run_metadata
32 rows where experiment.library_source = "TRANSCRIPTOMIC", technology = "10x" and tissue_curation = "Blood"
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| 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 |
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| 53001 | 53001 | SRR12173589 | SRX8688333 | SRS6966994 | SRP213938 | PRJNA553572 | A map of cis regulatory elements and 3D genome structures in zebrafish | GSE134055 | Other | The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records. | pubmed:33239788;pubmed:35649578 | YueLab RNA seq Blood rep2 | GSM4662086 | source name:YueLab RNA seq Blood|strain:Tuebingen|tissue:Blood | YueLab RNA seq Blood rep2 | RNA seq reads were aligned to zv10 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using Bowtie2;H3K27ac H3K4me3 ChIP seq were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5.For the ATAC seq the peak length were fixed to 500 bp. We only selected the peak with the most significant signal if several peaks overlap with each other in each tissue.Since the H3K9me3 and H3K9me2 makers are broad domain we called the peak using Homer with the parameter “ region size 1000” and peaks within 5 kb were merged together. HiC matrix was generated using HiC Pro WGBS data were mapped to in silico bisulfite converted zebrafish genome reference by using Bismark For the scATAC seq the BCL files generated from sequencing were used as inputs to the 10X Genomics Cell Ranger ATAC seq pipeline; then the FASTQ files were aligned to the GRCz10 genome using BWA and the fragments with MAPQ>30 were kept for further analysis and each fragment is associated with a single cell barcode. Genome build: zv10GRCz10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged | YueLab RNA seq Blood | RNA seq: For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP seq lysis buffer 20 mM Tris HCl pH 8.0 1% SDS 50 mM EDTA 1X proteinase inhibitor cocktail. Next 900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W duty factor 5 200 per burst. Sonication time is variable depending on tissue types. To check the chromatin fragmentation size 20 µL of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl pH 8.0 1% SDS 1 mM EDTA at 65 °C overnight treated with Rnase A and proteinase K and purified by phenol chloroform ext… | RNA seq: Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions ChIP seq ATAC seq Hi C and WGBS: Ault Tuebingen zebrafish were raised under standard laboratory conditions | strain:Tuebingen|tissue:Blood | GSM4662086 | GSM4662086: YueLab RNA seq Blood rep2; Danio rerio; RNA Seq | GSM4662086 | 1 | RNA seq: For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP seq lysis buffer 20 mM Tris HCl pH 8.0 1% SDS 50 mM EDTA 1X proteinase inhibitor cocktail. Next 900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W duty factor 5 200 per burst. Sonication time is variable depending on tissue types. To check the chromatin fragmentation size 20 µL of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl pH 8.0 1% SDS 1 mM EDTA at 65 °C overnight treated with Rnase A and proteinase K and purified by phenol chloroform ext… | GEO Accession:GSM4662086 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP213938 | YueLab-RNA-seq-Blood-rep2_2.fastq.gz YueLab-RNA-seq-Blood-rep2_1.fastq.gz | fastq fastq | 9750305560.0 | 32285780.0 | GSM4662086 r1 | 0:151 1:151 | A:2564237490;C:2313022617;G:2328740350;T:2544206938;N:98165 | 151 | 151 | 2564237490 | 2313022617 | 2328740350 | 2544206938 | 98165 | SRX8688333 | SRS6966994 | SRA919194 | GEO | Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine | 2 | 0.90976 | 0.90587 | 0.07014 | 0.06953 | 0.85415 | 0.85624 | 0.51898 | 0.51696 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | sc | single_cell_droplet | 10x | United States | 2020-07-08 | Pharyngula | Embryo | Blood | Hematopoietic System | |||||||||||
| 53002 | 53002 | SRR12173588 | SRX8688332 | SRS6966993 | SRP213938 | PRJNA553572 | A map of cis regulatory elements and 3D genome structures in zebrafish | GSE134055 | Other | The zebrafish has been widely used for the study of human disease and development as 70% of the protein coding genes are conserved between the two species. Annotation of functional control elements of the zebrafish genome however has lagged behind that of other model systems such as mouse and Drosophila. Based on multi omics approaches taken in the ENCODE and Roadmap Epigenomics projects we performed RNA seq ATAC seq ChIP seq and Hi C experiments in ten adult and two embryonic tissues to generate a comprehensive map of transcriptomes and regulatory elements in the zebrafish Tuebingen reference strain. Overall we have identified 235 596 cis regulatory elements which potentially shape the tissue specific and developmental stage specific gene expression in zebrafish. A comparison of zebrafish human and mouse regulatory elements allowed us to identify both evolutionarily conserved and species specific regulatory sequences. Furthermore through the analysis of Hi C data in zebrafish brain and muscle we observed different levels of 3D genome organization including compartment topological associating domains TADs and chromatin loops in zebrafish. A subset of TADs are deeply conserved between zebrafish and human. This work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionally conserved elements of 3D genome organization. Overall design: 13 tissues from adult and embryonic stage were examined using ChIP Seq H3K27ac and H3K4me3 RNA Seq 11 of them were examined using ATAC seq WGBS and ChIP seq H3K9me3 and H3K9me2 and one scATAC seq in brain. Additionally we performed HiC experiments in adult muscle and brain. Please note that for the samples GSM4661977 GSM4662088 [1] each processed data generated from both replicates is linked to the corresponding *rep1 sample records [2] the input sample used for each ChIP sample is indicated in the description field in the corresponding input sample records. | pubmed:33239788;pubmed:35649578 | YueLab RNA seq Blood rep1 | GSM4662085 | source name:YueLab RNA seq Blood|strain:Tuebingen|tissue:Blood | YueLab RNA seq Blood rep1 | RNA seq reads were aligned to zv10 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM ChIP seq and ATAC seq reads were aligned to zv10 genome assembly using Bowtie2;H3K27ac H3K4me3 ChIP seq were