207219;C:3824531650;G:4322736498;T:4324676442;N:13273745,8,133,,,4656207219,3824531650,4322736498,4324676442,13273745,SRX4996867,SRS4031876,SRA807619,University of Oregon|Institute of Neuroscience,University of Oregon,,,,,,,,,,,,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2018-11-08,Larval,Larval,Gonad,Reproductive System
67758,SRR17262950,SRX13441050,SRS11340479,SRP351377,PRJNA789855,Single cell transcriptome reveals insights into the development and function of the zebrafish ovary,GSE191137,Transcriptome Analysis,Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development  yet there are still significant gaps in our understanding of the genes that regulate gonad development  sex  and reproduction. Unlike the development of many organs  such as the brain and heart that form during the first few days of development  zebrafish gonads do not begin to form until the larval stage  =5 dpf. Thus  forward genetic screens have identified very few genes required for gonad development. In addition  bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations  we have used single cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10 658 germ cells and 14 431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types  including follicle cells  theca cells and interstitial stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance  we determined the location of these cell subpopulations within the ovary. Finally  for select examples  we used gene knockout experiments to determine the role of newly identified genes. Our results reveal novel insights into ovarian development and function and the sequencing information will provide a valuable resource for future studies. Overall design: Single cell RNA sequencing of 40 dpf zebrafish ovaries,,pubmed:35588359,,40 dpf zebrafish ovaries cells zx4,GSM5739896,,tissue:40 dpf zebrafish ovaries|cell type:Ovary cells|genotype:AB wildtype,40 dpf zebrafish ovaries cells zx4,A General Transfer Format GTF gene annotation filerelease 96 for the GRCz11 zebrafish genome was downloaded from Ensembl Genome Browser and filtered using the “mkgtf” function in Cell Ranger v3.0.2; 10x Genomic to retain the following attributes: protein coding  lincRNA  and antisense. A genome reference file was generated with Cell Ranger’s “mkref” function using the GRCz11 zebrafish genome obtained from the Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file. GRCz11 zebrafish genome FASTQ file from Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file described above were used to generate the count file using the “count” function in Cell Ranger v3.0.2; 10x Genomic. “expect cells” was setted to 10000 based on estimated cell recovery.  Genome build: GRCz11 Supplementary files format and content: Filtered or raw matrix files generated from Cell Ranger in one zip file.,40 dpf zebrafish ovaries,,Somatic ovary cells were dissociated using a modification of Elkouby and Mullins 2016. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfp transgenic fish Leu et al.  2010 were dissected and stored in a LoBind tube containing 2mL of L15. Tissues were minced with microdissection scissors into < 1 mm pieces. post the tissue had settled to the bottom of the tube  the media was replaced with 5mL of digestive enzyme mixture 3 mg/mL collagenase I Cat.No. C0130; Sigma Aldrich  3 mg/mL collagenase II Cat.No. C6885; Sigma Aldrich  and 1.6 mg/mL hyaluronidase Cat.No. H4272; Sigma Aldrich in L15 and incubated on an orbital rotator at room temperature . The suspension was monitored every 10 mins until a minimal number of cell clumps were observed 30 min.. Cells were centrifuged for 3 mins at 300 x g and resuspended in 5 mL of 5x TrypLE Cat.No. A1217701; Thermo Fisher in L15 and incubated on an orbital rotator at room temperature for 15 min. The trypsin reaction was stopped by adding 500 µL of 2.8 mg/mL trypsin inhibitor in L15 and incubated on an orbital rotator at room temperature for 1 min. The cell suspension was then added to 25 ml of L15 in a 50 ml conical tube to dilute the trypsin and centrifuged for 3 min at 300 x g. The cell pellet was resuspended and washed two times with 5 mL of L15 using a P1000 pipette and centrifuged for 3 mins at 300 x g. The cell pellet was then resuspended and filtered as described above. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly  barcoded 3’ single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell 3’ Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer’s recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent.  