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
70844,SRR20737630,SRX16758028,SRS14385048,SRP389175,PRJNA864829,Single nuclei profiling of chromatin accessibility and transcriptomes of jaw mesenchymal cells in wild type and nr5a2 mutant zebrafish embryos,GSE210251,Other,The functional jaw is composed of multiple connective tissues including skeletal components bone  cartilage  and teeth  tendon  ligament  and musculature. Cranial neural crest derived mesenchyme of the mandibular arch give rise to diverse tissue types within the lower jaw. To understand how the specification of diverse cell types with spatial and temporal precision is achieved  we profile multi omic chromatin accessibility snATACseq and transcriptome snRNAseq of jaw mesenchyme at single cell resolution from the developing zebrafish jaw. Overall design: To profile chromatin accessibility and transcriptome in the same cell from developing jaw  we collected nr5a2:GFP+ jaw mesenchyme from control and nr5a2 mutant zebrafish embryos at 2.5 dpf. The nuclei of FACS GFP+ cells were subjected to single cell profiling and sequencing by the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression platform of 10X Genomics.,,pubmed:36905926,,Multiome mutant nr5a2 GFP 2.5dpf head snRNA seq,GSM6424705,,source name:Jaw mesenchyme|tissue:Jaw mesenchyme|developmental stage:2.5 dpf|genotype:nr5a2:mGFP DBD del/oz3|transgene1:Tgnr5a2:GFP CAAX DBD delel875|transgene2:Tgscxa:mCherryfb301|facs markers:DAPI  / GFP+,Multiome mutant nr5a2 GFP 2.5dpf head snRNA seq,Multi omic libraries of snATACseq and snRNAseq from the same barcoded single nuclei were constructed per manufacturer’s instructions 10X Genomics  Chromium Next GEM Single Cell Multiome ATAC + Gene Expression  protocol CG000338. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit. Libraries were sequenced on Illumina HiSeq control or NextSeq mutant platforms. For sequencing snATACseq libraries  both Read1 and Read2 were extended to 60 cycles  whereas for sequencing snRNAseq libraries  Read2 was extended to 102 cycles for longer coverage. Sequencing reads were aligned to customized genome built with GRCz11.fa  GRCz11.104.gtf and JASPAR2020.pfm and added GFP CAAX and mCherry gene information. Alignment  peak calling for snATACseq data and cell calling were performed by Cell Ranger ARC v2.0.0 per manufacturer’s instructions 10X Genomics to generate peak by cell and gene by cell count matrices. Assembly: GRCz11 Supplementary files format and content: Each sample has one processed data output by Cell Ranger ARC v2.0.0: peak by cell and gene by cell count matrices in HDF5 format.,Jaw mesenchyme,,Zebrafish embryos are screened for nr5a2:mGFP DBD del+ / scxa:mCherry+ and fin tips are collected for PCR genotyping of oz3 allele mutant and wild type allele control before 2 dpf. Control and mutant heads were decapitated between the eye and ear post anesthesia at 2.5 dpf. Dissected heads twenty heads pre tube were washed twice with fresh and iced Ringer’s solution 116mM NaCl  2.6mM KCl  5mM HEPES  pH 7.0  followed by dissociation at 28.5 °C for 40 min by mechanical   nutating and pipetting every 5 min and enzymatic   in pre warmed protease solution 0.25% trypsin  1 mM EDTA  pH 8.0  and 20 mg/mL Collagenase D from stock of 400 mg/mL Collagenase D in HBSS in PBS until fully dissociated. Dissociation reaction is stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Dissociated cells were collected by centrifugation for 5 min  2000 rpm at 4°C and washed by suspension solution 1% FBS  0.8mM CaCl2  50U/ml Penicillin  0.05mg/ml Streptomycin in Leibovitz Medium twice and filtered by cell strainer before sorting. Live cells were fluorescence activated cell sorted FACS to isolate GFP+ and exclude the cytoplasmic stain Zombie Violet control or nuclear stain DAPI mutant into 0.04% BSA/ PBS at 4°C. Nuclei isolation was performed per manufacturer’s instructions 10X Genomics  protocol CG000169  low cell input protocol with optimalization for zebrafish mesenchyme. FACS cells were pelleted for 15 min  300 rcf at 4oC  and incubated with lysis buffer for 100 s on ice. Isolated nuclei were washed by Wash buffer and Nuclei buffer and checked for nucleus integrity under a fluorescence confocal microscope with DAPI staining before subjected to library construction. To capture accessible chromatin and transcripts from the same cells per manufacturer’s instructions  accessible chromatin regions from isolated nuclei were first targeted and tagged by transposase. Tagged chromatin and ployA mRNA from the same nuclei were pulled down and barcoded with the same sequences within isolated GEMs to achieve single nuclei separation. Chromatin fragments were further indexed with sample specific i7 indexes and linked with Illumina P5 and P7 sequences. Reverse transcription was performed in GEMs to synthesize cDNA from polyA mRNA. cDNAs were further fragmented and indexed with sample specific i7 and i5 indexes and linked with Illumina P5 and P7 sequences. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit.,All experiments on zebrafish Danio rerio were approved by the Institutional Animal Care and Use Committee of the University of Southern California IACUC protocol #20771 and #21151. Zebrafish are raised in vivarium under standard conditions maintained at 28.5°C with health and water conditions monitored daily.,tissue:Jaw mesenchyme|developmental stage:2.5 dpf|genotype:nr5a2:mGFP DBD del/oz3|transgene1:Tgnr5a2:GFP CAAX DBD delel875|transgene2:Tgscxa:mCherryfb301|facs markers:DAPI  / GFP+,GSM6424705,GSM6424705: Multiome mutant nr5a2 GFP 2.5dpf head snRNA seq; Danio rerio; RNA Seq,GSM6424705 r1,GSM6424705,1,Zebrafish embryos are screened for nr5a2:mGFP DBD del+ / scxa:mCherry+ and fin tips are collected for PCR genotyping of oz3 allele mutant and wild type allele control before 2 dpf. Control and mutant heads were decapitated between the eye and ear post anesthesia at 2.5 dpf. Dissected heads twenty heads pre tube were washed twice with fresh and iced Ringer's solution 116mM NaCl  2.6mM KCl  5mM HEPES  pH 7.0  followed by dissociation at 28.5 °C for 40 min by mechanical   nutating and pipetting every 5 min and enzymatic   in pre warmed protease solution 0.25% trypsin  1 mM EDTA  pH 8.0  and 20 mg/mL Collagenase D from stock of 400 mg/mL Collagenase D in HBSS in PBS until fully dissociated. Dissociation reaction is stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Dissociated cells were collected by centrifugation for 5 min  2000 rpm at 4°C and washed by suspension solution 1% FBS  0.8mM CaCl2  50U/ml Penicillin  0.05mg/ml Streptomycin in Leibovitz Medium twice and filtered by cell strainer before sorting. Live cells were fluorescence activated cell sorted FACS to isolate GFP+ and exclude the cytoplasmic stain Zombie Violet control or nuclear stain DAPI mutant into 0.04% BSA/ PBS at 4°C. Nuclei isolation was performed per manufacturer's instructions 10X Genomics  protocol CG000169  low cell input protocol with optimalization for zebrafish mesenchyme. FACS cells were pelleted for 15 min  300 rcf at 4oC  and incubated with lysis buffer for 100 s on ice. Isolated nuclei were washed by Wash buffer and Nuclei buffer and checked for nucleus integrity under a fluorescence confocal microscope with DAPI staining before subjected to library construction. To capture accessible chromatin and transcripts from the same cells per manufacturer's instructions  accessible chromatin regions from isolated nuclei were first targeted and tagged by transposase. Tagged chromatin and ployA mRNA from the same nuclei were pulled down and barcoded with the same sequences within isolated GEMs to achieve single nuclei separation. Chromatin fragments were further indexed with sample specific i7 indexes and linked with Illumina P5 and P7 sequences. Reverse transcription was performed in GEMs to synthesize cDNA from polyA mRNA. cDNAs were further fragmented and indexed with sample specific i7 and i5 indexes and linked with Illumina P5 and P7 sequences. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 550,,SRP389175,,loader:fastq load.py,Multiome_mutant_nr5a2_GFP_2.5dpf_head_RNA_S1_L001_R1_001.fastq.gz Multiome_mutant_nr5a2_GFP_2.5dpf_head_RNA_S1_L001_R2_001.fastq.gz,fastq fastq,24616183454.0,187429180.0,GSM6424705 r1,0:29 1:102.34,A:5661562219;C:4278027880;G:4357175731;T:5550818399;N:4768599225,29,102,,,5661562219,4278027880,4357175731,5550818399,4768599225,SRX16758028,SRS14385048,SRA1467000,Stem Cell Department at USC,Stem Cell Department at USC,2,0.01084,0.91331,0.00616,0.27551,0.99153,0.84447,0.51001,0.63176,29,102,T,B,sc-like readlen,illumina,nextseq,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2022-08-01,Hatching,Embryo,Jaw,Surface Structure