called using MACS2 with the following setting: ChIP seq q value <10e 2 p value<10e 5 Change>1 FC>2. ATAC seq: q value<10e 2 and p value<10e 5.For the ATAC seq the peak length were fixed to 500 bp. We only selected the peak with the most significant signal if several peaks overlap with each other in each tissue.Since the H3K9me3 and H3K9me2 makers are broad domain we called the peak using Homer with the parameter “ region size 1000” and peaks within 5 kb were merged together. HiC matrix was generated using HiC Pro WGBS data were mapped to in silico bisulfite converted zebrafish genome reference by using Bismark For the scATAC seq the BCL files generated from sequencing were used as inputs to the 10X Genomics Cell Ranger ATAC seq pipeline; then the FASTQ files were aligned to the GRCz10 genome using BWA and the fragments with MAPQ>30 were kept for further analysis and each fragment is associated with a single cell barcode. Genome build: zv10GRCz10 Supplementary files format and content: tab delimited text files include TPM values for each Sample; the narrowPeak files included the peaks for each Sample; The .hic file were the matrix of Hi C for each Sample.**All replicates were merged | YueLab RNA seq Blood | RNA seq: For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer’s protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP seq lysis buffer 20 mM Tris HCl pH 8.0 1% SDS 50 mM EDTA 1X proteinase inhibitor cocktail. Next 900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W duty factor 5 200 per burst. Sonication time is variable depending on tissue types. To check the chromatin fragmentation size 20 µL of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl pH 8.0 1% SDS 1 mM EDTA at 65 °C overnight treated with Rnase A and proteinase K and purified by phenol chloroform ext… | RNA seq: Embryonic and ault Tuebingen zebrafish were raised under standard laboratory conditions ChIP seq ATAC seq Hi C and WGBS: Ault Tuebingen zebrafish were raised under standard laboratory conditions | strain:Tuebingen|tissue:Blood | GSM4662085 | GSM4662085: YueLab RNA seq Blood rep1; Danio rerio; RNA Seq | GSM4662085 | 1 | RNA seq: For each RNA seq experiment the same tissues combined from at least two Tuebingen fish were used as one replicate. For embryonic trunk ten 1 dpf fish were dechorionated with pronase and trunk were cut off for RNA seq. For embryonic neuron green cells from TgHuc:Kaede cells were sorted by FACS and approxinately 20 000 cells were used for one replicate. The tissue RNA was extracted from Trizol® according to the protocol Invitrogen. RNA seq: The cDNA libraries were performed using SureSelect Strand Specific RNA Library Preparation Kit Agilent according to the manufacturer's protocol. Briefly polyA RNA was purified from 1000 ng of total RNA using oligo dT beads Invitrogen. Extracted RNA was first fragmented then followed by reverse transcription end repair adenylation adaptor ligation and subsequent PCR amplification. The final product was checked by size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit Agilent and Kapa Library Quantification Kit Kapa Biosystems and then followed by pair end 2X 50 bp high throughput sequencing using HiSeq 2500 Illumina. ChIP seq: All the tissues were ground in the liquid nitrogen and fixed by 1% formaldehyde at room temperature for 15 min. 0.2 M glycine was added and incubated at room temperature for 5 min to quench the fixation. Fixed tissues were then washed once by cold 1X PBS. Tissue pellet was resuspended and incubated on ice for 10 min in 100 µL of ChIP seq lysis buffer 20 mM Tris HCl pH 8.0 1% SDS 50 mM EDTA 1X proteinase inhibitor cocktail. Next 900 µL cold 1X TE buffer was added to dilute SDS concentration and the nuclei suspension was sonicated using Covaris E220 with the following parameters: 140 W duty factor 5 200 per burst. Sonication time is variable depending on tissue types. To check the chromatin fragmentation size 20 µL of input chromatin was reverse crosslinked in elution buffer 20 mM Tris HCl pH 8.0 1% SDS 1 mM EDTA at 65 °C overnight treated with Rnase A and proteinase K and purified by phenol chloroform ext… | GEO Accession:GSM4662085 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP213938 | YueLab-RNA-seq-Blood-rep1_1.fastq.gz YueLab-RNA-seq-Blood-rep1_2.fastq.gz | fastq fastq | 10181340496.0 | 33713048.0 | GSM4662085 r1 | 0:151 1:151 | A:2735674306;C:2352790027;G:2376786768;T:2715986044;N:103351 | 151 | 151 | 2735674306 | 2352790027 | 2376786768 | 2715986044 | 103351 | SRX8688332 | SRS6966993 | SRA919194 | GEO | Feng Yue, Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine | 2 | 0.91563 | 0.91373 | 0.11339 | 0.11315 | 0.82235 | 0.82266 | 0.48854 | 0.48669 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | trueseq | sc | single_cell_droplet | 10x | United States | 2020-07-08 | Pharyngula | Embryo | Blood | Hematopoietic System | |||||||||||
| 57171 | 57171 | SRR11243180 | SRX7854786 | SRS6264269 | SRP251673 | PRJNA610520 | A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish | GSE146404 | Transcriptome Analysis | To profile the developmental landscape of fetal HSPCs and their local niche here by using single cell RNA sequencing we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study. | pubmed:33785593 | 4.5 dpf CHT cells | GSM4384818 | source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | 4.5 dpf CHT cells | UMI tools was used to analysis our single cell data.Firstly in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples measured by UMI counts | zebrafish embryos | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture’s introduction. | genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | GSM4384818 | GSM4384818: 4.5 dpf CHT cells; Danio rerio; RNA Seq | GSM4384818 | 1 | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture's introduction. | GEO Accession:GSM4384818 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP251673 | 171353H-CHT-4dpf_3_2_R1.fq.gz 171353H-CHT-4dpf_3_2_R2.fq.gz | fastq fastq | 30131096700.0 | 100436989.0 | GSM4384818 r1 | 0:150 1:150 | A:6727746568;C:5761021689;G:10040248562;T:7601697440;N:382441 | 150 | 150 | 6727746568 | 5761021689 | 10040248562 | 7601697440 | 382441 | SRX7854786 | SRS6264269 | SRA1051251 | GEO | Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES | 2 | 0.0 | 0.9175 | 0.0 | 0.06023 | 1.0 | 0.84208 | 0.51614 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2020-03-05 | Larval | Larval | Blood | Hematopoietic System | |||||||||||||