The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.,Zebrafish husbandry was performed as previously described Westerfield  2000.,cell type:Ovary cells|genotype:AB wildtype,GSM5739896,GSM5739896: 40 dpf zebrafish ovaries cells zx4; Danio rerio; ssRNA seq,GSM5739896 r1,GSM5739896,1,Somatic ovary cells were dissociated using a modification of Elkouby and Mullins 2016. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfp transgenic fish Leu et al.  2010 were dissected and stored in a LoBind tube containing 2mL of L15. Tissues were minced with microdissection scissors into < 1 mm pieces. post the tissue had settled to the bottom of the tube  the media was replaced with 5mL of digestive enzyme mixture 3 mg/mL collagenase I Cat.No. C0130; Sigma Aldrich  3 mg/mL collagenase II Cat.No. C6885; Sigma Aldrich  and 1.6 mg/mL hyaluronidase Cat.No. H4272; Sigma Aldrich in L15 and incubated on an orbital rotator at room temperature . The suspension was monitored every 10 mins until a minimal number of cell clumps were observed 30 min.. Cells were centrifuged for 3 mins at 300 x g and resuspended in 5 mL of 5x TrypLE Cat.No. A1217701; Thermo Fisher in L15 and incubated on an orbital rotator at room temperature for 15 min. The trypsin reaction was stopped by adding 500 µL of 2.8 mg/mL trypsin inhibitor in L15 and incubated on an orbital rotator at room temperature for 1 min. The cell suspension was then added to 25 ml of L15 in a 50 ml conical tube to dilute the trypsin and centrifuged for 3 min at 300 x g. The cell pellet was resuspended and washed two times with 5 mL of L15 using a P1000 pipette and centrifuged for 3 mins at 300 x g. The cell pellet was then resuspended and filtered as described above. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly  barcoded three prime single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell three prime Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer's recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent.  The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP351377,,,40dpf_ova_2_S1_L001_R1_001.fastq.gz 40dpf_ova_2_S1_L001_R2_001.fastq.gz,fastq fastq,109199255578.0,361586939.0,GSM5739896 r1,0:151 1:151,A:26889567766;C:19012911507;G:17705256458;T:45580417154;N:11102693,151,151,,,26889567766,19012911507,17705256458,45580417154,11102693,SRX13441050,SRS11340479,SRA1345465,"Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis","Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis",2,0.00012,0.84311,5e-05,0.10842,0.99997,0.78486,1.0,0.53946,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-17,Juvenile,Juvenile,Gonad,Reproductive System
67759,SRR17262951,SRX13441049,SRS11340478,SRP351377,PRJNA789855,Single cell transcriptome reveals insights into the development and function of the zebrafish ovary,GSE191137,Transcriptome Analysis,Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development  yet there are still significant gaps in our understanding of the genes that regulate gonad development  sex  and reproduction. Unlike the development of many organs  such as the brain and heart that form during the first few days of development  zebrafish gonads do not begin to form until the larval stage  =5 dpf. Thus  forward genetic screens have identified very few genes required for gonad development. In addition  bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations  we have used single cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10 658 germ cells and 14 431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types  including follicle cells  theca cells and interstitial stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance  we determined the location of these cell subpopulations within the ovary. Finally  for select examples  we used gene knockout experiments to determine the role of newly identified genes. Our results reveal novel insights into ovarian development and function and the sequencing information will provide a valuable resource for future studies. Overall design: Single cell RNA sequencing of 40 dpf zebrafish ovaries,,pubmed:35588359,,40 dpf zebrafish ovaries cells zx2,GSM5739895,,tissue:40 dpf zebrafish ovaries|cell type:Ovary cells|genotype:AB wildtype,40 dpf zebrafish ovaries cells zx2,A General Transfer Format GTF gene annotation filerelease 96 for the GRCz11 zebrafish genome was downloaded from Ensembl Genome Browser and filtered using the “mkgtf” function in Cell Ranger v3.0.2; 10x Genomic to retain the following attributes: protein coding  lincRNA  and antisense. A genome reference file was generated with Cell Ranger’s “mkref” function using the GRCz11 zebrafish genome obtained from the Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file. GRCz11 zebrafish genome FASTQ file from Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file described above were used to generate the count file using the “count” function in Cell Ranger v3.0.2; 10x Genomic. “expect cells” was setted to 10000 based on estimated cell recovery.  