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52 rows where experiment.library_selection = "cDNA", technology = "celseq" and tissue_curation = "Multi-tissue"

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devstage_curation_coarse 2

devstage_curation 2

tissue_curation_coarse 1

tissue_curation 1

  • Multi-tissue · 52 ✖

technology 1

  • celseq · 52 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

  • cDNA · 52 ✖

experiment.library_layout 1

Link 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
47881 47881 SRR6908731 SRX3856805 SRS3100397 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM8 eosinophils and lymphocytes GSM3070143   tissue:WKM8 eosinophils and lymphocytes|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM8 eosinophils and lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM8 eosinophils and lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070143 GSM3070143: WKM8 eosinophils and lymphocytes; Danio rerio; RNA Seq GSM3070143   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070143 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM8_eosinophils_and_lymphocytes_L001_R2_001.fastq.gz WKM8_eosinophils_and_lymphocytes_L001_R1_001.fastq.gz fastq fastq 1375061469.0 9111725.0 GSM3070143 r1 0:75.43 1:75.48 A:397639171;C:207855377;G:230813601;T:538747052;N:6268 75 75     397639171 207855377 230813601 538747052 6268 SRX3856805 SRS3100397 SRA675960 GEO Hubrecht Institute 2 0.4147 0.81295 0.33835 0.48636 0.94951 0.85942 0.48903 0.52414 76 75 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Multi-tissue Multi-system
47882 47882 SRR6908732 SRX3856805 SRS3100397 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM8 eosinophils and lymphocytes GSM3070143   tissue:WKM8 eosinophils and lymphocytes|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM8 eosinophils and lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM8 eosinophils and lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070143 GSM3070143: WKM8 eosinophils and lymphocytes; Danio rerio; RNA Seq GSM3070143   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070143 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM8_eosinophils_and_lymphocytes_L002_R1_001.fastq.gz WKM8_eosinophils_and_lymphocytes_L002_R2_001.fastq.gz fastq fastq 1349675695.0 8943335.0 GSM3070143 r2 0:75.43 1:75.48 A:387332778;C:203252981;G:231137130;T:527949327;N:3479 75 75     387332778 203252981 231137130 527949327 3479 SRX3856805 SRS3100397 SRA675960 GEO Hubrecht Institute 2 0.40287 0.80137 0.3286 0.47191 0.95446 0.86354 0.4748 0.49423 76 74 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Multi-tissue Multi-system
47883 47883 SRR6908733 SRX3856805 SRS3100397 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM8 eosinophils and lymphocytes GSM3070143   tissue:WKM8 eosinophils and lymphocytes|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM8 eosinophils and lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM8 eosinophils and lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070143 GSM3070143: WKM8 eosinophils and lymphocytes; Danio rerio; RNA Seq GSM3070143   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070143 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM8_eosinophils_and_lymphocytes_L003_R1_001.fastq.gz WKM8_eosinophils_and_lymphocytes_L003_R2_001.fastq.gz fastq fastq 1228039195.0 8136994.0 GSM3070143 r3 0:75.44 1:75.48 A:352677291;C:185534334;G:208351378;T:481454385;N:21807 75 75     352677291 185534334 208351378 481454385 21807 SRX3856805 SRS3100397 SRA675960 GEO Hubrecht Institute 2 0.40303 0.80734 0.33097 0.48111 0.95812 0.86709 0.47702 0.5199 76 75 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Multi-tissue Multi-system
47884 47884 SRR6908734 SRX3856805 SRS3100397 SRP136633 PRJNA446034 Cell type purification by single cell transcriptome trained sorting GSE112438 Other Traditional cell type enrichment using fluorescence activated cell sorting FACS relies on methods that specifically label the cell type of interest. Here we propose GateID a computational method that combines single cell transcriptomics for unbiased cell type identification with FACS index sorting to purify cell types of choice. We validate GateID by purifying various cell types from the zebrafish kidney marrow and the human pancreas without xxx to specific antibodies or transgenes. Overall design: Single cell mRNA sequencing data of unenriched and enriched cells from zebrafish whole kidney marrow and human pancreas using GateID. For each cell we provide libraries with transcriptome information. An unenriched sample is transcriptome data from a live single cell FACS sort while an enriched library has transcriptome data for GateID enriched single cells for a given cell type.   pubmed:31585086   WKM8 eosinophils and lymphocytes GSM3070143   tissue:WKM8 eosinophils and lymphocytes|FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:lymphocytes WKM8 eosinophils and lymphocytes In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Multimappers are not considered as valid. The cell specific barcode file is added as a part of processed data files. Genome build: All transcriptome libraries were mapped to Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: Tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID. The cell specific barcode file is provided in the celseq2 bc.csv.gz 1st column represents index of the cell specific barcode and the second column is the barcode WKM8 eosinophils and lymphocytes   post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters   FISHid:WKM8|cell type:whole kidney marrow single cells|cell subtype:lymphocytes GSM3070143 GSM3070143: WKM8 eosinophils and lymphocytes; Danio rerio; RNA Seq GSM3070143   1 post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for mRNA detection Spike in controls and and RNAse inhibitor. cellseq2 Illumina TruSeq adapaters GEO Accession:GSM3070143 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP136633     WKM8_eosinophils_and_lymphocytes_L004_R1_001.fastq.gz WKM8_eosinophils_and_lymphocytes_L004_R2_001.fastq.gz fastq fastq 1192405777.0 7901058.0 GSM3070143 r4 0:75.44 1:75.48 A:341927110;C:179070080;G:204590907;T:466800667;N:17013 75 75     341927110 179070080 204590907 466800667 17013 SRX3856805 SRS3100397 SRA675960 GEO Hubrecht Institute 2 0.40935 0.80524 0.33588 0.48 0.95899 0.87377 0.47516 0.52985 75 75 T B mate1 technical by mapping diff illumina nextseq unknown random_priming trueseq sc single_cell_plate celseq   Netherlands 2018-03-28 Undetermined Undetermined Multi-tissue Multi-system