| 57172 | 57172 | SRR11243181 | SRX7854786 | SRS6264269 | SRP251673 | PRJNA610520 | A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish | GSE146404 | Transcriptome Analysis | To profile the developmental landscape of fetal HSPCs and their local niche here by using single cell RNA sequencing we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study. | pubmed:33785593 | 4.5 dpf CHT cells | GSM4384818 | source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | 4.5 dpf CHT cells | UMI tools was used to analysis our single cell data.Firstly in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples measured by UMI counts | zebrafish embryos | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture’s introduction. | genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | GSM4384818 | GSM4384818: 4.5 dpf CHT cells; Danio rerio; RNA Seq | GSM4384818 | 1 | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture's introduction. | GEO Accession:GSM4384818 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP251673 | 171353H-CHT-4dpf_2-2_R1.fq.gz 171353H-CHT-4dpf_2-2_R2.fq.gz | fastq fastq | 35454747300.0 | 118182491.0 | GSM4384818 r2 | 0:150 1:150 | A:7924515815;C:6769046954;G:11812021964;T:8948714749;N:447818 | 150 | 150 | 7924515815 | 6769046954 | 11812021964 | 8948714749 | 447818 | SRX7854786 | SRS6264269 | SRA1051251 | GEO | Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES | 2 | 0.0 | 0.91808 | 0.0 | 0.05945 | 1.0 | 0.83938 | 0.52604 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2020-03-05 | Larval | Larval | Blood | Hematopoietic System | |||||||||||||
| 57173 | 57173 | SRR11243182 | SRX7854786 | SRS6264269 | SRP251673 | PRJNA610520 | A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish | GSE146404 | Transcriptome Analysis | To profile the developmental landscape of fetal HSPCs and their local niche here by using single cell RNA sequencing we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study. | pubmed:33785593 | 4.5 dpf CHT cells | GSM4384818 | source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | 4.5 dpf CHT cells | UMI tools was used to analysis our single cell data.Firstly in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples measured by UMI counts | zebrafish embryos | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture’s introduction. | genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | GSM4384818 | GSM4384818: 4.5 dpf CHT cells; Danio rerio; RNA Seq | GSM4384818 | 1 | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture's introduction. | GEO Accession:GSM4384818 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP251673 | 171353H-CHT-4dpf_2_R1.fq.gz 171353H-CHT-4dpf_2_R2.fq.gz | fastq fastq | 15872844300.0 | 52909481.0 | GSM4384818 r3 | 0:150 1:150 | A:3729663981;C:3022353413;G:5072752670;T:4047900723;N:173513 | 150 | 150 | 3729663981 | 3022353413 | 5072752670 | 4047900723 | 173513 | SRX7854786 | SRS6264269 | SRA1051251 | GEO | Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES | 2 | 0.0 | 0.92013 | 0.0 | 0.0618 | 1.0 | 0.83871 | 0.51823 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2020-03-05 | Larval | Larval | Blood | Hematopoietic System | |||||||||||||
| 57174 | 57174 | SRR11243183 | SRX7854786 | SRS6264269 | SRP251673 | PRJNA610520 | A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish | GSE146404 | Transcriptome Analysis | To profile the developmental landscape of fetal HSPCs and their local niche here by using single cell RNA sequencing we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study. | pubmed:33785593 | 4.5 dpf CHT cells | GSM4384818 | source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | 4.5 dpf CHT cells | UMI tools was used to analysis our single cell data.Firstly in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples measured by UMI counts | zebrafish embryos | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture’s introduction. | genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | GSM4384818 | GSM4384818: 4.5 dpf CHT cells; Danio rerio; RNA Seq | GSM4384818 | 1 | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture's introduction. | GEO Accession:GSM4384818 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP251673 | 171353H-CHT-4dpf_1_R1.fq.gz 171353H-CHT-4dpf_1_R2.fq.gz | fastq fastq | 17996156400.0 | 59987188.0 | GSM4384818 r4 | 0:150 1:150 | A:4218380165;C:3448565478;G:5754713324;T:4574296718;N:200715 | 150 | 150 | 4218380165 | 3448565478 | 5754713324 | 4574296718 | 200715 | SRX7854786 | SRS6264269 | SRA1051251 | GEO | Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES | 2 | 0.0 | 0.92379 | 0.0 | 0.06035 | 1.0 | 0.83857 | 0.52292 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2020-03-05 | Larval | Larval | Blood | Hematopoietic System | |||||||||||||
| 57175 | 57175 | SRR11243184 | SRX7854786 | SRS6264269 | SRP251673 | PRJNA610520 | A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish | GSE146404 | Transcriptome Analysis | To profile the developmental landscape of fetal HSPCs and their local niche here by using single cell RNA sequencing we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study. | pubmed:33785593 | 4.5 dpf CHT cells | GSM4384818 | source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | 4.5 dpf CHT cells | UMI tools was used to analysis our single cell data.Firstly in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples measured by UMI counts | zebrafish embryos | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture’s introduction. | genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:4.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | GSM4384818 | GSM4384818: 4.5 dpf CHT cells; Danio rerio; RNA Seq | GSM4384818 | 1 | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture's introduction. | GEO Accession:GSM4384818 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP251673 | 171353H-CHT-4dpf_1-2_R1.fq.gz 171353H-CHT-4dpf_1-2_R2.fq.gz | fastq fastq | 39542324700.0 | 131807749.0 | GSM4384818 r5 | 0:150 1:150 | A:8830009820;C:7582391853;G:13173552664;T:9955867355;N:503008 | 150 | 150 | 8830009820 | 7582391853 | 13173552664 | 9955867355 | 503008 | SRX7854786 | SRS6264269 | SRA1051251 | GEO | Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES | 2 | 0.0 | 0.91925 | 0.0 | 0.05821 | 1.0 | 0.83989 | 0.50837 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2020-03-05 | Larval | Larval | Blood | Hematopoietic System | |||||||||||||