Genome build: GRCz11 Supplementary files format and content: Filtered or raw matrix files generated from Cell Ranger in one zip file.,40 dpf zebrafish ovaries,,Somatic ovary cells were dissociated using a modification of Elkouby and Mullins 2016. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfp transgenic fish Leu et al.  2010 were dissected and stored in a LoBind tube containing 2mL of L15. Tissues were minced with microdissection scissors into < 1 mm pieces. post the tissue had settled to the bottom of the tube  the media was replaced with 5mL of digestive enzyme mixture 3 mg/mL collagenase I Cat.No. C0130; Sigma Aldrich  3 mg/mL collagenase II Cat.No. C6885; Sigma Aldrich  and 1.6 mg/mL hyaluronidase Cat.No. H4272; Sigma Aldrich in L15 and incubated on an orbital rotator at room temperature . The suspension was monitored every 10 mins until a minimal number of cell clumps were observed 30 min.. Cells were centrifuged for 3 mins at 300 x g and resuspended in 5 mL of 5x TrypLE Cat.No. A1217701; Thermo Fisher in L15 and incubated on an orbital rotator at room temperature for 15 min. The trypsin reaction was stopped by adding 500 µL of 2.8 mg/mL trypsin inhibitor in L15 and incubated on an orbital rotator at room temperature for 1 min. The cell suspension was then added to 25 ml of L15 in a 50 ml conical tube to dilute the trypsin and centrifuged for 3 min at 300 x g. The cell pellet was resuspended and washed two times with 5 mL of L15 using a P1000 pipette and centrifuged for 3 mins at 300 x g. The cell pellet was then resuspended and filtered as described above. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly  barcoded 3’ single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell 3’ Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer’s recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent.  The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.,Zebrafish husbandry was performed as previously described Westerfield  2000.,cell type:Ovary cells|genotype:AB wildtype,GSM5739895,GSM5739895: 40 dpf zebrafish ovaries cells zx2; Danio rerio; ssRNA seq,GSM5739895 r1,GSM5739895,1,Somatic ovary cells were dissociated using a modification of Elkouby and Mullins 2016. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfp transgenic fish Leu et al.  2010 were dissected and stored in a LoBind tube containing 2mL of L15. Tissues were minced with microdissection scissors into < 1 mm pieces. post the tissue had settled to the bottom of the tube  the media was replaced with 5mL of digestive enzyme mixture 3 mg/mL collagenase I Cat.No. C0130; Sigma Aldrich  3 mg/mL collagenase II Cat.No. C6885; Sigma Aldrich  and 1.6 mg/mL hyaluronidase Cat.No. H4272; Sigma Aldrich in L15 and incubated on an orbital rotator at room temperature . The suspension was monitored every 10 mins until a minimal number of cell clumps were observed 30 min.. Cells were centrifuged for 3 mins at 300 x g and resuspended in 5 mL of 5x TrypLE Cat.No. A1217701; Thermo Fisher in L15 and incubated on an orbital rotator at room temperature for 15 min. The trypsin reaction was stopped by adding 500 µL of 2.8 mg/mL trypsin inhibitor in L15 and incubated on an orbital rotator at room temperature for 1 min. The cell suspension was then added to 25 ml of L15 in a 50 ml conical tube to dilute the trypsin and centrifuged for 3 min at 300 x g. The cell pellet was resuspended and washed two times with 5 mL of L15 using a P1000 pipette and centrifuged for 3 mins at 300 x g. The cell pellet was then resuspended and filtered as described above. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly  barcoded three prime single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell three prime Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer's recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent.  The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP351377,,,40dpf_ova_1_S146_L004_R2_001.fastq.gz 40dpf_ova_1_S146_L004_R1_001.fastq.gz,fastq fastq,109753922368.0,363423584.0,GSM5739895 r1,0:151 1:151,A:26550231612;C:18985464266;G:18837331344;T:45367377509;N:13517637,151,151,,,26550231612,18985464266,18837331344,45367377509,13517637,SRX13441049,SRS11340478,SRA1345465,"Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis","Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis",2,9e-05,0.84548,8e-05,0.09287,1.0,0.78589,,0.54454,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-17,Juvenile,Juvenile,Gonad,Reproductive System
