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
74455,SRR23804140,SRX19635460,SRS17004492,SRP426651,PRJNA943248,Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Adult Kidney],GSE227115,Transcriptome Analysis,We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry or kdrlflk1:GFP positive cells collected from adult kidneys. Overall design: kdrl:mCherry or kdrl:GFP positive transgenic adult kidneys were dissected  homogenized  filtered  and then 25 000 mCherry+ or GFP+ cells were FACS sorted into PBS. 2 000 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.,parent bioproject:PRJNA510836,,,kdrl:GFP+  adult kidney,GSM7091842,,source name:kdrl:GFP transgenic zebrafish adult kidney wild type|developmental stage:adult|genotype:wild type|tissue:kidney,kdrl:GFP+  adult kidney,the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode,kdrl:GFP transgenic zebrafish adult kidney wild type,No treatments,Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,Transgenic kdrl:GFP or kdrl:GFP zebrafish were grown under standard conditions at 28C in E3 buffer.  Adult kidneys were dissected then homogenized  filtered  and sorted using FACS into PBS  collecting at least 25 000 cells.,developmental stage:adult|genotype:wild type|tissue:kidney,GSM7091842,GSM7091842: kdrl:GFP+  adult kidney; Danio rerio; RNA Seq,GSM7091842 r1,GSM7091842,1,Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP426651,,,FLK-G_Single_Cell_ACTCTAGG.fastq.sorted.fastq.gz,fastq,10648313404.0,80407702.0,GSM7091842 r1,0:132.43,A:3393628100;C:2087372845;G:1953079760;T:3213786135;N:446564,132,,,,3393628100,2087372845,1953079760,3213786135,446564,SRX19635460,SRS17004492,,,"Oncology/Hematology, Boston Children's Hospital",1,0.60891,,0.10525,,0.81903,,0.52577,,150,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,indrops,,United States,2023-03-10,Adult,Adult,Kidney,Renal System
74456,SRR23804141,SRX19635459,SRS17004491,SRP426651,PRJNA943248,Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Adult Kidney],GSE227115,Transcriptome Analysis,We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry or kdrlflk1:GFP positive cells collected from adult kidneys. Overall design: kdrl:mCherry or kdrl:GFP positive transgenic adult kidneys were dissected  homogenized  filtered  and then 25 000 mCherry+ or GFP+ cells were FACS sorted into PBS. 2 000 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.,parent bioproject:PRJNA510836,,,kdrl:mCherry+  adult kidney  rep2,GSM7091841,,source name:kdrl:mCherry transgenic zebrafish adult kidney wild type|developmental stage:adult|genotype:wild type|tissue:kidney,kdrl:mCherry+  adult kidney  rep2,the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode,kdrl:mCherry transgenic zebrafish adult kidney wild type,No treatments,Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,Transgenic kdrl:GFP or kdrl:GFP zebrafish were grown under standard conditions at 28C in E3 buffer.  Adult kidneys were dissected then homogenized  filtered  and sorted using FACS into PBS  collecting at least 25 000 cells.,developmental stage:adult|genotype:wild type|tissue:kidney,GSM7091841,GSM7091841: kdrl:mCherry+  adult kidney  rep2; Danio rerio; RNA Seq,GSM7091841 r1,GSM7091841,1,Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP426651,,,FLK-R_Single_Cell_CTAGTCGA.fastq.sorted.fastq.gz,fastq,13922952441.0,105098464.0,GSM7091841 r1,0:132.48,A:4341235438;C:2807868369;G:2579519980;T:4193742000;N:586654,132,,,,4341235438,2807868369,2579519980,4193742000,586654,SRX19635459,SRS17004491,,,"Oncology/Hematology, Boston Children's Hospital",1,0.64512,,0.12315,,0.81712,,0.52922,,100,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,indrops,,United States,2023-03-10,Adult,Adult,Kidney,Renal System