| 57176 | 57176 | SRR11243176 | SRX7854785 | SRS6264267 | SRP251673 | PRJNA610520 | A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish | GSE146404 | Transcriptome Analysis | To profile the developmental landscape of fetal HSPCs and their local niche here by using single cell RNA sequencing we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study. | pubmed:33785593 | 3.5 dpf CHT cells | GSM4384817 | source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | 3.5 dpf CHT cells | UMI tools was used to analysis our single cell data.Firstly in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples measured by UMI counts | zebrafish embryos | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture’s introduction. | genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | GSM4384817 | GSM4384817: 3.5 dpf CHT cells; Danio rerio; RNA Seq | GSM4384817 | 1 | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture's introduction. | GEO Accession:GSM4384817 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP251673 | 171353F_CHT-3dpf_4_R1.fq.gz 171353F_CHT-3dpf_4_R2.fq.gz | fastq fastq | 71692100700.0 | 238973669.0 | GSM4384817 r1 | 0:150 1:150 | A:17020567059;C:13566816873;G:21814800469;T:19287755240;N:2161059 | 150 | 150 | 17020567059 | 13566816873 | 21814800469 | 19287755240 | 2161059 | SRX7854785 | SRS6264267 | SRA1051251 | GEO | Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES | 2 | 0.0 | 0.9088 | 0.0 | 0.06027 | 1.0 | 0.82733 | 0.50573 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2020-03-05 | Larval | Larval | Blood | Hematopoietic System | |||||||||||||
| 57177 | 57177 | SRR11243177 | SRX7854785 | SRS6264267 | SRP251673 | PRJNA610520 | A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish | GSE146404 | Transcriptome Analysis | To profile the developmental landscape of fetal HSPCs and their local niche here by using single cell RNA sequencing we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study. | pubmed:33785593 | 3.5 dpf CHT cells | GSM4384817 | source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | 3.5 dpf CHT cells | UMI tools was used to analysis our single cell data.Firstly in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples measured by UMI counts | zebrafish embryos | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture’s introduction. | genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | GSM4384817 | GSM4384817: 3.5 dpf CHT cells; Danio rerio; RNA Seq | GSM4384817 | 1 | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture's introduction. | GEO Accession:GSM4384817 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP251673 | 171353F_CHT-3dpf_1_R2.fq.gz 171353F_CHT-3dpf_1_R1.fq.gz | fastq fastq | 57793587900.0 | 192645293.0 | GSM4384817 r2 | 0:150 1:150 | A:13736253697;C:10912235777;G:17579141926;T:15564212842;N:1743658 | 150 | 150 | 13736253697 | 10912235777 | 17579141926 | 15564212842 | 1743658 | SRX7854785 | SRS6264267 | SRA1051251 | GEO | Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES | 2 | 0.0 | 0.90774 | 0.0 | 0.06058 | 1.0 | 0.82875 | 0.49524 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2020-03-05 | Larval | Larval | Blood | Hematopoietic System | |||||||||||||
| 57178 | 57178 | SRR11243178 | SRX7854785 | SRS6264267 | SRP251673 | PRJNA610520 | A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish | GSE146404 | Transcriptome Analysis | To profile the developmental landscape of fetal HSPCs and their local niche here by using single cell RNA sequencing we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study. | pubmed:33785593 | 3.5 dpf CHT cells | GSM4384817 | source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | 3.5 dpf CHT cells | UMI tools was used to analysis our single cell data.Firstly in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples measured by UMI counts | zebrafish embryos | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture’s introduction. | genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | GSM4384817 | GSM4384817: 3.5 dpf CHT cells; Danio rerio; RNA Seq | GSM4384817 | 1 | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture's introduction. | GEO Accession:GSM4384817 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP251673 | 171353F_CHT-3dpf_3_R2.fq.gz 171353F_CHT-3dpf_3_R1.fq.gz | fastq fastq | 63713003700.0 | 212376679.0 | GSM4384817 r3 | 0:150 1:150 | A:15098662178;C:12078656688;G:19421188669;T:17112576360;N:1919805 | 150 | 150 | 15098662178 | 12078656688 | 19421188669 | 17112576360 | 1919805 | SRX7854785 | SRS6264267 | SRA1051251 | GEO | Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES | 2 | 0.0 | 0.90945 | 0.0 | 0.06034 | 1.0 | 0.83149 | 0.50559 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2020-03-05 | Larval | Larval | Blood | Hematopoietic System | |||||||||||||
| 57179 | 57179 | SRR11243179 | SRX7854785 | SRS6264267 | SRP251673 | PRJNA610520 | A Single Cell Resolution Atlas of expanding hematopoietic organ in zebrafish | GSE146404 | Transcriptome Analysis | To profile the developmental landscape of fetal HSPCs and their local niche here by using single cell RNA sequencing we decoded the expanding hematopoietic organ in zebrafish Overall design: The tails of 3.5 dpf and 4.5 dpf Tg kdrl:mCherry/CD41:GFP embryos were collected and digested with 2.5% trypsin for dissociation.The 50 000 kdrl:mCherry+ cells plus 50000 CD41:GFP+ cells and double negative cells were isolated by fluorescence activated cell sorting FACS for 10× Genomics analysis CapitalBio Technology Corporation. Please note that the GSE120503 GSM3402061 55hpf CHT single cell RNA seq data raw data been re analyzed in the current study. | pubmed:33785593 | 3.5 dpf CHT cells | GSM4384817 | source name:zebrafish embryos|genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | 3.5 dpf CHT cells | UMI tools was used to analysis our single cell data.Firstly in “whitelist” step we set 5000 as cell number and check quality plots.The R1 fastq file is the technical read including barcode and UMI and R2 is biological sequencing. Then