63260 63260 SRR13724987 SRX10113011 SRS8268907 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 26 GSM5087790   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 26 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11|genotype or treatment see plate layout:LY294002 treated GSM5087790 GSM5087790: SBF 26; Danio rerio; RNA Seq GSM5087790   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087790 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-026_HNN3JBGXC_S4_L001_R1_001.fastq.gz HUB-SF-026_HNN3JBGXC_S4_L001_R2_001.fastq.gz fastq fastq 724015252.0 8418782.0 GSM5087790 r1 0:26 1:60 A:181448033;C:140181369;G:139987828;T:262155531;N:242491 26 60     181448033 140181369 139987828 262155531 242491 SRX10113011 SRS8268907 SRA1196923 GEO Hubrecht Institute 2 0.10352 0.78777 0.09808 0.22696 0.99078 0.81389 0.60135 0.52625 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63261 63261 SRR13724988 SRX10113011 SRS8268907 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 26 GSM5087790   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 26 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11|genotype or treatment see plate layout:LY294002 treated GSM5087790 GSM5087790: SBF 26; Danio rerio; RNA Seq GSM5087790   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087790 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-026_HNN3JBGXC_S4_L002_R1_001.fastq.gz HUB-SF-026_HNN3JBGXC_S4_L002_R2_001.fastq.gz fastq fastq 710763770.0 8264695.0 GSM5087790 r2 0:26 1:60 A:177328072;C:137060064;G:139543912;T:256619367;N:212355 26 60     177328072 137060064 139543912 256619367 212355 SRX10113011 SRS8268907 SRA1196923 GEO Hubrecht Institute 2 0.10309 0.78735 0.09769 0.22712 0.9907 0.81434 0.59399 0.51403 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63262 63262 SRR13724989 SRX10113011 SRS8268907 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 26 GSM5087790   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 26 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11|genotype or treatment see plate layout:LY294002 treated GSM5087790 GSM5087790: SBF 26; Danio rerio; RNA Seq GSM5087790   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087790 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-026_HNN3JBGXC_S4_L003_R1_001.fastq.gz HUB-SF-026_HNN3JBGXC_S4_L003_R2_001.fastq.gz fastq fastq 733552222.0 8529677.0 GSM5087790 r3 0:26 1:60 A:183770046;C:141936571;G:141851405;T:265713964;N:280236 26 60     183770046 141936571 141851405 265713964 280236 SRX10113011 SRS8268907 SRA1196923 GEO Hubrecht Institute 2 0.10305 0.78993 0.0974 0.22773 0.99058 0.81477 0.59145 0.52341 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63263 63263 SRR13724990 SRX10113011 SRS8268907 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 26 GSM5087790   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 26 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11|genotype or treatment see plate layout:LY294002 treated GSM5087790 GSM5087790: SBF 26; Danio rerio; RNA Seq GSM5087790   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087790 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-026_HNN3JBGXC_S4_L004_R1_001.fastq.gz HUB-SF-026_HNN3JBGXC_S4_L004_R2_001.fastq.gz fastq fastq 721320614.0 8387449.0 GSM5087790 r4 0:26 1:60 A:179946156;C:139058546;G:141752407;T:260320288;N:243217 26 60     179946156 139058546 141752407 260320288 243217 SRX10113011 SRS8268907 SRA1196923 GEO Hubrecht Institute 2 0.10209 0.7864 0.09672 0.22655 0.99088 0.81688 0.56585 0.52923 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63264 63264 SRR13724983 SRX10113010 SRS8268906 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 25 GSM5087789   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 25 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11 and 12|genotype or treatment see plate layout:LY294002 treated GSM5087789 GSM5087789: SBF 25; Danio rerio; RNA Seq GSM5087789   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087789 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-025_HNN3JBGXC_S3_L001_R1_001.fastq.gz HUB-SF-025_HNN3JBGXC_S3_L001_R2_001.fastq.gz fastq fastq 563057824.0 6547184.0 GSM5087789 r1 0:26 1:60 A:133647343;C:107580359;G:102130933;T:219507850;N:191339 26 60     133647343 107580359 102130933 219507850 191339 SRX10113010 SRS8268906 SRA1196923 GEO Hubrecht Institute 2 0.09959 0.88637 0.09191 0.22223 0.98841 0.7893 0.60149 0.5034 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63265 63265 SRR13724984 SRX10113010 SRS8268906 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 25 GSM5087789   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 25 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11 and 12|genotype or treatment see plate layout:LY294002 treated GSM5087789 GSM5087789: SBF 25; Danio rerio; RNA Seq GSM5087789   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087789 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-025_HNN3JBGXC_S3_L002_R1_001.fastq.gz HUB-SF-025_HNN3JBGXC_S3_L002_R2_001.fastq.gz fastq fastq 554827796.0 6451486.0 GSM5087789 r2 0:26 1:60 A:131279108;C:105552087;G:102233068;T:215597875;N:165658 26 60     131279108 105552087 102233068 215597875 165658 SRX10113010 SRS8268906 SRA1196923 GEO Hubrecht Institute 2 0.09895 0.88574 0.09115 0.22146 0.98849 0.79048 0.60201 0.50402 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63266 63266 SRR13724985 SRX10113010 SRS8268906 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 25 GSM5087789   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 25 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11 and 12|genotype or treatment see plate layout:LY294002 treated GSM5087789 GSM5087789: SBF 25; Danio rerio; RNA Seq GSM5087789   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087789 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-025_HNN3JBGXC_S3_L003_R1_001.fastq.gz HUB-SF-025_HNN3JBGXC_S3_L003_R2_001.fastq.gz fastq fastq 572299814.0 6654649.0 GSM5087789 r3 0:26 1:60 A:135756854;C:109312452;G:103917320;T:223090484;N:222704 26 60     135756854 109312452 103917320 223090484 222704 SRX10113010 SRS8268906 SRA1196923 GEO Hubrecht Institute 2 0.09998 0.88647 0.09216 0.22088 0.98841 0.7881 0.56617 0.49783 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63267 63267 SRR13724986 SRX10113010 SRS8268906 