74457,SRR23804142,SRX19635458,SRS17004490,SRP426651,PRJNA943248,Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Adult Kidney],GSE227115,Transcriptome Analysis,We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry or kdrlflk1:GFP positive cells collected from adult kidneys. Overall design: kdrl:mCherry or kdrl:GFP positive transgenic adult kidneys were dissected  homogenized  filtered  and then 25 000 mCherry+ or GFP+ cells were FACS sorted into PBS. 2 000 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.,parent bioproject:PRJNA510836,,,kdrl:mCherry+  adult kidney  rep1,GSM7091840,,source name:kdrl:mCherry transgenic zebrafish adult kidney wild type|developmental stage:adult|genotype:wild type|tissue:kidney,kdrl:mCherry+  adult kidney  rep1,the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode,kdrl:mCherry transgenic zebrafish adult kidney wild type,No treatments,Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,Transgenic kdrl:GFP or kdrl:GFP zebrafish were grown under standard conditions at 28C in E3 buffer.  Adult kidneys were dissected then homogenized  filtered  and sorted using FACS into PBS  collecting at least 25 000 cells.,developmental stage:adult|genotype:wild type|tissue:kidney,GSM7091840,GSM7091840: kdrl:mCherry+  adult kidney  rep1; Danio rerio; RNA Seq,GSM7091840 r1,GSM7091840,1,Approximately 2 000 3 000 kdrl:mCherry or kdrl:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP426651,,,KLR_Single_Cell_ATTAGACG.fastq.sorted.fastq.gz,fastq,8774502682.0,64692571.0,GSM7091840 r1,0:135.63,A:2791773089;C:1725088037;G:1633088372;T:2624197073;N:356111,135,,,,2791773089,1725088037,1633088372,2624197073,356111,SRX19635458,SRS17004490,,,"Oncology/Hematology, Boston Children's Hospital",1,0.66981,,0.10372,,0.81357,,0.5394,,38,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,indrops,,United States,2023-03-10,Adult,Adult,Kidney,Renal System
74458,SRR23802705,SRX19634573,SRS17003744,SRP426627,PRJNA943249,Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Embryo Niche],GSE227117,Transcriptome Analysis,We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry and mrc1a.125:GFP double positive cells collected from whole embryos at 72 hpf. Overall design: kdrl:mCherry and mrc1a.125:GFP double positive transgenic embryos were homogenized  filtered  and then 25 000 GFP+ cells were FACS sorted into PBS. 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.,parent bioproject:PRJNA510836,,,kdrl:GFP+  mrc1a.125:GFP+ 72 hpf  rep2,GSM7091919,,source name:kdrl:GFP  mrc1a.125:GFP transgenic zebrafish embryos wild type|tissue:embryos|genotype:wild type,kdrl:GFP+  mrc1a.125:GFP+ 72 hpf  rep2,the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode,kdrl:GFP  mrc1a.125:GFP transgenic zebrafish embryos wild type,No treatments,Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,Double transgenic kdrl:mCherry and mrc1a.125:GFP zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were screened for transgene expression and then homogenized  filtered  and sorted using FACS into PBS  collecting at least 25 000 cells.,tissue:embryos|genotype:wild type,GSM7091919,GSM7091919: kdrl:GFP+  mrc1a.125:GFP+ 72 hpf  rep2; Danio rerio; RNA Seq,GSM7091919 r1,GSM7091919,1,Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP426627,,,GR4_Single_Cell_TCTTACGC.fastq.sorted.fastq.gz,fastq,13661225700.0,102550405.0,GSM7091919 r1,0:133.21,A:4263167363;C:2771561232;G:2605236063;T:4020689114;N:571928,133,,,,4263167363,2771561232,2605236063,4020689114,571928,SRX19634573,SRS17003744,,,"Oncology/Hematology, Boston Children's Hospital",1,0.64929,,0.08349,,0.80462,,0.50638,,149,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,indrops,,United States,2023-03-10,Larval,Larval,Embryo Imprecise,All anatomical structures