67760,SRR17262952,SRX13441048,SRS11340477,SRP351377,PRJNA789855,Single cell transcriptome reveals insights into the development and function of the zebrafish ovary,GSE191137,Transcriptome Analysis,Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development  yet there are still significant gaps in our understanding of the genes that regulate gonad development  sex  and reproduction. Unlike the development of many organs  such as the brain and heart that form during the first few days of development  zebrafish gonads do not begin to form until the larval stage  =5 dpf. Thus  forward genetic screens have identified very few genes required for gonad development. In addition  bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations  we have used single cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10 658 germ cells and 14 431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types  including follicle cells  theca cells and interstitial stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance  we determined the location of these cell subpopulations within the ovary. Finally  for select examples  we used gene knockout experiments to determine the role of newly identified genes. Our results reveal novel insights into ovarian development and function and the sequencing information will provide a valuable resource for future studies. Overall design: Single cell RNA sequencing of 40 dpf zebrafish ovaries,,pubmed:35588359,,40 dpf zebrafish ovaries cells  sorted germ cells,GSM5739894,,tissue:40 dpf zebrafish ovaries|cell type:Germ cells|genotype:AB wildtype,40 dpf zebrafish ovaries cells  sorted germ cells,A General Transfer Format GTF gene annotation filerelease 96 for the GRCz11 zebrafish genome was downloaded from Ensembl Genome Browser and filtered using the “mkgtf” function in Cell Ranger v3.0.2; 10x Genomic to retain the following attributes: protein coding  lincRNA  and antisense. A genome reference file was generated with Cell Ranger’s “mkref” function using the GRCz11 zebrafish genome obtained from the Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file. GRCz11 zebrafish genome FASTQ file from Ensembl Genome Browser with alternative loci scaffolds removed and the filtered GTF file described above were used to generate the count file using the “count” function in Cell Ranger v3.0.2; 10x Genomic. “expect cells” was setted to 10000 based on estimated cell recovery.  Genome build: GRCz11 Supplementary files format and content: Filtered or raw matrix files generated from Cell Ranger in one zip file.,40 dpf zebrafish ovaries,,Germ cells were dissociated from the somatic gonad using a modification of Blokhina et al.  2019. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfpuc02 transgenic fish Leu et al.  2010 and stored in a LoBind tube Cat.No. 0030108302; Eppendorf containing 2 mL of L15 mediumCat.No. L5520; Sigma Aldrich. The tissue was minced with small scissors into <1 mm pieces. 200 µL of 20 mg/mL of type 2 collagenase in L15  Cat.No. NC9870009; Worthington were added and incubated on an orbital rotator at 28°C for 35 min. The cell suspension was then gently passed through a 23g needle five times to break up large cell clumps. 200 µL of 7 mg/mL trypsin Cat.No. LS003708; Worthington in L15 were added and incubated on an orbital rotator for 10 min or until a minimal amount of cell clumps was observed. The trypsin reaction was stopped by adding 500 µL of 20 mg/mL trypsin Inhibitor Cat.No. 100612; MP Biomedicals in L15. The cells were centrifuged for 3 min at 300 x g and the supernatant carefully removed. The cells were then resuspended and washed two times with 5 mL of L15 using  a P1000 pipette tip and then centrifuged for 3 min at 300 x g. Cells were then resuspended in 1 mL L15 and filtered through a 100 µm nylon filter Cat.No. 431752; Corning and then through a 40 µm nylon filter Cat.No. 431750; Corning to remove cell clumps. The filtrate was centrifuged for 3 min at 300 x g and resuspended in 1 mL of 50 mg/mL BSA Cat.No. A8806; Sigma Aldrich in Phosphate Buffered Saline. Cell viability and number were assessed using propidium iodine Cat. No. P1304MP; Thermo Fisher and Hoechst 33342 Cat.No. H3570; Thermo Fisher staining on a Fuchs Rosenthal hemocytometer Cat.No. DHC F01; Incyto. Following cell dissociation of Tgpiwil1:egfp transgenic ovaries  GFP+ germ cells were sorted using a MoFlo Astrios EQ Cell Sorter Beckman Coulter with a 70 µm nozzle. Cells were sorted using side scatter and GFP purify to identify single germ cells. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly  barcoded 3’ single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell 3’ Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer’s recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent.  The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.,Zebrafish husbandry was performed as previously described Westerfield  2000.,cell type:Germ cells|genotype:AB wildtype,GSM5739894,GSM5739894: 40 dpf zebrafish ovaries cells  sorted germ cells; Danio rerio; ssRNA seq,GSM5739894 r1,GSM5739894,1,Germ cells were dissociated from the somatic gonad using a modification of Blokhina et al.  2019. 40 pairs of 40 dpf ovaries were dissected from Tgpiwil1:egfpuc02 transgenic fish Leu et al.  2010 and stored in a LoBind tube Cat.No. 0030108302; Eppendorf containing 2 mL of L15 mediumCat.No. L5520; Sigma Aldrich. The tissue was minced with small scissors into <1 mm pieces. 200 µL of 20 mg/mL of type 2 collagenase in L15  Cat.No. NC9870009; Worthington were added and incubated on an orbital rotator at 28°C for 35 min. The cell suspension was then gently passed through a 23g needle five times to break up large cell clumps. 200 µL of 7 mg/mL trypsin Cat.No. LS003708; Worthington in L15 were added and incubated on an orbital rotator for 10 min or until a minimal amount of cell clumps was observed. The trypsin reaction was stopped by adding 500 µL of 20 mg/mL trypsin Inhibitor Cat.No. 100612; MP Biomedicals in L15. The cells were centrifuged for 3 min at 300 x g and the supernatant carefully removed. The cells were then resuspended and washed two times with 5 mL of L15 using  a P1000 pipette tip and then centrifuged for 3 min at 300 x g. Cells were then resuspended in 1 mL L15 and filtered through a 100 µm nylon filter Cat.No. 431752; Corning and then through a 40 µm nylon filter Cat.No. 431750; Corning to remove cell clumps. The filtrate was centrifuged for 3 min at 300 x g and resuspended in 1 mL of 50 mg/mL BSA Cat.No. A8806; Sigma Aldrich in Phosphate Buffered Saline. Cell viability and number were assessed using propidium iodine Cat. No. P1304MP; Thermo Fisher and Hoechst 33342 Cat.No. H3570; Thermo Fisher staining on a Fuchs Rosenthal hemocytometer Cat.No. DHC F01; Incyto. Following cell dissociation of Tgpiwil1:egfp transgenic ovaries  GFP+ germ cells were sorted using a MoFlo Astrios EQ Cell Sorter Beckman Coulter with a 70 µm nozzle. Cells were sorted using side scatter and GFP purify to identify single germ cells. Single cell RNA sequencing libraries were prepared by the UC Davis DNA Technologies core. Briefly  barcoded three prime single cell libraries were prepared from dissociated cell suspensions or sorted cells using the Chromium Single Cell three prime Library and Gel Bead kit V3 10X Genomics for sequencing according to the manufacturer's recommendations. All libraries were targeted at 10 000 cell recovery and were amplified using 11 cycles. The cDNA and library fragment size distribution was verified via micro capillary gel electrophoresis on a Bioanalyzer 2100 Agilent.  The libraries were quantified by fluorometry on a Qubit instrument LifeTechnologies and by qPCR with a Kapa Library Quant kit Kapa Biosystems prior to sequencing. Libraries were sequenced on a HiSeq 4000 sequencer Illumina with paired end 100 bp reads.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP351377,,,40d_Germ_S67_L007_R1_001.fastq.gz 40d_Germ_S67_L007_R2_001.fastq.gz,fastq fastq,97157899800.0,321714900.0,GSM5739894 r1,0:151 1:151,A:25130180865;C:15016964022;G:17255588720;T:39751154898;N:4011295,151,151,,,25130180865,15016964022,17255588720,39751154898,4011295,SRX13441048,SRS11340477,SRA1345465,"Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis","Bruce Draper Lab, Molecular and Cellular Biology, University of California, Davis",2,0.00058,0.83872,0.00016,0.05616,0.99989,0.77873,0.4,0.51521,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-12-17,Juvenile,Juvenile,Gonad,Reproductive System
68139,SRR17630961,SRX13799339,SRS11681628,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,,scRNA seq TCDD testes   rep 2,GSM5820556,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq TCDD 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 TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820556,GSM5820556: scRNA seq TCDD testes   rep 2; Danio rerio; RNA Seq,GSM5820556 r1,GSM5820556,1,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,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_T2_S5_L001_I1_001.fastq.gz SC_T2_S5_L001_R1_001.fastq.gz SC_T2_S5_L001_R2_001.fastq.gz,fastq fastq fastq,11262679659.0,88682517.0,GSM5820556 r1,0:8 1:28 2:91,A:2329833844;C:1736580490;G:2028746154;T:1974513391;N:435168,8,28,91,,2329833844,1736580490,2028746154,1974513391,435168,SRX13799339,SRS11681628,SRA1357269,University of Florida,University of Florida,1,0.89663,,0.23137,,0.75166,,0.55299,,91,,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