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 25 GSM5087789   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 25 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11 and 12|genotype or treatment see plate layout:LY294002 treated GSM5087789 GSM5087789: SBF 25; Danio rerio; RNA Seq GSM5087789   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087789 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-025_HNN3JBGXC_S3_L004_R1_001.fastq.gz HUB-SF-025_HNN3JBGXC_S3_L004_R2_001.fastq.gz fastq fastq 561898716.0 6533706.0 GSM5087789 r4 0:26 1:60 A:132858077;C:106892850;G:103648903;T:218299356;N:199530 26 60     132858077 106892850 103648903 218299356 199530 SRX10113010 SRS8268906 SRA1196923 GEO Hubrecht Institute 2 0.09901 0.88605 0.09109 0.22144 0.98965 0.79074 0.51912 0.50131 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63268 63268 SRR13724979 SRX10113009 SRS8268905 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 24 GSM5087788   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 24 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11|genotype or treatment see plate layout:LY294002 treated GSM5087788 GSM5087788: SBF 24; Danio rerio; RNA Seq GSM5087788   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087788 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-024_HNN3JBGXC_S2_L001_R1_001.fastq.gz HUB-SF-024_HNN3JBGXC_S2_L001_R2_001.fastq.gz fastq fastq 453515324.0 5273434.0 GSM5087788 r1 0:26 1:60 A:109074977;C:85225133;G:81350727;T:177710223;N:154264 26 60     109074977 85225133 81350727 177710223 154264 SRX10113009 SRS8268905 SRA1196923 GEO Hubrecht Institute 2 0.10905 0.86212 0.10222 0.18864 0.9919 0.79261 0.6034 0.53442 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63269 63269 SRR13724980 SRX10113009 SRS8268905 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 24 GSM5087788   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 24 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11|genotype or treatment see plate layout:LY294002 treated GSM5087788 GSM5087788: SBF 24; Danio rerio; RNA Seq GSM5087788   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087788 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-024_HNN3JBGXC_S2_L002_R1_001.fastq.gz HUB-SF-024_HNN3JBGXC_S2_L002_R2_001.fastq.gz fastq fastq 446302418.0 5189563.0 GSM5087788 r2 0:26 1:60 A:106865192;C:83450626;G:81614410;T:174238330;N:133860 26 60     106865192 83450626 81614410 174238330 133860 SRX10113009 SRS8268905 SRA1196923 GEO Hubrecht Institute 2 0.10841 0.8604 0.10133 0.1894 0.99153 0.79448 0.5982 0.54405 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63270 63270 SRR13724981 SRX10113009 SRS8268905 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 24 GSM5087788   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 24 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11|genotype or treatment see plate layout:LY294002 treated GSM5087788 GSM5087788: SBF 24; Danio rerio; RNA Seq GSM5087788   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087788 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-024_HNN3JBGXC_S2_L003_R1_001.fastq.gz HUB-SF-024_HNN3JBGXC_S2_L003_R2_001.fastq.gz fastq fastq 460232096.0 5351536.0 GSM5087788 r3 0:26 1:60 A:110609261;C:86416065;G:82666816;T:180361735;N:178219 26 60     110609261 86416065 82666816 180361735 178219 SRX10113009 SRS8268905 SRA1196923 GEO Hubrecht Institute 2 0.10769 0.86203 0.1007 0.18972 0.99127 0.79147 0.61515 0.51848 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63271 63271 SRR13724982 SRX10113009 SRS8268905 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 24 GSM5087788   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 24 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11|genotype or treatment see plate layout:LY294002 treated GSM5087788 GSM5087788: SBF 24; Danio rerio; RNA Seq GSM5087788   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087788 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-024_HNN3JBGXC_S2_L004_R1_001.fastq.gz HUB-SF-024_HNN3JBGXC_S2_L004_R2_001.fastq.gz fastq fastq 452332050.0 5259675.0 GSM5087788 r4 0:26 1:60 A:108267618;C:84551070;G:82750927;T:176603395;N:159040 26 60     108267618 84551070 82750927 176603395 159040 SRX10113009 SRS8268905 SRA1196923 GEO Hubrecht Institute 2 0.10794 0.85996 0.10109 0.18768 0.99186 0.79155 0.60436 0.53563 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63288 63288 SRR13724959 SRX10113004 SRS8268900 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 19 GSM5087783   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 19 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11 and 12|genotype or treatment see plate layout:wildtype and LY294002 treated GSM5087783 GSM5087783: SBF 19; Danio rerio; RNA Seq GSM5087783   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087783 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-019_HNN3JBGXC_S1_L001_R1_001.fastq.gz HUB-SF-019_HNN3JBGXC_S1_L001_R2_001.fastq.gz fastq fastq 512895658.0 5963903.0 GSM5087783 r1 0:26 1:60 A:120657922;C:97018481;G:93066359;T:201974967;N:177929 26 60     120657922 97018481 93066359 201974967 177929 SRX10113004 SRS8268900 SRA1196923 GEO Hubrecht Institute 2 0.10618 0.89183 0.09932 0.15723 0.99289 0.79697 0.64665 0.51501 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63289 63289 SRR13724960 SRX10113004 SRS8268900 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 19 GSM5087783   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 19 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11 and 12|genotype or treatment see plate layout:wildtype and LY294002 treated GSM5087783 GSM5087783: SBF 19; Danio rerio; RNA Seq GSM5087783   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087783 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-019_HNN3JBGXC_S1_L002_R1_001.fastq.gz HUB-SF-019_HNN3JBGXC_S1_L002_R2_001.fastq.gz fastq fastq 505286894.0 5875429.0 GSM5087783 r2 0:26 1:60 A:118287675;C:95129666;G:93501877;T:198218457;N:149219 26 60     118287675 95129666 93501877 198218457 149219 SRX10113004 SRS8268900 SRA1196923 GEO Hubrecht Institute 2 0.10457 0.88947 0.0982 0.15596 0.99245 0.79717 0.6419 0.51385 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63290 63290 SRR13724961 SRX10113004 SRS8268900 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 19 GSM5087783   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 19 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11 and 12|genotype or treatment