74459,SRR23802706,SRX19634572,SRS17003743,SRP426627,PRJNA943249,Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Embryo Niche],GSE227117,Transcriptome Analysis,We report single cell gene expression data for FACS isolated zebrafish kdrlflk1:mCherry and mrc1a.125:GFP double positive cells collected from whole embryos at 72 hpf. Overall design: kdrl:mCherry and mrc1a.125:GFP double positive transgenic embryos were homogenized  filtered  and then 25 000 GFP+ cells were FACS sorted into PBS. 3 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.,parent bioproject:PRJNA510836,,,kdrl:GFP+  mrc1a.125:GFP+ 72 hpf  rep1,GSM7091918,,source name:kdrl:GFP  mrc1a.125:GFP transgenic zebrafish embryos wild type|tissue:embryos|genotype:wild type,kdrl:GFP+  mrc1a.125:GFP+ 72 hpf  rep1,the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode,kdrl:GFP  mrc1a.125:GFP transgenic zebrafish embryos wild type,No treatments,Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,Double transgenic kdrl:mCherry and mrc1a.125:GFP zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were screened for transgene expression and then homogenized  filtered  and sorted using FACS into PBS  collecting at least 25 000 cells.,tissue:embryos|genotype:wild type,GSM7091918,GSM7091918: kdrl:GFP+  mrc1a.125:GFP+ 72 hpf  rep1; Danio rerio; RNA Seq,GSM7091918 r1,GSM7091918,1,Approximately 3 000 kdrl:GFP+ and mrc1a.125:GFP+ cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP426627,,,GR_Single_Cell_AGGCTTAG.fastq.sorted.fastq.gz,fastq,15177402828.0,110023820.0,GSM7091918 r1,0:137.95,A:4661865038;C:2940634835;G:2919070311;T:4655218796;N:613848,137,,,,4661865038,2940634835,2919070311,4655218796,613848,SRX19634572,SRS17003743,,,"Oncology/Hematology, Boston Children's Hospital",1,0.73316,,0.12888,,0.79594,,0.5247,,127,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,indrops,,United States,2023-03-10,Larval,Larval,Embryo Imprecise,All anatomical structures
74460,SRR23802569,SRX19634451,SRS17003621,SRP426621,PRJNA943252,Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail],GSE227118,Other,We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized  filtered  and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.,parent bioproject:PRJNA510836,,,Whole tail  72 hpf,GSM7091920,,source name:transgenic zebrafish embryos wild type|tissue:Whole tail|developmental stage:72 hpf,Whole tail  72 hpf,the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode,transgenic zebrafish embryos wild type,No treatments,Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were bisected on the axial plane towards the caudal end of the yolk extension  tail tissues were then homogenized  filtered  and viable cells sorted using live dead staining FACS into PBS  collecting at least 25 000 cells.,tissue:Whole tail|developmental stage:72 hpf,GSM7091920,GSM7091920: Whole tail  72 hpf; Danio rerio; RNA Seq,GSM7091920 r1,GSM7091920,1,Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP426621,,,EH_Tails_Single_Cell_GAGACGGA_L001.fastq.sorted.fastq.gz,fastq,715456535.0,12017381.0,GSM7091920 r1,0:59.54,A:205982879;C:141307848;G:135221384;T:232940601;N:3823,59,,,,205982879,141307848,135221384,232940601,3823,SRX19634451,SRS17003621,,,"Oncology/Hematology, Boston Children's Hospital",1,0.88315,,0.14516,,0.78257,,0.49661,,61,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,indrops,,United States,2023-03-10,Larval,Larval,Tail,Multi-system
74461,SRR23802570,SRX19634451,SRS17003621,SRP426621,PRJNA943252,Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail],GSE227118,Other,We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized  filtered  and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.,parent bioproject:PRJNA510836,,,Whole tail  72 hpf,GSM7091920,,source name:transgenic zebrafish embryos wild type|tissue:Whole tail|developmental stage:72 hpf,Whole tail  72 hpf,the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode,transgenic zebrafish embryos wild type,No treatments,Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were bisected on the axial plane towards the caudal end of the yolk extension  tail tissues were then homogenized  filtered  and viable cells sorted using live dead staining