in “extract” step we filter some low quality reads and non UMI reads with recommend parameters so that we can use STAR to map to the reference genome. Finally in “count” step we generate a gene expression matrix for following analysis. Genome build: GRCz10 Supplementary files format and content: Contains the expression level of all three samples measured by UMI counts | zebrafish embryos | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture’s introduction. | genotype/variation:Tg kdrl:mCherry/CD41:GFP|age:3.5 dpf|tissue:caudal hematopoietic tissue CHT region|cell type:endothelial cells+hematopoietic cells+ double negative niche cells | GSM4384817 | GSM4384817: 3.5 dpf CHT cells; Danio rerio; RNA Seq | GSM4384817 | 1 | Then single cell suspensions 300 1 000 living cells per microliter determined by trypan blue staining were loaded on a Chromium Single Cell Controller 10× Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell 30 Library and Gel Bead Kit V2 10× Genomics 120237. Captured cells were lysed and the released RNAs were barcoded through reverse transcription in individual GEMs. Barcoded cDNAs were pooled and cleaned up using beads Invitrogen 37002D. 10X genomics scRNA Seq: Single cell RNA sequencing scRNA seq libraries were prepared using Single Cell 30 Library Gel Bead Kit V2 10× Genomics 120237 following the manufacture's introduction. | GEO Accession:GSM4384817 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP251673 | 171353F_CHT-3dpf_2_R1.fq.gz 171353F_CHT-3dpf_2_R2.fq.gz | fastq fastq | 71620433400.0 | 238734778.0 | GSM4384817 r4 | 0:150 1:150 | A:16843285494;C:13823957864;G:21855431757;T:19095628638;N:2129647 | 150 | 150 | 16843285494 | 13823957864 | 21855431757 | 19095628638 | 2129647 | SRX7854785 | SRS6264267 | SRA1051251 | GEO | Group of Hematopoiesis and Cardiovascular Development, INSTITUTE OF ZOOLOGY, CHINESE ACADEMY OF SCIENCES | 2 | 0.0 | 0.90995 | 0.0 | 0.06019 | 1.0 | 0.82767 | 0.49515 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | China | 2020-03-05 | Larval | Larval | Blood | Hematopoietic System | |||||||||||||
| 60923 | 60923 | SRR12658672 | SRX9139730 | SRS7381396 | SRP282672 | PRJNA663960 | Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development | GSE158099 | Transcriptome Analysis | We used single cell RNA sequencing to investigate the expression and the heterogeneity of wild type and runx1 mutant cd41 GFPLow cd41GFP hematopoietic stem and progenitor cells at embryonic 2.5 dpf dpf and larval stages 6 10 dpf 16 dpf. Overall design: Single cell RNA seq with FACS sorted cd41 GFPlow cells from wild type and runx1 / at 2.5 6 10 dpf 16 dpf. | parent bioproject:PRJNA663961 | pubmed:34492681 | cd41:GFPlow runx1 / bloodless 16dpf | GSM4792215 | tissue:sorted cd41:GFPlow|strain:EK|genotype/variation:runx1 / del8 hg96 tgcd41:GFP|age:16 dpf|cell subset:sorted cd41:GFPlow | cd41:GFPlow runx1 / bloodless 16dpf | Sequences from the Chromium platform were de multiplexed and aligned using CellRanger ver. 2.0.2 from 10x Genomics using custom zebrafish reference genome GRCz10 and transcript annotation reference GRCz10.87 with default parameters. Genome build: GRCz10 Supplementary files format and content: barcodes.tsv genes.tsv features.tsv matrix.mtx | sorted cd41:GFPlow | Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol. | strain:EK|genotype/variation:runx1 / del8 hg96 tgcd41:GFP|age:16 dpf|cell subset:sorted cd41:GFPlow | GSM4792215 | GSM4792215: cd41:GFPlow runx1 / bloodless 16dpf; Danio rerio; RNA Seq | GSM4792215 | 1 | Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium. Single cell RNA seq libraries were prepared using Chromium Single Cell three prime Library & Gel Bead Kit v3. Cell lysis cDNA preparation and library construction were prepared following the manufacturer's protocol. | GEO Accession:GSM4792215 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 550 | SRP282672 | loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=SC8.EB200211 2.R1.fastq.gz read2PairFiles=SC8.EB200211 2.R2.fastq.gz read3PairFiles=SC8.EB200211 2.I1.fastq.gz | SC8.EB200211_2.I1.fastq.gz SC8.EB200211_2.R1.fastq.gz SC8.EB200211_2.R2.fastq.gz | fastq fastq fastq | 31985659032.0 | 238698948.0 | GSM4792215 r1 | 0:28 1:98 2:8 | A:8834796646;C:7245480386;G:7345360172;T:8558850270;N:1171558 | 28 | 98 | 8 | 8834796646 | 7245480386 | 7345360172 | 8558850270 | 1171558 | SRX9139730 | SRS7381396 | SRA1126726 | GEO | NHGRI | 1 | 0.93838 | 0.0839 | 0.7558 | 0.51065 | 98 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-09-16 | Larval | Larval | Blood | Hematopoietic System | |||||||||||||||
| 61983 | 61983 | SRR13080692 | SRX9527457 | SRS7734428 | SRP293088 | PRJNA679243 | A Non Canonical Type 2 Immune Response Coordinates Tuberculous Granuloma Formation and Epithelialization | GSE161712 | Other | Using the zebrafish M. marinum model we identify the basis of granuloma macrophage transformation. Single cell RNA seq analysis of zebrafish granulomas as well as analysis of M. tuberculosis infected macaques reveal that even in the presence of robust type 1 immune responses countervailing type 2 signals associate with macrophage epithelialization. We find that type 2 immune signaling mediated via stat6 is absolutely required for epithelialization and granuloma formation. Overall design: Wildtype zebrafish M. marinum granuloma single cell RNAseq profile. | pubmed:33761328 | *AB wildtype zebrafish M.marinum granuloma cells | GSM4913139 | source name:WT Zebrafish granuloma cels|tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB | *AB wildtype zebrafish M.marinum granuloma cells | 10X Cell Ranger was used to demultiplex raw base call BCL files generated by an Illumina sequencer into FASTQ before aligning them to the Ensembl zebrafish genome assembly GRCz11.96 performed filtering barcode and UMI counting. Genome build: GRCz11.96 Supplementary files format and content: WTGran.matrix.mtx: Gene barcode matrix in Market Exchange Format MEX for Mus musculus Uninjured Control & Injured1d tibialis anterior muscle cells. Columns correspond to individual cellsbarcodes while rows correspond to genes. Supplementary files format and content: WTGran.features.