70845,SRR20737632,SRX16758026,SRS14385046,SRP389175,PRJNA864829,Single nuclei profiling of chromatin accessibility and transcriptomes of jaw mesenchymal cells in wild type and nr5a2 mutant zebrafish embryos,GSE210251,Other,The functional jaw is composed of multiple connective tissues including skeletal components bone  cartilage  and teeth  tendon  ligament  and musculature. Cranial neural crest derived mesenchyme of the mandibular arch give rise to diverse tissue types within the lower jaw. To understand how the specification of diverse cell types with spatial and temporal precision is achieved  we profile multi omic chromatin accessibility snATACseq and transcriptome snRNAseq of jaw mesenchyme at single cell resolution from the developing zebrafish jaw. Overall design: To profile chromatin accessibility and transcriptome in the same cell from developing jaw  we collected nr5a2:GFP+ jaw mesenchyme from control and nr5a2 mutant zebrafish embryos at 2.5 dpf. The nuclei of FACS GFP+ cells were subjected to single cell profiling and sequencing by the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression platform of 10X Genomics.,,pubmed:36905926,,Multiome control nr5a2 GFP 2.5dpf head snRNA seq,GSM6424703,,source name:Jaw mesenchyme|tissue:Jaw mesenchyme|developmental stage:2.5 dpf|genotype:nr5a2:mGFP DBD del/+|transgene1:Tgnr5a2:GFP CAAX DBD delel875|transgene2:Tgscxa:mCherryfb301|facs markers:Zombie  / GFP+,Multiome control nr5a2 GFP 2.5dpf head snRNA seq,Multi omic libraries of snATACseq and snRNAseq from the same barcoded single nuclei were constructed per manufacturer’s instructions 10X Genomics  Chromium Next GEM Single Cell Multiome ATAC + Gene Expression  protocol CG000338. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit. Libraries were sequenced on Illumina HiSeq control or NextSeq mutant platforms. For sequencing snATACseq libraries  both Read1 and Read2 were extended to 60 cycles  whereas for sequencing snRNAseq libraries  Read2 was extended to 102 cycles for longer coverage. Sequencing reads were aligned to customized genome built with GRCz11.fa  GRCz11.104.gtf and JASPAR2020.pfm and added GFP CAAX and mCherry gene information. Alignment  peak calling for snATACseq data and cell calling were performed by Cell Ranger ARC v2.0.0 per manufacturer’s instructions 10X Genomics to generate peak by cell and gene by cell count matrices. Assembly: GRCz11 Supplementary files format and content: Each sample has one processed data output by Cell Ranger ARC v2.0.0: peak by cell and gene by cell count matrices in HDF5 format.,Jaw mesenchyme,,Zebrafish embryos are screened for nr5a2:mGFP DBD del+ / scxa:mCherry+ and fin tips are collected for PCR genotyping of oz3 allele mutant and wild type allele control before 2 dpf. Control and mutant heads were decapitated between the eye and ear post anesthesia at 2.5 dpf. Dissected heads twenty heads pre tube were washed twice with fresh and iced Ringer’s solution 116mM NaCl  2.6mM KCl  5mM HEPES  pH 7.0  followed by dissociation at 28.5 °C for 40 min by mechanical   nutating and pipetting every 5 min and enzymatic   in pre warmed protease solution 0.25% trypsin  1 mM EDTA  pH 8.0  and 20 mg/mL Collagenase D from stock of 400 mg/mL Collagenase D in HBSS in PBS until fully dissociated. Dissociation reaction is stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Dissociated cells were collected by centrifugation for 5 min  2000 rpm at 4°C and washed by suspension solution 1% FBS  0.8mM CaCl2  50U/ml Penicillin  0.05mg/ml Streptomycin in Leibovitz Medium twice and filtered by cell strainer before sorting. Live cells were fluorescence activated cell sorted FACS to isolate GFP+ and exclude the cytoplasmic stain Zombie Violet control or nuclear stain DAPI mutant into 0.04% BSA/ PBS at 4°C. Nuclei isolation was performed per manufacturer’s instructions 10X Genomics  protocol CG000169  low cell input protocol with optimalization for zebrafish mesenchyme. FACS cells were pelleted for 15 min  300 rcf at 4oC  and incubated with lysis buffer for 100 s on ice. Isolated nuclei were washed by Wash buffer and Nuclei buffer and checked for nucleus integrity under a fluorescence confocal microscope with DAPI staining before subjected to library construction. To capture accessible chromatin and transcripts from the same cells per manufacturer’s instructions  accessible chromatin regions from isolated nuclei were first targeted and tagged by transposase. Tagged chromatin and ployA mRNA from the same nuclei were pulled down and barcoded with the same sequences within isolated GEMs to achieve single nuclei separation. Chromatin fragments were further indexed with sample specific i7 indexes and linked with Illumina P5 and P7 sequences. Reverse transcription was performed in GEMs to synthesize cDNA from polyA mRNA. cDNAs were further fragmented and indexed with sample specific i7 and i5 indexes and linked with Illumina P5 and P7 sequences. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit.,All experiments on zebrafish Danio rerio were approved by the Institutional Animal Care and Use Committee of the University of Southern California IACUC protocol #20771 and #21151. Zebrafish are raised in vivarium under standard conditions maintained at 28.5°C with health and water conditions monitored daily.,tissue:Jaw mesenchyme|developmental stage:2.5 dpf|genotype:nr5a2:mGFP DBD del/+|transgene1:Tgnr5a2:GFP CAAX DBD delel875|transgene2:Tgscxa:mCherryfb301|facs markers:Zombie  / GFP+,GSM6424703,GSM6424703: Multiome control nr5a2 GFP 2.5dpf head snRNA seq; Danio rerio; RNA Seq,GSM6424703 r1,GSM6424703,1,Zebrafish embryos are screened for nr5a2:mGFP DBD del+ / scxa:mCherry+ and fin tips are collected for PCR genotyping of oz3 allele mutant and wild type allele control before 2 dpf. Control and mutant heads were decapitated between the eye and ear post anesthesia at 2.5 dpf. Dissected heads twenty heads pre tube were washed twice with fresh and iced Ringer's solution 116mM NaCl  2.6mM KCl  5mM HEPES  pH 7.0  followed by dissociation at 28.5 °C for 40 min by mechanical   nutating and pipetting every 5 min and enzymatic   in pre warmed protease solution 0.25% trypsin  1 mM EDTA  pH 8.0  and 20 mg/mL Collagenase D from stock of 400 mg/mL Collagenase D in HBSS in PBS until fully dissociated. Dissociation reaction is stopped by 6X stop solution 6 mM CaCl2 and 30% fetal bovine serum FBS in PBS. Dissociated cells were collected by centrifugation for 5 min  2000 rpm at 4°C and washed by suspension solution 1% FBS  0.8mM CaCl2  50U/ml Penicillin  0.05mg/ml Streptomycin in Leibovitz Medium twice and filtered by cell strainer before sorting. Live cells were fluorescence activated cell sorted FACS to isolate GFP+ and exclude the cytoplasmic stain Zombie Violet control or nuclear stain DAPI mutant into 0.04% BSA/ PBS at 4°C. Nuclei isolation was performed per manufacturer's instructions 10X Genomics  protocol CG000169  low cell input protocol with optimalization for zebrafish mesenchyme. FACS cells were pelleted for 15 min  300 rcf at 4oC  and incubated with lysis buffer for 100 s on ice. Isolated nuclei were washed by Wash buffer and Nuclei buffer and checked for nucleus integrity under a fluorescence confocal microscope with DAPI staining before subjected to library construction. To capture accessible chromatin and transcripts from the same cells per manufacturer's instructions  accessible chromatin regions from isolated nuclei were first targeted and tagged by transposase. Tagged chromatin and ployA mRNA from the same nuclei were pulled down and barcoded with the same sequences within isolated GEMs to achieve single nuclei separation. Chromatin fragments were further indexed with sample specific i7 indexes and linked with Illumina P5 and P7 sequences. Reverse transcription was performed in GEMs to synthesize cDNA from polyA mRNA. cDNAs were further fragmented and indexed with sample specific i7 and i5 indexes and linked with Illumina P5 and P7 sequences. QC of libraries were checked with 4200 TapeStation system and Qubit dsDNA HS assay kit.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP389175,,loader:fastq load.py,Multiome_control_nr5a2_GFP_2.5dpf_head_RNA_S4_L001_R1_001.fastq.gz Multiome_control_nr5a2_GFP_2.5dpf_head_RNA_S4_L001_R2_001.fastq.gz,fastq fastq,64154124610.0,487905462.0,GSM6424703 r1,0:29 1:102.49,A:18612889696;C:13758862487;G:13948126717;T:17774530698;N:59715012,29,102,,,18612889696,13758862487,13948126717,17774530698,59715012,SRX16758026,SRS14385046,SRA1467000,Stem Cell Department at USC,Stem Cell Department at USC,2,0.01181,0.86488,0.00641,0.29997,0.99093,0.80795,0.50941,0.6767,29,102,T,B,sc-like readlen,illumina,hiseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United States,2022-08-01,Hatching,Embryo,Jaw,Surface Structure