see plate layout:wildtype and LY294002 treated GSM5087783 GSM5087783: SBF 19; Danio rerio; RNA Seq GSM5087783   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087783 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-019_HNN3JBGXC_S1_L003_R1_001.fastq.gz HUB-SF-019_HNN3JBGXC_S1_L003_R2_001.fastq.gz fastq fastq 520563590.0 6053065.0 GSM5087783 r3 0:26 1:60 A:122370650;C:98437640;G:94573308;T:204982625;N:199367 26 60     122370650 98437640 94573308 204982625 199367 SRX10113004 SRS8268900 SRA1196923 GEO Hubrecht Institute 2 0.10455 0.89316 0.09799 0.15826 0.99352 0.79602 0.64228 0.51728 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63291 63291 SRR13724962 SRX10113004 SRS8268900 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 19 GSM5087783   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 19 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:11 and 12|genotype or treatment see plate layout:wildtype and LY294002 treated GSM5087783 GSM5087783: SBF 19; Danio rerio; RNA Seq GSM5087783   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087783 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-019_HNN3JBGXC_S1_L004_R1_001.fastq.gz HUB-SF-019_HNN3JBGXC_S1_L004_R2_001.fastq.gz fastq fastq 511418178.0 5946723.0 GSM5087783 r4 0:26 1:60 A:119653614;C:96220209;G:94759226;T:200596303;N:188826 26 60     119653614 96220209 94759226 200596303 188826 SRX10113004 SRS8268900 SRA1196923 GEO Hubrecht Institute 2 0.10519 0.88809 0.09876 0.15771 0.9932 0.7976 0.64098 0.51551 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63292 63292 SRR13724955 SRX10113003 SRS8268899 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 18 GSM5087782   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 18 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:10 and 11|genotype or treatment see plate layout:wildtype GSM5087782 GSM5087782: SBF 18; Danio rerio; RNA Seq GSM5087782   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087782 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-018_HNMNYBGXC_S4_L001_R1_001.fastq.gz HUB-SF-018_HNMNYBGXC_S4_L001_R2_001.fastq.gz fastq fastq 607020680.0 7058380.0 GSM5087782 r1 0:26 1:60 A:140183095;C:115207153;G:112295533;T:239312982;N:21917 26 60     140183095 115207153 112295533 239312982 21917 SRX10113003 SRS8268899 SRA1196923 GEO Hubrecht Institute 2 0.1065 0.90122 0.09986 0.12875 0.99409 0.79886 0.54213 0.49434 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63293 63293 SRR13724956 SRX10113003 SRS8268899 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 18 GSM5087782   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 18 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:10 and 11|genotype or treatment see plate layout:wildtype GSM5087782 GSM5087782: SBF 18; Danio rerio; RNA Seq GSM5087782   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087782 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-018_HNMNYBGXC_S4_L002_R1_001.fastq.gz HUB-SF-018_HNMNYBGXC_S4_L002_R2_001.fastq.gz fastq fastq 601756276.0 6997166.0 GSM5087782 r2 0:26 1:60 A:138291767;C:113586795;G:113460316;T:236406500;N:10898 26 60     138291767 113586795 113460316 236406500 10898 SRX10113003 SRS8268899 SRA1196923 GEO Hubrecht Institute 2 0.10623 0.89793 0.1 0.12868 0.99373 0.79736 0.56624 0.48875 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63294 63294 SRR13724957 SRX10113003 SRS8268899 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 18 GSM5087782   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 18 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:10 and 11|genotype or treatment see plate layout:wildtype GSM5087782 GSM5087782: SBF 18; Danio rerio; RNA Seq GSM5087782   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087782 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-018_HNMNYBGXC_S4_L003_R1_001.fastq.gz HUB-SF-018_HNMNYBGXC_S4_L003_R2_001.fastq.gz fastq fastq 609228472.0 7084052.0 GSM5087782 r3 0:26 1:60 A:140535790;C:115667471;G:112769371;T:240222708;N:33132 26 60     140535790 115667471 112769371 240222708 33132 SRX10113003 SRS8268899 SRA1196923 GEO Hubrecht Institute 2 0.10644 0.90117 0.10007 0.12821 0.99373 0.79555 0.57799 0.49876 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63295 63295 SRR13724958 SRX10113003 SRS8268899 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 18 GSM5087782   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 18 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:10 and 11|genotype or treatment see plate layout:wildtype GSM5087782 GSM5087782: SBF 18; Danio rerio; RNA Seq GSM5087782   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087782 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-018_HNMNYBGXC_S4_L004_R1_001.fastq.gz HUB-SF-018_HNMNYBGXC_S4_L004_R2_001.fastq.gz fastq fastq 611656080.0 7112280.0 GSM5087782 r4 0:26 1:60 A:140638258;C:115528635;G:114971815;T:240469585;N:47787 26 60     140638258 115528635 114971815 240469585 47787 SRX10113003 SRS8268899 SRA1196923 GEO Hubrecht Institute 2 0.10488 0.89678 0.09883 0.12836 0.99401 0.79874 0.53879 0.50271 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63296 63296 SRR13724951 SRX10113002 SRS8268898 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 17 GSM5087781   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 17 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:10|genotype or treatment see plate layout:wildtype GSM5087781 GSM5087781: SBF 17; Danio rerio; RNA Seq GSM5087781   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087781 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-017_HNMNYBGXC_S3_L001_R1_001.fastq.gz HUB-SF-017_HNMNYBGXC_S3_L001_R2_001.fastq.gz fastq fastq 550210542.0 6397797.0 GSM5087781 r1 0:26 1:60 A:129629378;C:105408321;G:101310529;T:213842712;N:19602 26 60     129629378 105408321 101310529 213842712 19602 SRX10113002 SRS8268898 SRA1196923 GEO Hubrecht Institute 2 0.10176 0.85145 0.09561 0.12666 0.99228 0.79715 0.65986 0.49363 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63297 63297 SRR13724952 SRX10113002 SRS8268898 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 17 GSM5087781   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 17 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:10|genotype or treatment see plate layout:wildtype GSM5087781 GSM5087781: SBF 17; Danio rerio; RNA Seq GSM5087781   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087781 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-017_HNMNYBGXC_S3_L002_R1_001.fastq.gz