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column. Supplementary files format and content: WTGran.barcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx. | WT Zebrafish granuloma cels | Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell 3’ GEM Library and Gel Bead Kit v3. | Adult wildtype *AB zebrafish were infected with 350 fluorescent bacteria of M. marinum. | tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB | GSM4913139 | GSM4913139: *AB wildtype zebrafish M.marinum granuloma cells; Danio rerio; RNA Seq | GSM4913139 | 1 | Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell three prime GEM Library and Gel Bead Kit v3. | GEO Accession:GSM4913139 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP293088 | loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=5761 S1 L001 I1 001.fastq.gz read2PairFiles=5761 S1 L001 R1 001.fastq.gz read3PairFiles=5761 S1 L001 R2 001.fastq.gz | 5761_S1_L001_I1_001.fastq.gz 5761_S1_L001_R1_001.fastq.gz 5761_S1_L001_R2_001.fastq.gz | fastq fastq fastq | 13295345266.0 | 104687758.0 | GSM4913139 r1 | 0:8 1:28 2:91 | A:3755348831;C:2900888340;G:2979576059;T:3656820253;N:2711783 | 8 | 28 | 91 | 3755348831 | 2900888340 | 2979576059 | 3656820253 | 2711783 | SRX9527457 | SRS7734428 | SRA1160946 | GEO | Tobin, Molecular Genetics and Microbiology, Duke University | 1 | 0.92709 | 0.13791 | 0.81929 | 0.57724 | 91 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-11-18 | Adult | Adult | Blood | Hematopoietic System | |||||||||||||||
| 61984 | 61984 | SRR13080693 | SRX9527457 | SRS7734428 | SRP293088 | PRJNA679243 | A Non Canonical Type 2 Immune Response Coordinates Tuberculous Granuloma Formation and Epithelialization | GSE161712 | Other | Using the zebrafish M. marinum model we identify the basis of granuloma macrophage transformation. Single cell RNA seq analysis of zebrafish granulomas as well as analysis of M. tuberculosis infected macaques reveal that even in the presence of robust type 1 immune responses countervailing type 2 signals associate with macrophage epithelialization. We find that type 2 immune signaling mediated via stat6 is absolutely required for epithelialization and granuloma formation. Overall design: Wildtype zebrafish M. marinum granuloma single cell RNAseq profile. | pubmed:33761328 | *AB wildtype zebrafish M.marinum granuloma cells | GSM4913139 | source name:WT Zebrafish granuloma cels|tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB | *AB wildtype zebrafish M.marinum granuloma cells | 10X Cell Ranger was used to demultiplex raw base call BCL files generated by an Illumina sequencer into FASTQ before aligning them to the Ensembl zebrafish genome assembly GRCz11.96 performed filtering barcode and UMI counting. Genome build: GRCz11.96 Supplementary files format and content: WTGran.matrix.mtx: Gene barcode matrix in Market Exchange Format MEX for Mus musculus Uninjured Control & Injured1d tibialis anterior muscle cells. Columns correspond to individual cellsbarcodes while rows correspond to genes. Supplementary files format and content: WTGran.features.tsv: Genes corresponding to row indices in matrix.mtx. Gene ID and gene name are stored in the first and second column. Supplementary files format and content: WTGran.barcodes.tsv: Barcode sequences that correspond to column indices in matrix.mtx. | WT Zebrafish granuloma cels | Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell 3’ GEM Library and Gel Bead Kit v3. | Adult wildtype *AB zebrafish were infected with 350 fluorescent bacteria of M. marinum. | tissue:Granulomas|cell type:Granuloma cells|zebrafish strain:*AB | GSM4913139 | GSM4913139: *AB wildtype zebrafish M.marinum granuloma cells; Danio rerio; RNA Seq | GSM4913139 | 1 | Granulomas were microdissected from of tissues 14 days post infection and cells dissociated using 30 minute incubation with 0.05% trypsin/EDTA Library preparation was done using Chromium Single Cell three prime GEM Library and Gel Bead Kit v3. | GEO Accession:GSM4913139 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP293088 | loader:fastq load.py|options: platform=Illumina readTypes=TTB read1PairFiles=5895 S1 L001 I1 001.fastq.gz read2PairFiles=5895 S1 L001 R1 001.fastq.gz read3PairFiles=5895 S1 L001 R2 001.fastq.gz | 5895_S1_L001_I1_001.fastq.gz 5895_S1_L001_R1_001.fastq.gz 5895_S1_L001_R2_001.fastq.gz | fastq fastq fastq | 17723636384.0 | 139556192.0 | GSM4913139 r2 | 0:8 1:28 2:91 | A:4955483447;C:3902218538;G:4036183306;T:4807856940;N:21894153 | 8 | 28 | 91 | 4955483447 | 3902218538 | 4036183306 | 4807856940 | 21894153 | SRX9527457 | SRS7734428 | SRA1160946 | GEO | Tobin, Molecular Genetics and Microbiology, Duke University | 1 | 0.9176 | 0.13304 | 0.81462 | 0.57616 | 91 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2020-11-18 | Adult | Adult | Blood | Hematopoietic System | |||||||||||||||
| 65651 | 65651 | SRR15483596 | SRX11783413 | SRS9786611 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | runx1:mCherry+ at 52 hpf #2 replicate | GSM5525118 | tissue:hematopoietic cells|developmental stage:52 hpf line:runx1+23:nls mCherry | runx1:mCherry+ at 52 hpf #2 replicate | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:52 hpf line:runx1+23:nls mCherry | GSM5525118 | GSM5525118: runx1:mCherry+ at 52 hpf #2 replicate; Danio rerio; RNA Seq | GSM5525118 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525118 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=R2 2 S1 L001 R1 001.fastq.gz read2PairFiles=R2 2 S1 L001 R2 001.fastq.gz read3PairFiles=R2 2 S1 L001 I1 001.fastq.gz | R2-2_S1_L001_I1_001.fastq.gz R2-2_S1_L001_R1_001.fastq.gz R2-2_S1_L001_R2_001.fastq.gz | fastq fastq fastq | 59162946612.0 | 192087489.0 | GSM5525118 r1 | 0:150 1:150 2:8 | A:6826510360;C:7720741166;G:7033747534;T:7231279942;N:844348 | 150 | 150 | 8 | 6826510360 | 7720741166 | 7033747534 | 7231279942 | 844348 | SRX11783413 | SRS9786611 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 1 | 0.95266 | 0.01784 | 0.93022 | 0.46235 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Hatching | Embryo | Blood | Hematopoietic System | ||||||||||||||||