68140,SRR17630962,SRX13799339,SRS11681628,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,,scRNA seq TCDD testes   rep 2,GSM5820556,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq TCDD 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 TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820556,GSM5820556: scRNA seq TCDD testes   rep 2; Danio rerio; RNA Seq,GSM5820556 r1,GSM5820556,1,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,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_T2_S5_L002_I1_001.fastq.gz SC_T2_S5_L002_R1_001.fastq.gz SC_T2_S5_L002_R2_001.fastq.gz,fastq fastq fastq,11384315052.0,89640276.0,GSM5820556 r2,0:8 1:28 2:91,A:2351124750;C:1758531934;G:2054452297;T:1992620872;N:535263,8,28,91,,2351124750,1758531934,2054452297,1992620872,535263,SRX13799339,SRS11681628,SRA1357269,University of Florida,University of Florida,1,0.89836,,0.23263,,0.7543,,0.55738,,91,,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
68141,SRR17630963,SRX13799338,SRS11681627,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,,scRNA seq TCDD testes   rep 1,GSM5820555,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq TCDD 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 TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820555,GSM5820555: scRNA seq TCDD testes   rep 1; Danio rerio; RNA Seq,GSM5820555 r1,GSM5820555,1,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,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_T1_S4_L001_I1_001.fastq.gz SC_T1_S4_L001_R1_001.fastq.gz SC_T1_S4_L001_R2_001.fastq.gz,fastq fastq fastq,10978768873.0,86446999.0,GSM5820555 r1,0:8 1:28 2:91,A:2363149906;C:1616901304;G:1945888469;T:1940298056;N:439174,8,28,91,,2363149906,1616901304,1945888469,1940298056,439174,SRX13799338,SRS11681627,SRA1357269,University of Florida,University of Florida,1,0.87562,,0.208,,0.75511,,0.5329,,91,,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
68142,SRR17630964,SRX13799338,SRS11681627,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,,scRNA seq TCDD testes   rep 1,GSM5820555,,tissue:testes|strain:AB|treatment:50 pg/mL TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq TCDD 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 TCDD in 0.1% DMSO|sample preparation:dissociated cell suspension,GSM5820555,GSM5820555: scRNA seq TCDD testes   rep 1; Danio rerio; RNA Seq,GSM5820555 r1,GSM5820555,1,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,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_T1_S4_L002_I1_001.fastq.gz SC_T1_S4_L002_R1_001.fastq.gz SC_T1_S4_L002_R2_001.fastq.gz,fastq fastq fastq,11084990022.0,87283386.0,GSM5820555 r2,0:8 1:28 2:91,A:2382115862;C:1635424114;G:1968060449;T:1956671635;N:516066,8,28,91,,2382115862,1635424114,1968060449,1956671635,516066,SRX13799338,SRS11681627,SRA1357269,University of Florida,University of Florida,1,0.8745,,0.20808,,0.7585,,0.52692,,91,,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
68143,SRR17630965,SRX13799337,SRS11681626,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,,scRNA seq control testes   rep 3,GSM5820554,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq 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:dissociated cell suspension,GSM5820554,GSM5820554: scRNA seq control testes   rep 3; Danio rerio; RNA Seq,GSM5820554 r1,GSM5820554,1,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,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_C3_S3_L001_I1_001.fastq.gz SC_C3_S3_L001_R1_001.fastq.gz SC_C3_S3_L001_R2_001.fastq.gz,fastq fastq fastq,11736916836.0,92416668.0,GSM5820554 r1,0:8 1:28 2:91,A:2491182657;C:1749727321;G:2001921423;T:2166620469;N:464918,8,28,91,,2491182657,1749727321,2001921423,2166620469,464918,SRX13799337,SRS11681626,SRA1357269,University of Florida,University of Florida,1,0.89927,,0.17983,,0.71601,,0.52261,,91,,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
