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
10186,ERR6212423,ERX5847531,ERS7094943,ERP130388,PRJEB46176,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10379_3,Transcriptome Analysis,To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution  we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Naive,SAMEA9361876,University Of Edinburgh,ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361876|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Naive|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|organism part:spinal cord|sample name:E MTAB 10379 3:Naive|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10379 3:Naive p,Naive p,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP130388,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,Mpeg_Naive_I1.fastq.gz Mpeg_Naive_R1.fastq.gz Mpeg_Naive_R2.fastq.gz,fastq fastq fastq,60168324125.0,481346593.0,E MTAB 10379 3:Naive,0:8 1:27 2:90,A:12424400694;C:9366563781;G:10029312355;T:11497237299;N:3679241,8,27,90,,12424400694,9366563781,10029312355,11497237299,3679241,ERX5847531,ERS7094943,ERA5186263,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.94834,,0.09482,,0.802,,0.5277,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-07-08,Larval,Larval,Multi-tissue,Multi-system
10187,ERR6212422,ERX5847530,ERS7094942,ERP130388,PRJEB46176,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,E-MTAB-10379_3,Transcriptome Analysis,To analyse lesion induced gene regulation in macrophage and microglia at single cell resolution  we performed single cell RNAseq on FACS isolated mpeg1.1:GFP cells from the spinal cord at 24 hours post lesion hpl post spinal injury at 3 dpf dpf  compared to age matched uninjured animals.,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,,Protocols: Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Lesi1d,SAMEA9361875,University Of Edinburgh,ENA first public:2021 07 08|ENA last update:2021 07 08|External Id:SAMEA9361875|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 07 08T11:18:57Z|INSDC last update:2021 07 08T11:18:57Z|INSDC status:public|Submitter Id:E MTAB 10379 3:Lesi1d|age:4|broker name:ArrayExpress|cell type:mixed macrophage and microglia|common name:zebrafish|developmental stage:larval day 4|immunophenotype:mpeg1.1 positive|injury:spinal cord lesion|organism part:spinal cord|sample name:E MTAB 10379 3:Lesi1d|sex:mixed|strain:WIK,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesi1d and unlesi1d zebrafish larvae spinal cord,E MTAB 10379 3:Lesioned p,Lesioned p,scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,Trunks containing the lesion sites or equivalent site from unlesioned fish are collected and kept in PBS on ice.Incubate the trunks up to 300 in 1 mL of 1X Trypsin EDTA at 37C for 5 7 mins.Stop dissociation by adding FBS to a final concentration of 5%.Centrifuge at 200g for 7 mins.Discard Sups.Resuspend in 500 uL of PBS.Add the cell suspension into a 40 uM cell strainer.Centrifuge at 200g for 7 mins.Resuspend in the buffer for FACS PBS 5% FBS Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines  Following cell dissociation and FAC sorting  samples were processed on the 10X Chromium platform using 10X Single Cell three prime v3 chemistry following the manufacturer's guidelines,Experimental Factor: injury:spinal cord lesion,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,Oligo-dT,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP130388,Illumina NovaSeq 6000 sequencing; scRNAseq of mpeg1.1+ cells from lesioned and unlesioned zebrafish larvae spinal cord,ENA FIRST PUBLIC:2021 07 08|ENA LAST UPDATE:2021 07 08,Mpeg_Lesioned_I1.fastq.gz Mpeg_Lesioned_R1.fastq.gz Mpeg_Lesioned_R2.fastq.gz,fastq fastq fastq,61701873000.0,493614984.0,E MTAB 10379 3:Lesioned,0:8 1:27 2:90,A:12952533019;C:9222397450;G:9920185920;T:12326470894;N:3761277,8,27,90,,12952533019,9222397450,9920185920,12326470894,3761277,ERX5847530,ERS7094942,ERA5186263,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,1,0.93082,,0.10862,,0.80302,,0.54924,,90,,B,,usable mapping rate,illumina,novaseq_era,unknown,poly_a,unknown,sc,single_cell_droplet,10x,,United Kingdom,2021-07-08,Larval,Larval,Multi-tissue,Multi-system
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