| 65652 | 65652 | SRR15483597 | SRX11783413 | SRS9786611 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | runx1:mCherry+ at 52 hpf #2 replicate | GSM5525118 | tissue:hematopoietic cells|developmental stage:52 hpf line:runx1+23:nls mCherry | runx1:mCherry+ at 52 hpf #2 replicate | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:52 hpf line:runx1+23:nls mCherry | GSM5525118 | GSM5525118: runx1:mCherry+ at 52 hpf #2 replicate; Danio rerio; RNA Seq | GSM5525118 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525118 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=R2 2 S1 L002 R1 001.fastq.gz read2PairFiles=R2 2 S1 L002 R2 001.fastq.gz read3PairFiles=R2 2 S1 L002 I1 001.fastq.gz | R2-2_S1_L002_I1_001.fastq.gz R2-2_S1_L002_R1_001.fastq.gz R2-2_S1_L002_R2_001.fastq.gz | fastq fastq fastq | 67940768588.0 | 220586911.0 | GSM5525118 r2 | 0:150 1:150 2:8 | A:7901205395;C:8819719149;G:8118311347;T:8243562587;N:5238172 | 150 | 150 | 8 | 7901205395 | 8819719149 | 8118311347 | 8243562587 | 5238172 | SRX11783413 | SRS9786611 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 1 | 0.94536 | 0.018 | 0.92839 | 0.45489 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Hatching | Embryo | Blood | Hematopoietic System | ||||||||||||||||
| 65653 | 65653 | SRR15483594 | SRX11783412 | SRS9786609 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | runx1:mCherry+ at 52 hpf #1 | GSM5525117 | tissue:hematopoietic cells|developmental stage:52 hpf line:runx1+23:nls mCherry | runx1:mCherry+ at 52 hpf #1 | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:52 hpf line:runx1+23:nls mCherry | GSM5525117 | GSM5525117: runx1:mCherry+ at 52 hpf #1; Danio rerio; RNA Seq | GSM5525117 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525117 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=R2 1 S1 L001 R1 001.fastq.gz read2PairFiles=R2 1 S1 L001 R2 001.fastq.gz read3PairFiles=R2 1 S1 L001 I1 001.fastq.gz | R2-1_S1_L001_I1_001.fastq.gz R2-1_S1_L001_R1_001.fastq.gz R2-1_S1_L001_R2_001.fastq.gz | fastq fastq fastq | 64542996056.0 | 209555182.0 | GSM5525117 r1 | 0:150 1:150 2:8 | A:7500200023;C:8401456631;G:7492567345;T:8038123819;N:929482 | 150 | 150 | 8 | 7500200023 | 8401456631 | 7492567345 | 8038123819 | 929482 | SRX11783412 | SRS9786609 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 1 | 0.94027 | 0.01204 | 0.94107 | 0.46801 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Hatching | Embryo | Blood | Hematopoietic System | ||||||||||||||||
| 65654 | 65654 | SRR15483595 | SRX11783412 | SRS9786609 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | runx1:mCherry+ at 52 hpf #1 | GSM5525117 | tissue:hematopoietic cells|developmental stage:52 hpf line:runx1+23:nls mCherry | runx1:mCherry+ at 52 hpf #1 | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:52 hpf line:runx1+23:nls mCherry | GSM5525117 | GSM5525117: runx1:mCherry+ at 52 hpf #1; Danio rerio; RNA Seq | GSM5525117 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525117 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=R2 1 S1 L002 R1 001.fastq.gz read2PairFiles=R2 1 S1 L002 R2 001.fastq.gz read3PairFiles=R2 1 S1 L002 I1 001.fastq.gz | R2-1_S1_L002_I1_001.fastq.gz R2-1_S1_L002_R1_001.fastq.gz R2-1_S1_L002_R2_001.fastq.gz | fastq fastq fastq | 61129147772.0 | 198471259.0 | GSM5525117 r2 | 0:150 1:150 2:8 | A:7164346674;C:7911114850;G:7135136885;T:7555336618;N:4753823 | 150 | 150 | 8 | 7164346674 | 7911114850 | 7135136885 | 7555336618 | 4753823 | SRX11783412 | SRS9786609 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 1 | 0.93152 | 0.01164 | 0.94152 | 0.46255 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Hatching | Embryo | Blood | Hematopoietic System | ||||||||||||||||
| 65655 | 65655 | SRR15483588 | SRX11783411 | SRS9786608 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate | GSM5525116 | tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | GSM5525116 | GSM5525116: draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate; Danio rerio; RNA Seq | GSM5525116 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525116 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=DG2 2 S1 L001 R1 001.fastq.gz read2PairFiles=DG2 2 S1 L001 R2 001.fastq.gz read3PairFiles=DG2 2 S1 L001 I1 001.fastq.gz | DG2-2_S1_L001_I1_001.fastq.gz DG2-2_S1_L001_R1_001.fastq.gz DG2-2_S1_L001_R2_001.fastq.gz | fastq fastq fastq | 58062154920.0 | 188513490.0 | GSM5525116 r1 | 0:150 1:150 2:8 | A:6786904201;C:7461082970;G:6741279762;T:7286929534;N:827033 | 150 | 150 | 8 | 6786904201 | 7461082970 | 6741279762 | 7286929534 | 827033 | SRX11783411 | SRS9786608 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 1 | 0.9442 | 0.02532 | 0.92577 | 0.45185 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Hatching | Embryo | Blood | Hematopoietic System | ||||||||||||||||
| 65656 | 65656 | SRR15483589 | SRX11783411 | SRS9786608 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate | GSM5525116 | tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | GSM5525116 | GSM5525116: draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate; Danio rerio; RNA Seq | GSM5525116 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525116 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=DG2 2 S1 L002 R1 001.fastq.gz read2PairFiles=DG2 2 S1 L002 R2 001.fastq.gz read3PairFiles=DG2 2 S1 L002 I1 001.fastq.gz | DG2-2_S1_L002_I1_001.fastq.gz DG2-2_S1_L002_R1_001.fastq.gz DG2-2_S1_L002_R2_001.fastq.gz | fastq fastq fastq | 71629010068.0 | 232561721.0 | GSM5525116 r2 | 0:150 1:150 2:8 | A:8422157482;C:9164931651;G:8346143692;T:8946552575;N:4472750 | 150 | 150 | 8 | 8422157482 | 9164931651 | 8346143692 | 8946552575 | 4472750 | SRX11783411 | SRS9786608 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 1 | 0.93666 | 0.02678 | 0.92232 | 0.44942 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Hatching | Embryo | Blood | Hematopoietic System | ||||||||||||||||
| 65657 | 65657 | SRR15483590 | SRX11783411 | SRS9786608 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate | GSM5525116 | tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | GSM5525116 | GSM5525116: draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate; Danio rerio; RNA Seq | GSM5525116 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525116 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | DG2-2_S1_L003_R1_001.fastq.gz DG2-2_S1_L003_R2_001.fastq.gz | fastq fastq | 32047702200.0 | 106825674.0 | GSM5525116 r3 | 0:150 1:150 | A:7309683350;C:6236246000;G:6254785333;T:12244316725;N:2670792 | 150 | 150 | 7309683350 | 6236246000 | 6254785333 | 12244316725 | 2670792 | SRX11783411 | SRS9786608 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 2 | 0.01831 | 0.94417 | 0.00206 | 0.02463 | 0.99691 | 0.92423 | 0.53203 | 0.45728 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Hatching | Embryo | Blood | Hematopoietic System | ||||||||||||