HUB-SF-017_HNMNYBGXC_S3_L002_R2_001.fastq.gz fastq fastq 544852140.0 6335490.0 GSM5087781 r2 0:26 1:60 A:127605846;C:103730258;G:102606915;T:210899244;N:9877 26 60     127605846 103730258 102606915 210899244 9877 SRX10113002 SRS8268898 SRA1196923 GEO Hubrecht Institute 2 0.10057 0.84909 0.09431 0.12623 0.99285 0.79809 0.66527 0.49628 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63298 63298 SRR13724953 SRX10113002 SRS8268898 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 17 GSM5087781   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 17 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:10|genotype or treatment see plate layout:wildtype GSM5087781 GSM5087781: SBF 17; Danio rerio; RNA Seq GSM5087781   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087781 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-017_HNMNYBGXC_S3_L003_R1_001.fastq.gz HUB-SF-017_HNMNYBGXC_S3_L003_R2_001.fastq.gz fastq fastq 552000976.0 6418616.0 GSM5087781 r3 0:26 1:60 A:129943041;C:105738992;G:101687286;T:214600933;N:30724 26 60     129943041 105738992 101687286 214600933 30724 SRX10113002 SRS8268898 SRA1196923 GEO Hubrecht Institute 2 0.10203 0.85152 0.09564 0.12515 0.99212 0.79693 0.66008 0.49617 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63299 63299 SRR13724954 SRX10113002 SRS8268898 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 17 GSM5087781   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 17 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:10|genotype or treatment see plate layout:wildtype GSM5087781 GSM5087781: SBF 17; Danio rerio; RNA Seq GSM5087781   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087781 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     HUB-SF-017_HNMNYBGXC_S3_L004_R1_001.fastq.gz HUB-SF-017_HNMNYBGXC_S3_L004_R2_001.fastq.gz fastq fastq 554433572.0 6446902.0 GSM5087781 r4 0:26 1:60 A:129958370;C:105617900;G:104105493;T:214710300;N:41509 26 60     129958370 105617900 104105493 214710300 41509 SRX10113002 SRS8268898 SRA1196923 GEO Hubrecht Institute 2 0.101 0.84666 0.09491 0.12434 0.99271 0.80052 0.65868 0.50218 26 60 T B sc-like readlen illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63316 63316 SRR13724931 SRX10112997 SRS8268893 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 6 GSM5087776   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 6 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:4|genotype or treatment see plate layout:LY294002 treated GSM5087776 GSM5087776: SBF 6; Danio rerio; RNA Seq GSM5087776   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087776 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBF6_AH333MBGX9_S2_L001_R1_001.fastq.gz SBF6_AH333MBGX9_S2_L001_R2_001.fastq.gz fastq fastq 1277423615.0 8461048.0 GSM5087776 r1 0:75.53 1:75.45 A:355718095;C:180588233;G:186496300;T:554167681;N:453306 75 75     355718095 180588233 186496300 554167681 453306 SRX10112997 SRS8268893 SRA1196923 GEO Hubrecht Institute 2 0.1772 0.84028 0.11265 0.22285 0.98946 0.89936 0.50938 0.51879 76 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63317 63317 SRR13724932 SRX10112997 SRS8268893 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 6 GSM5087776   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 6 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:4|genotype or treatment see plate layout:LY294002 treated GSM5087776 GSM5087776: SBF 6; Danio rerio; RNA Seq GSM5087776   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087776 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBF6_AH333MBGX9_S2_L002_R1_001.fastq.gz SBF6_AH333MBGX9_S2_L002_R2_001.fastq.gz fastq fastq 1428463292.0 9460235.0 GSM5087776 r2 0:75.53 1:75.47 A:393204544;C:206178548;G:226631642;T:601950555;N:498003 75 75     393204544 206178548 226631642 601950555 498003 SRX10112997 SRS8268893 SRA1196923 GEO Hubrecht Institute 2 0.19986 0.8458 0.12219 0.22132 0.97822 0.8616 0.48286 0.50011 75 74 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63318 63318 SRR13724933 SRX10112997 SRS8268893 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 6 GSM5087776   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 6 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:4|genotype or treatment see plate layout:LY294002 treated GSM5087776 GSM5087776: SBF 6; Danio rerio; RNA Seq GSM5087776   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087776 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBF6_AH333MBGX9_S2_L003_R1_001.fastq.gz SBF6_AH333MBGX9_S2_L003_R2_001.fastq.gz fastq fastq 1197534302.0 7935963.0 GSM5087776 r3 0:75.45 1:75.45 A:343317356;C:167744193;G:179840173;T:506420153;N:212427 75 75     343317356 167744193 179840173 506420153 212427 SRX10112997 SRS8268893 SRA1196923 GEO Hubrecht Institute 2 0.16914 0.83932 0.11169 0.22325 0.99036 0.88745 0.45846 0.51895 75 75 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63319 63319 SRR13724934 SRX10112997 SRS8268893 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 6 GSM5087776   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 6 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:4|genotype or treatment see plate layout:LY294002 treated GSM5087776 GSM5087776: SBF 6; Danio rerio; RNA Seq GSM5087776   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087776 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBF6_AH333MBGX9_S2_L004_R1_001.fastq.gz SBF6_AH333MBGX9_S2_L004_R2_001.fastq.gz fastq fastq 1154537853.0 7651049.0 GSM5087776 r4 0:75.44 1:75.46 A:330092661;C:161606869;G:181064371;T:481566601;N:207351 75 75     330092661 161606869 181064371 481566601 207351 SRX10112997 SRS8268893 SRA1196923 GEO Hubrecht Institute 2 0.18689 0.83323 0.11629 0.22137 0.98524 0.87677 0.50562 0.52611 76 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63320 63320 SRR13724927 SRX10112996 SRS8268892 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 5 GSM5087775   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 5 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:4|genotype or treatment see plate layout:LY294002 treated GSM5087775 GSM5087775: SBF 5; Danio rerio; RNA Seq GSM5087775   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087775 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBF5_AH333MBGX9_S1_L001_R1_001.fastq.gz SBF5_AH333MBGX9_S1_L001_R2_001.fastq.gz fastq fastq 1088370818.0 7206853.0 GSM5087775 r1 0:75.54 1:75.48 