FACS into PBS  collecting at least 25 000 cells.,tissue:Whole tail|developmental stage:72 hpf,GSM7091920,GSM7091920: Whole tail  72 hpf; Danio rerio; RNA Seq,GSM7091920 r1,GSM7091920,1,Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP426621,,,EH_Tails_Single_Cell_GAGACGGA_L002.fastq.sorted.fastq.gz,fastq,589786185.0,9927008.0,GSM7091920 r2,0:59.41,A:170171480;C:115960508;G:111370241;T:192283114;N:842,59,,,,170171480,115960508,111370241,192283114,842,SRX19634451,SRS17003621,,,"Oncology/Hematology, Boston Children's Hospital",1,0.88418,,0.1452,,0.78173,,0.48617,,61,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,indrops,,United States,2023-03-10,Larval,Larval,Tail,Multi-system
74462,SRR23802571,SRX19634451,SRS17003621,SRP426621,PRJNA943252,Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail],GSE227118,Other,We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized  filtered  and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.,parent bioproject:PRJNA510836,,,Whole tail  72 hpf,GSM7091920,,source name:transgenic zebrafish embryos wild type|tissue:Whole tail|developmental stage:72 hpf,Whole tail  72 hpf,the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode,transgenic zebrafish embryos wild type,No treatments,Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were bisected on the axial plane towards the caudal end of the yolk extension  tail tissues were then homogenized  filtered  and viable cells sorted using live dead staining FACS into PBS  collecting at least 25 000 cells.,tissue:Whole tail|developmental stage:72 hpf,GSM7091920,GSM7091920: Whole tail  72 hpf; Danio rerio; RNA Seq,GSM7091920 r1,GSM7091920,1,Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP426621,,,EH_Tails_Single_Cell_GAGACGGA_L003.fastq.sorted.fastq.gz,fastq,683131915.0,11477240.0,GSM7091920 r3,0:59.52,A:196805573;C:134822600;G:129142852;T:222358115;N:2775,59,,,,196805573,134822600,129142852,222358115,2775,SRX19634451,SRS17003621,,,"Oncology/Hematology, Boston Children's Hospital",1,0.88169,,0.14457,,0.78054,,0.49459,,61,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,indrops,,United States,2023-03-10,Larval,Larval,Tail,Multi-system
74463,SRR23802572,SRX19634451,SRS17003621,SRP426621,PRJNA943252,Transcription factor induction of vascular blood stem cell niches in vivo [scRNA Seq.Whole tail],GSE227118,Other,We report single cell gene expression data for caudal tail tissue cells collected from embryos at 72 hpf. Overall design: Wild type embryos were homogenized  filtered  and then 25 000 live cells were FACS sorted into PBS. 5 000 cells were then encapsulated using the inDrops method and libraries were prepared for sequencing.,parent bioproject:PRJNA510836,,,Whole tail  72 hpf,GSM7091920,,source name:transgenic zebrafish embryos wild type|tissue:Whole tail|developmental stage:72 hpf,Whole tail  72 hpf,the inDrops single cell RNA seq analysis follows the instruction as descriibed in https://github.com/indrops/indrops. inDrops Library v3 requires manual demultiplex raw bcl into different samples. Zebrafish Bowtie transcriptome index was build based on Ensembl GRCz10 genome sequenc and gene annotation. Assembly: GRCz11 Supplementary files format and content: The output data matrix contains the raw count of each gene for each cell barcode,transgenic zebrafish embryos wild type,No treatments,Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,Wild type zebrafish embryos were grown under standard conditions at 28C in E3 buffer until 72 hpf.  