68144,SRR17630966,SRX13799337,SRS11681626,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,,scRNA seq control testes   rep 3,GSM5820554,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq 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:dissociated cell suspension,GSM5820554,GSM5820554: scRNA seq control testes   rep 3; Danio rerio; RNA Seq,GSM5820554 r1,GSM5820554,1,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,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_C3_S3_L002_I1_001.fastq.gz SC_C3_S3_L002_R1_001.fastq.gz SC_C3_S3_L002_R2_001.fastq.gz,fastq fastq fastq,11862480339.0,93405357.0,GSM5820554 r2,0:8 1:28 2:91,A:2515246562;C:1770645118;G:2026263526;T:2187182415;N:549866,8,28,91,,2515246562,1770645118,2026263526,2187182415,549866,SRX13799337,SRS11681626,SRA1357269,University of Florida,University of Florida,1,0.89922,,0.1803,,0.71419,,0.52093,,91,,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
68145,SRR17630967,SRX13799336,SRS11681625,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,,scRNA seq control testes   rep 2,GSM5820553,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq 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:dissociated cell suspension,GSM5820553,GSM5820553: scRNA seq control testes   rep 2; Danio rerio; RNA Seq,GSM5820553 r1,GSM5820553,1,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,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_C2_S2_L001_I1_001.fastq.gz SC_C2_S2_L001_R1_001.fastq.gz SC_C2_S2_L001_R2_001.fastq.gz,fastq fastq fastq,11597196897.0,91316511.0,GSM5820553 r1,0:8 1:28 2:91,A:2441188567;C:1731265684;G:2062239362;T:2074648513;N:460375,8,28,91,,2441188567,1731265684,2062239362,2074648513,460375,SRX13799336,SRS11681625,SRA1357269,University of Florida,University of Florida,1,0.87524,,0.22302,,0.75893,,0.55047,,91,,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
68146,SRR17630968,SRX13799336,SRS11681625,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,,scRNA seq control testes   rep 2,GSM5820553,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq 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:dissociated cell suspension,GSM5820553,GSM5820553: scRNA seq control testes   rep 2; Danio rerio; RNA Seq,GSM5820553 r1,GSM5820553,1,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,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_C2_S2_L002_I1_001.fastq.gz SC_C2_S2_L002_R1_001.fastq.gz SC_C2_S2_L002_R2_001.fastq.gz,fastq fastq fastq,11724309038.0,92317394.0,GSM5820553 r2,0:8 1:28 2:91,A:2464546352;C:1753014248;G:2088164317;T:2094592155;N:565782,8,28,91,,2464546352,1753014248,2088164317,2094592155,565782,SRX13799336,SRS11681625,SRA1357269,University of Florida,University of Florida,1,0.87809,,0.22205,,0.75272,,0.55306,,91,,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
68147,SRR17630969,SRX13799335,SRS11681624,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,,scRNA seq control testes   rep 1,GSM5820552,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq 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:dissociated cell suspension,GSM5820552,GSM5820552: scRNA seq control testes   rep 1; Danio rerio; RNA Seq,GSM5820552 r1,GSM5820552,1,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,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_C1_S1_L001_I1_001.fastq.gz SC_C1_S1_L001_R1_001.fastq.gz SC_C1_S1_L001_R2_001.fastq.gz,fastq fastq fastq,11845124392.0,93268696.0,GSM5820552 r1,0:8 1:28 2:91,A:2554285232;C:1757437977;G:2060709302;T:2114543968;N:474857,8,28,91,,2554285232,1757437977,2060709302,2114543968,474857,SRX13799335,SRS11681624,SRA1357269,University of Florida,University of Florida,1,0.89006,,0.16375,,0.74714,,0.51816,,91,,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
68148,SRR17630970,SRX13799335,SRS11681624,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,,scRNA seq control testes   rep 1,GSM5820552,,tissue:testes|strain:AB|treatment:50 pg/mL 0.1% DMSO|sample preparation:dissociated cell suspension,scRNA seq 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:dissociated cell suspension,GSM5820552,GSM5820552: scRNA seq control testes   rep 1; Danio rerio; RNA Seq,GSM5820552 r1,GSM5820552,1,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,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP355202,,loader:fastq load.py,SC_C1_S1_L002_I1_001.fastq.gz SC_C1_S1_L002_R1_001.fastq.gz SC_C1_S1_L002_R2_001.fastq.gz,fastq fastq fastq,11974253293.0,94285459.0,GSM5820552 r2,0:8 1:28 2:91,A:2577816465;C:1779883368;G:2086781140;T:2134925822;N:569974,8,28,91,,2577816465,1779883368,2086781140,2134925822,569974,SRX13799335,SRS11681624,SRA1357269,University of Florida,University of Florida,1,0.89007,,0.16458,,0.74986,,0.52005,,91,,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
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