A:295469865;C:163970733;G:170086472;T:458445260;N:398488 75 75     295469865 163970733 170086472 458445260 398488 SRX10112996 SRS8268892 SRA1196923 GEO Hubrecht Institute 2 0.26005 0.85502 0.19687 0.28684 0.9847 0.89161 0.48864 0.54017 74 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63321 63321 SRR13724928 SRX10112996 SRS8268892 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 5 GSM5087775   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 5 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:4|genotype or treatment see plate layout:LY294002 treated GSM5087775 GSM5087775: SBF 5; Danio rerio; RNA Seq GSM5087775   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087775 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBF5_AH333MBGX9_S1_L002_R1_001.fastq.gz SBF5_AH333MBGX9_S1_L002_R2_001.fastq.gz fastq fastq 1295570350.0 8577614.0 GSM5087775 r2 0:75.55 1:75.49 A:348091187;C:198053540;G:214980570;T:533988605;N:456448 75 75     348091187 198053540 214980570 533988605 456448 SRX10112996 SRS8268892 SRA1196923 GEO Hubrecht Institute 2 0.28518 0.83096 0.21289 0.27752 0.97021 0.85729 0.48622 0.52931 75 74 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63322 63322 SRR13724929 SRX10112996 SRS8268892 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 5 GSM5087775   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 5 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:4|genotype or treatment see plate layout:LY294002 treated GSM5087775 GSM5087775: SBF 5; Danio rerio; RNA Seq GSM5087775   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087775 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBF5_AH333MBGX9_S1_L003_R1_001.fastq.gz SBF5_AH333MBGX9_S1_L003_R2_001.fastq.gz fastq fastq 1101611186.0 7297680.0 GSM5087775 r3 0:75.48 1:75.48 A:305906619;C:164420793;G:175650639;T:455425822;N:207313 75 75     305906619 164420793 175650639 455425822 207313 SRX10112996 SRS8268892 SRA1196923 GEO Hubrecht Institute 2 0.25329 0.85303 0.19276 0.28474 0.98636 0.88055 0.50839 0.55071 76 75 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63323 63323 SRR13724930 SRX10112996 SRS8268892 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 5 GSM5087775   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 5 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:4|genotype or treatment see plate layout:LY294002 treated GSM5087775 GSM5087775: SBF 5; Danio rerio; RNA Seq GSM5087775   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087775 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBF5_AH333MBGX9_S1_L004_R1_001.fastq.gz SBF5_AH333MBGX9_S1_L004_R2_001.fastq.gz fastq fastq 1032362340.0 6839045.0 GSM5087775 r4 0:75.47 1:75.49 A:286580573;C:153625198;G:170370416;T:421602918;N:183235 75 75     286580573 153625198 170370416 421602918 183235 SRX10112996 SRS8268892 SRA1196923 GEO Hubrecht Institute 2 0.26925 0.84457 0.2052 0.28507 0.98048 0.86815 0.49424 0.54795 75 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63324 63324 SRR13724923 SRX10112995 SRS8268891 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 4 GSM5087774   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 4 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:3|genotype or treatment see plate layout:wildtype and LY294002 treated GSM5087774 GSM5087774: SBF 4; Danio rerio; RNA Seq GSM5087774   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087774 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBF-4_AH5WKHBGX3_S5_L001_R1_001.fastq.gz SBF-4_AH5WKHBGX3_S5_L001_R2_001.fastq.gz fastq fastq 2411223196.0 15966823.0 GSM5087774 r1 0:75.52 1:75.49 A:644674430;C:333992035;G:384770311;T:1047444511;N:341909 75 75     644674430 333992035 384770311 1047444511 341909 SRX10112995 SRS8268891 SRA1196923 GEO Hubrecht Institute 2 0.33554 0.83519 0.19659 0.21757 0.97402 0.80062 0.49709 0.50299 74 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63325 63325 SRR13724924 SRX10112995 SRS8268891 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 4 GSM5087774   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 4 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:3|genotype or treatment see plate layout:wildtype and LY294002 treated GSM5087774 GSM5087774: SBF 4; Danio rerio; RNA Seq GSM5087774   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087774 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBF-4_AH5WKHBGX3_S5_L002_R1_001.fastq.gz SBF-4_AH5WKHBGX3_S5_L002_R2_001.fastq.gz fastq fastq 2451975555.0 16238043.0 GSM5087774 r2 0:75.51 1:75.49 A:657663872;C:335089008;G:401426684;T:1057502726;N:293265 75 75     657663872 335089008 401426684 1057502726 293265 SRX10112995 SRS8268891 SRA1196923 GEO Hubrecht Institute 2 0.34808 0.82817 0.20122 0.21406 0.96952 0.80624 0.5081 0.51204 75 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63326 63326 SRR13724925 SRX10112995 SRS8268891 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 4 GSM5087774   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 4 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:3|genotype or treatment see plate layout:wildtype and LY294002 treated GSM5087774 GSM5087774: SBF 4; Danio rerio; RNA Seq GSM5087774   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087774 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBF-4_AH5WKHBGX3_S5_L003_R1_001.fastq.gz SBF-4_AH5WKHBGX3_S5_L003_R2_001.fastq.gz fastq fastq 2433467285.0 16115065.0 GSM5087774 r3 0:75.51 1:75.49 A:649651175;C:332209980;G:393925739;T:1057547874;N:132517 75 75     649651175 332209980 393925739 1057547874 132517 SRX10112995 SRS8268891 SRA1196923 GEO Hubrecht Institute 2 0.35242 0.83424 0.20776 0.2186 0.97561 0.80255 0.505 0.51812 76 75 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63327 63327 SRR13724926 SRX10112995 SRS8268891 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 4 GSM5087774   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 4 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:3|genotype or treatment see plate layout:wildtype and LY294002 treated GSM5087774 GSM5087774: SBF 4; Danio rerio; RNA Seq GSM5087774   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087774 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBF-4_AH5WKHBGX3_S5_L004_R1_001.fastq.gz SBF-4_AH5WKHBGX3_S5_L004_R2_001.fastq.gz fastq fastq 2398267715.0 15883759.0 GSM5087774 r4 0:75.50 1:75.49 A:643613425;C:328877849;G:388880564;T:1036811141;N:84736 75 75     643613425 328877849 388880564 1036811141 84736 SRX10112995 SRS8268891 SRA1196923 