Embryos were bisected on the axial plane towards the caudal end of the yolk extension  tail tissues were then homogenized  filtered  and viable cells sorted using live dead staining FACS into PBS  collecting at least 25 000 cells.,tissue:Whole tail|developmental stage:72 hpf,GSM7091920,GSM7091920: Whole tail  72 hpf; Danio rerio; RNA Seq,GSM7091920 r1,GSM7091920,1,Approximately 5 000 cells were encapsulated using the inDrops method Zilionis et al.  2017. Libraries were prepared for sequencing as previously described. Libraries were prepared as previously described Zilionis et al.  2017 and sequenced on an Illumina Hiseq 2500 Single cell RNA seq inDrops,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 4000,,SRP426621,,,EH_Tails_Single_Cell_GAGACGGA_L004.fastq.sorted.fastq.gz,fastq,584432554.0,9840065.0,GSM7091920 r4,0:59.39,A:168684456;C:114891950;G:110562368;T:190292465;N:1315,59,,,,168684456,114891950,110562368,190292465,1315,SRX19634451,SRS17003621,,,"Oncology/Hematology, Boston Children's Hospital",1,0.88266,,0.14397,,0.78001,,0.49223,,61,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,indrops,,United States,2023-03-10,Larval,Larval,Tail,Multi-system
75092,SRR24239717,SRX20035842,SRS17374857,SRP433739,PRJNA958104,The secreted neuronal signal Spock1 regulates the blood brain barrier,GSE230236,Transcriptome Analysis,The blood brain barrier BBB is a unique set of properties of the brain vasculature which severely restricts its permeability to proteins and small molecules. Classic chick quail chimera studies showed that these properties are not intrinsic to the brain vasculature but rather are induced by surrounding neural tissue. Here we identify Spock1 as a candidate neuronal signal for regulating BBB permeability in zebrafish and mice. Mosaic genetic analysis shows that neuronally expressed Spock1 is cell non autonomously required for a functional BBB. Leakage in spock1 mutants is associated with altered extracellular matrix ECM  increased endothelial transcytosis  and altered pericyte endothelial interactions. Furthermore  a single dose of recombinant SPOCK1  into spock1 mutants quenches gelatinase activity  restores vascular expression of BBB genes including mcamb   and partially restores barrier function. These analyses support a model in which neuronally secreted Spock1 induces BBB properties by altering the ECM  thereby regulating pericyte endothelial interactions and downstream vascular gene expression. Overall design: Bulk RNAseq Libraries 66 71 of leaky mutant and wild type siblings to identify the genetic lesion responsible for the leaky phenotype. These analyses revealed linkage to chr14  and more specifically to the spock1 gene. scRNAseq Library scDRBrain of dissected spock1 mutant and wild type brains was then used to identify all cell type specific changes in gene expression in the mutant background.,,pubmed:37437574,,scRNA seq for WT and hm41 larval heads  3 and 5dpf,GSM7208220,,tissue:mixed|cell type:mixed|genotype:mixed|time:3 dpf  5 dpf|geo loc name:missing|collection date:missing,scRNA seq for WT and hm41 larval heads  3 and 5dpf,Sequencing reads were mapped to the Zebrafish GRCz11 R101 genome assembly using a custom python pipeline as previously described see Zilionis et al.  Nature Protocols 2017 and https://github.com/indrops/. Multi seq hashtags were identified using custom code available at: https://github.com/AllonKleinLab/klunctions/tree/master/Ignas/Hashing. We first removed background cell barcodes by only considering transcriptomes with greater than 350 UMIs for downstream analysis. In order to remove dead cells  transcriptomes were further filtered by mitochondrial read percentage >20%. Cell demultiplexing was performed by manual inspection. Specifically  thresholds were drawn to delineate single cells from background and multiplet populations. The resulting counts matrix was normalized to the mean UMIs per cell in the dataset. Assembly: GRCz11 Supplementary files format and content: The gene counts matrix is an output from rsem differential gene expression analysis and is a raw counts estimate   not normalized for each gene. The first column is gene name and then post that each column represents an individual sample WT for the first 3 and then MUT for the last 3. Supplementary files format and content: The h5ad file contains the counts matrix for the demultiplexed single cell data. This file also holds relevant genotype and timepoint annotations as well as Multi seq barcode counts for each cell.,mixed,,Dissected brain tissues were dissociated using a modified protocol adapted from Bresciani et. al. 2018 PMID: 30364607. Briefly  chemical dissociations were performed at 30.5°C using a mixture of 0.25% Trypsin EDTA  Collagenase/Dispase 8 mg/mL and DNaseI 20 µg/mL for 15 20 minutes with gentle pipetting every 2.5 minutes. The dissociations were quenched using DMEM + 10% fetal bovine serum and filtered through a 40 µM cell strainer. The dissociation mixtures were spun down twice at 700g for 5 min and washed with PBS. The mixtures were then resuspended in PBS and barcoded using Multi seq as described in McGinnis et. al. 2019 PMID: 31209384 with slight modifications. For each sample  80 pmoles of Lipid modified oligos LMOs were used to hash every 500k cells. The hashing reaction was quenched using PBS + 1% BSA. The barcoded samples were pooled into a single tube and washed twice with PBS + 1% BSA 700g for 5 min.. The pooled cell mixture was resuspended in PBS + 0.1%BSA + 18% Optiprep at a final concentration of 300k cells/mL prior to single cell capture with inDrops. Single cell transcriptomes were captured by the Single cell Core SCC at the Harvard Medical School as previously described Zilionis et al.  Nature Protocols 2017 using the inDrops V3 chemistry. The Single cell Core at the Harvard Medical School prepared the gene expression inDrops v3 chemistry and Multi seq libraries.,,cell type:mixed|genotype:mixed|time:3 dpf  5 dpf,GSM7208220,GSM7208220: scRNA seq for WT and hm41 larval heads  3 and 5dpf; Danio rerio; RNA Seq,GSM7208220 r1,GSM7208220,1,Dissected brain tissues were dissociated using a modified protocol adapted from Bresciani et. al. 2018 PMID: 30364607. Briefly  chemical dissociations were performed at 30.5°C using a mixture of 0.25% Trypsin EDTA  Collagenase/Dispase 8 mg/mL and DNaseI 20 µg/mL for 15 20 minutes with gentle pipetting every 2.5 minutes. The dissociations were quenched using DMEM + 10% fetal bovine serum and filtered through a 40 µM cell strainer. The dissociation mixtures were spun down twice at 700g for 5 min and washed with PBS. The mixtures were then resuspended in PBS and barcoded using Multi seq as described in McGinnis et. al. 2019 PMID: 31209384 with slight modifications. For each sample  80 pmoles of Lipid modified oligos LMOs were used to hash every 500k cells. The hashing reaction was quenched using PBS + 1% BSA. The barcoded samples were pooled into a single tube and washed twice with PBS + 1% BSA 700g for 5 min.. The pooled cell mixture was resuspended in PBS + 0.1%BSA + 18% Optiprep at a final concentration of 300k cells/mL prior to single cell capture with inDrops. Single cell transcriptomes were captured by the Single cell Core SCC at the Harvard Medical School as previously described Zilionis et al.  Nature Protocols 2017 using the inDrops V3 chemistry. The Single cell Core at the Harvard Medical School prepared the gene expression inDrops v3 chemistry and Multi seq libraries.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP433739,,loader:fastq load.py|options:  readTypes=BTBT   read1PairFiles=Undetermined S0 L001 R1 001.fastq.gz   read2PairFiles=Undetermined S0 L001 R2 001.fastq.gz   read3PairFiles=Undetermined S0 L001 R3 001.fastq.gz   read4PairFiles=Undetermined S0 L001 R4 001.fastq.gz,,,548653863228.0,4729774683.0,GSM7208220 r1,,,,,,,,,,,,SRX20035842,SRS17374857,SRA1728506,"Megason Lab, Systems Biology, Harvard Medical School","Megason Lab, Systems Biology, Harvard Medical School",2,0.83589,0.0,0.23127,0.0,0.7723,1.0,0.46689,,86,8,B,T,sc-like readlen,illumina,novaseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,indrops,,United States,2023-04-21,Larval,Larval,Multi-tissue,Multi-system