GEO Hubrecht Institute 2 0.33562 0.83085 0.20341 0.21767 0.97735 0.80184 0.50029 0.51498 76 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63328 63328 SRR13724919 SRX10112994 SRS8268890 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 3 GSM5087773   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 3 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:3|genotype or treatment see plate layout:wildtype and LY294002 treated GSM5087773 GSM5087773: SBF 3; Danio rerio; RNA Seq GSM5087773   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087773 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBF-3_AH5WKHBGX3_S4_L001_R1_001.fastq.gz SBF-3_AH5WKHBGX3_S4_L001_R2_001.fastq.gz fastq fastq 3195541787.0 21161310.0 GSM5087773 r1 0:75.54 1:75.47 A:903731324;C:453063501;G:545122790;T:1293158952;N:465220 75 75     903731324 453063501 545122790 1293158952 465220 SRX10112994 SRS8268890 SRA1196923 GEO Hubrecht Institute 2 0.31678 0.74007 0.23751 0.27632 0.97344 0.82548 0.46646 0.46858 76 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63329 63329 SRR13724920 SRX10112994 SRS8268890 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 3 GSM5087773   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 3 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:3|genotype or treatment see plate layout:wildtype and LY294002 treated GSM5087773 GSM5087773: SBF 3; Danio rerio; RNA Seq GSM5087773   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087773 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBF-3_AH5WKHBGX3_S4_L002_R1_001.fastq.gz SBF-3_AH5WKHBGX3_S4_L002_R2_001.fastq.gz fastq fastq 3222130047.0 21338414.0 GSM5087773 r2 0:75.53 1:75.47 A:911955596;C:450527126;G:564151778;T:1295111718;N:383829 75 75     911955596 450527126 564151778 1295111718 383829 SRX10112994 SRS8268890 SRA1196923 GEO Hubrecht Institute 2 0.31155 0.73818 0.23573 0.27589 0.96968 0.83114 0.46101 0.52203 76 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63330 63330 SRR13724921 SRX10112994 SRS8268890 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 3 GSM5087773   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 3 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:3|genotype or treatment see plate layout:wildtype and LY294002 treated GSM5087773 GSM5087773: SBF 3; Danio rerio; RNA Seq GSM5087773   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087773 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBF-3_AH5WKHBGX3_S4_L003_R1_001.fastq.gz SBF-3_AH5WKHBGX3_S4_L003_R2_001.fastq.gz fastq fastq 3222462119.0 21339984.0 GSM5087773 r3 0:75.53 1:75.47 A:909869219;C:451636784;G:557091828;T:1303683831;N:180457 75 75     909869219 451636784 557091828 1303683831 180457 SRX10112994 SRS8268890 SRA1196923 GEO Hubrecht Institute 2 0.29341 0.74071 0.22113 0.27868 0.97546 0.82869 0.47864 0.53241 76 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63331 63331 SRR13724922 SRX10112994 SRS8268890 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF 3 GSM5087773   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF 3 Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:3|genotype or treatment see plate layout:wildtype and LY294002 treated GSM5087773 GSM5087773: SBF 3; Danio rerio; RNA Seq GSM5087773   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087773 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBF-3_AH5WKHBGX3_S4_L004_R1_001.fastq.gz SBF-3_AH5WKHBGX3_S4_L004_R2_001.fastq.gz fastq fastq 3198542940.0 21184892.0 GSM5087773 r4 0:75.51 1:75.47 A:908150005;C:449327559;G:554336886;T:1286617646;N:110844 75 75     908150005 449327559 554336886 1286617646 110844 SRX10112994 SRS8268890 SRA1196923 GEO Hubrecht Institute 2 0.31174 0.73875 0.2333 0.27833 0.97587 0.82735 0.44495 0.52152 75 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63332 63332 SRR13724915 SRX10112993 SRS8268889 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF b GSM5087772   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF b Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:1|genotype or treatment see plate layout:wildtype GSM5087772 GSM5087772: SBF b; Danio rerio; RNA Seq GSM5087772   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087772 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBFb_AHMK3CBGXY_S6_L001_R1_001.fastq.gz SBFb_AHMK3CBGXY_S6_L001_R2_001.fastq.gz fastq fastq 1371717182.0 9096160.0 GSM5087772 r1 0:75.32 1:75.49 A:431208814;C:182975788;G:191474217;T:565708541;N:349822 75 75     431208814 182975788 191474217 565708541 349822 SRX10112993 SRS8268889 SRA1196923 GEO Hubrecht Institute 2 0.20858 0.86563 0.09681 0.16003 0.97417 0.80977 0.4986 0.5051 76 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63333 63333 SRR13724916 SRX10112993 SRS8268889 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF b GSM5087772   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF b Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:1|genotype or treatment see plate layout:wildtype GSM5087772 GSM5087772: SBF b; Danio rerio; RNA Seq GSM5087772   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087772 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBFb_AHMK3CBGXY_S6_L002_R1_001.fastq.gz SBFb_AHMK3CBGXY_S6_L002_R2_001.fastq.gz fastq fastq 1389974740.0 9216925.0 GSM5087772 r2 0:75.32 1:75.49 A:432611387;C:185298654;G:195582180;T:576097261;N:385258 75 75     432611387 185298654 195582180 576097261 385258 SRX10112993 SRS8268889 SRA1196923 GEO Hubrecht Institute 2 0.19445 0.86622 0.08995 0.16164 0.97486 0.81107 0.49507 0.51217 76 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63334 63334 SRR13724917 SRX10112993 SRS8268889 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF b GSM5087772   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF b Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:1|genotype or treatment see plate layout:wildtype GSM5087772 GSM5087772: SBF b; Danio rerio; RNA Seq GSM5087772   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087772 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBFb_AHMK3CBGXY_S6_L003_R1_001.fastq.gz SBFb_AHMK3CBGXY_S6_L003_R2_001.fastq.gz fastq fastq 1344249576.0 8912874.0 GSM5087772 r3 0:75.34 1:75.49 A:417103394;C:179153160;G:189101644;T:558793788;N:97590 75 75     417103394 179153160 189101644 558793788 97590 SRX10112993 SRS8268889 SRA1196923 GEO Hubrecht Institute 2 0.20291 0.86448 0.09728 0.16345 0.97589 0.81331 0.51276 0.48907 75 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63335 63335 SRR13724918 SRX10112993 SRS8268889 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF b GSM5087772   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF b Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:1|genotype or treatment see plate layout:wildtype GSM5087772 GSM5087772: SBF b; Danio rerio; RNA Seq GSM5087772   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087772 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBFb_AHMK3CBGXY_S6_L004_R1_001.fastq.gz SBFb_AHMK3CBGXY_S6_L004_R2_001.fastq.gz fastq fastq 1406958228.0 9327733.0 GSM5087772 r4 0:75.34 1:75.49 A:425247477;C:188248952;G:203730376;T:589616502;N:114921 75 75     425247477 188248952 203730376 589616502 114921 SRX10112993 SRS8268889 SRA1196923 GEO Hubrecht Institute 2 0.20529 0.86237 0.09578 0.15898 0.97364 0.80533 0.5159 0.51177 76 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63336 63336 SRR13724911 SRX10112992 SRS8268888 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF a GSM5087771   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF a Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:1|genotype or treatment see plate layout:wildtype GSM5087771 GSM5087771: SBF a; Danio rerio; RNA Seq GSM5087771   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087771 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBFa_AHMK3CBGXY_S5_L001_R1_001.fastq.gz SBFa_AHMK3CBGXY_S5_L001_R2_001.fastq.gz fastq fastq 1795957614.0 11906763.0 GSM5087771 r1 0:75.36 1:75.48 A:556557758;C:271831603;G:276684005;T:690436759;N:447489 75 75     556557758 271831603 276684005 690436759 447489 SRX10112992 SRS8268888 SRA1196923 GEO Hubrecht Institute 2 0.27373 0.79114 0.20032 0.33403 0.96207 0.81639 0.50247 0.51409 76 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63337 63337 SRR13724912 SRX10112992 SRS8268888 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF a GSM5087771   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF a Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:1|genotype or treatment see plate layout:wildtype GSM5087771 GSM5087771: SBF a; Danio rerio; RNA Seq GSM5087771   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087771 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBFa_AHMK3CBGXY_S5_L002_R1_001.fastq.gz SBFa_AHMK3CBGXY_S5_L002_R2_001.fastq.gz fastq fastq 1834336394.0 12160842.0 GSM5087771 r2 0:75.36 1:75.48 A:564737521;C:276699534;G:284366491;T:708014403;N:518445 75 75     564737521 276699534 284366491 708014403 518445 SRX10112992 SRS8268888 SRA1196923 GEO Hubrecht Institute 2 0.26884 0.78787 0.19458 0.33465 0.96004 0.82079 0.50759 0.51672 76 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63338 63338 SRR13724913 SRX10112992 SRS8268888 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF a GSM5087771   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF a Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:1|genotype or treatment see plate layout:wildtype GSM5087771 GSM5087771: SBF a; Danio rerio; RNA Seq GSM5087771   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087771 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBFa_AHMK3CBGXY_S5_L003_R1_001.fastq.gz SBFa_AHMK3CBGXY_S5_L003_R2_001.fastq.gz fastq fastq 1756417626.0 11643382.0 GSM5087771 r3 0:75.37 1:75.48 A:538991548;C:264988843;G:272348964;T:679970786;N:117485 75 75     538991548 264988843 272348964 679970786 117485 SRX10112992 SRS8268888 SRA1196923 GEO Hubrecht Institute 2 0.27143 0.79064 0.19748 0.33283 0.96266 0.823 0.50907 0.50684 75 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system
63339 63339 SRR13724914 SRX10112992 SRS8268888 SRP306756 PRJNA702191 Phosphatidylinositol 3 kinase signaling controls survival and stemness of hematopoietic stem and progenitor cells GSE166900 Transcriptome Analysis Loss of Pten and inhibition of PI3K induced apoptosis of hematopoietic stem/progenitor cells upon endothelial to hematopoietic transition and surviving hematopoietic stem/progenitor cells committed to all blood lineages but displayed reduced stemness Overall design: AGMs 36hpf or CHTs 5dpf were dissected and dissociated using FACS sorting HSPCs were isolated and single cell RNA seq was performed.   pubmed:33714985   SBF a GSM5087771   tissue:Aorta Gonad Mes1phros|developmental stage:36hpf SBF a Well numbers X001 X384 in *.TranscriptCounts.tsv refer to well numbers of the 384 well plate in the following order: A1 to A24 B1 to B24 until P24. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. During sequencing Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA Anders and Huber 2010. Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna alemany/transcriptomics/tree/master/mapandgo Tabular separated file indicating number of transcripts per section obtained as previously described Grün Dominic Lennart Kester and Alexander Van Oudenaarden. "Validation of noise models for single cell transcriptomics." Nature methods 11.6 2014: 637. We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI corrected transcripts per gene per cell The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier UMI. The remainder of the left read contains a polyT stretch followed by a number <40 of transcript derived bases. Read 1 was not used for quantification. cell specific barcodes are specified in the file “cel seq2 barcodes.csv” Genome build: zV9 Danio Rerio Aorta Gonad Mesonephros   Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols   developmental stage:36hpf|sort day see plate layout:1|genotype or treatment see plate layout:wildtype GSM5087771 GSM5087771: SBF a; Danio rerio; RNA Seq GSM5087771   1 Cells were sorted into 384 well plates. All wells underwent Cel Seq2 protocol RNA libraries were prepared for sequencing using standard Illumina protocols GEO Accession:GSM5087771 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP306756     SBFa_AHMK3CBGXY_S5_L004_R1_001.fastq.gz SBFa_AHMK3CBGXY_S5_L004_R2_001.fastq.gz fastq fastq 1939499436.0 12856118.0 GSM5087771 r4 0:75.38 1:75.48 A:582243992;C:292051417;G:306410955;T:758635889;N:157183 75 75     582243992 292051417 306410955 758635889 157183 SRX10112992 SRS8268888 SRA1196923 GEO Hubrecht Institute 2 0.26584 0.79482 0.19411 0.33124 0.96173 0.81225 0.52607 0.515 75 76 T B mate1 technical by mapping diff illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate celseq   Netherlands 2021-02-16 Pharyngula Embryo Multi-tissue Multi-system

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;