| 65658 | 65658 | SRR15483591 | SRX11783411 | SRS9786608 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate | GSM5525116 | tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | GSM5525116 | GSM5525116: draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate; Danio rerio; RNA Seq | GSM5525116 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525116 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | DG2-2_S1_L004_R1_001.fastq.gz DG2-2_S1_L004_R2_001.fastq.gz | fastq fastq | 37463959500.0 | 124879865.0 | GSM5525116 r4 | 0:150 1:150 | A:8552446843;C:7287672885;G:7301637904;T:14319175980;N:3025888 | 150 | 150 | 8552446843 | 7287672885 | 7301637904 | 14319175980 | 3025888 | SRX11783411 | SRS9786608 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 2 | 0.0179 | 0.94533 | 0.00191 | 0.0243 | 0.99691 | 0.92261 | 0.49722 | 0.45421 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Hatching | Embryo | Blood | Hematopoietic System | ||||||||||||
| 65659 | 65659 | SRR15483592 | SRX11783411 | SRS9786608 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate | GSM5525116 | tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | GSM5525116 | GSM5525116: draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate; Danio rerio; RNA Seq | GSM5525116 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525116 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | DG2-2_S1_L005_R1_001.fastq.gz DG2-2_S1_L005_R2_001.fastq.gz | fastq fastq | 30981057900.0 | 103270193.0 | GSM5525116 r5 | 0:150 1:150 | A:7076201480;C:6026934261;G:6065200560;T:11810111130;N:2610469 | 150 | 150 | 7076201480 | 6026934261 | 6065200560 | 11810111130 | 2610469 | SRX11783411 | SRS9786608 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 2 | 0.01658 | 0.93855 | 0.00198 | 0.02394 | 0.99734 | 0.92476 | 0.53823 | 0.45548 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Hatching | Embryo | Blood | Hematopoietic System | ||||||||||||
| 65660 | 65660 | SRR15483593 | SRX11783411 | SRS9786608 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate | GSM5525116 | tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | GSM5525116 | GSM5525116: draculin:mCherry+;gata1:GFP at 52 hpf #2 replicate; Danio rerio; RNA Seq | GSM5525116 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525116 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | DG2-2_S1_L006_R1_001.fastq.gz DG2-2_S1_L006_R2_001.fastq.gz | fastq fastq | 33497811000.0 | 111659370.0 | GSM5525116 r6 | 0:150 1:150 | A:7673047524;C:6494998239;G:6520425795;T:12806463581;N:2875861 | 150 | 150 | 7673047524 | 6494998239 | 6520425795 | 12806463581 | 2875861 | SRX11783411 | SRS9786608 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 2 | 0.01712 | 0.94074 | 0.00206 | 0.02516 | 0.99701 | 0.92318 | 0.56268 | 0.45333 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Hatching | Embryo | Blood | Hematopoietic System | ||||||||||||
| 65661 | 65661 | SRR15483582 | SRX11783410 | SRS9786606 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | draculin:mCherry+;gata1:GFP at 52 hpf #1 | GSM5525115 | tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | draculin:mCherry+;gata1:GFP at 52 hpf #1 | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | GSM5525115 | GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq | GSM5525115 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525115 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=DG2 1 S1 L001 R1 001.fastq.gz read2PairFiles=DG2 1 S1 L001 R2 001.fastq.gz read3PairFiles=DG2 1 S1 L001 I1 001.fastq.gz | DG2-1_S1_L001_I1_001.fastq.gz DG2-1_S1_L001_R1_001.fastq.gz DG2-1_S1_L001_R2_001.fastq.gz | fastq fastq fastq | 53816019796.0 | 174727337.0 | GSM5525115 r1 | 0:150 1:150 2:8 | A:6268319263;C:6935405810;G:6236287882;T:6768309909;N:777686 | 150 | 150 | 8 | 6268319263 | 6935405810 | 6236287882 | 6768309909 | 777686 | SRX11783410 | SRS9786606 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 1 | 0.94373 | 0.02418 | 0.93206 | 0.4538 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Hatching | Embryo | Blood | Hematopoietic System | ||||||||||||||||
| 65662 | 65662 | SRR15483583 | SRX11783410 | SRS9786606 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | draculin:mCherry+;gata1:GFP at 52 hpf #1 | GSM5525115 | tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | draculin:mCherry+;gata1:GFP at 52 hpf #1 | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | GSM5525115 | GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq | GSM5525115 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525115 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=DG2 1 S1 L002 R1 001.fastq.gz read2PairFiles=DG2 1 S1 L002 R2 001.fastq.gz read3PairFiles=DG2 1 S1 L002 I1 001.fastq.gz | DG2-1_S1_L002_I1_001.fastq.gz DG2-1_S1_L002_R1_001.fastq.gz DG2-1_S1_L002_R2_001.fastq.gz | fastq fastq fastq | 56656687472.0 | 183950284.0 | GSM5525115 r2 | 0:150 1:150 2:8 | A:6636746214;C:7271043747;G:6588518102;T:7092648593;N:3585944 | 150 | 150 | 8 | 6636746214 | 7271043747 | 6588518102 | 7092648593 | 3585944 | SRX11783410 | SRS9786606 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 1 | 0.9348 | 0.02385 | 0.93156 | 0.45273 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Hatching | Embryo | Blood | Hematopoietic System | ||||||||||||||||
| 65663 | 65663 | SRR15483584 | SRX11783410 | SRS9786606 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | draculin:mCherry+;gata1:GFP at 52 hpf #1 | GSM5525115 | tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | draculin:mCherry+;gata1:GFP at 52 hpf #1 | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | GSM5525115 | GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq | GSM5525115 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525115 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | DG2-1_S1_L003_R1_001.fastq.gz DG2-1_S1_L003_R2_001.fastq.gz | fastq fastq | 33218500800.0 | 110728336.0 | GSM5525115 r3 | 0:150 1:150 | A:7550847416;C:6408594085;G:6405597564;T:12826295610;N:27166125 | 150 | 150 | 7550847416 | 6408594085 | 6405597564 | 12826295610 | 27166125 | SRX11783410 | SRS9786606 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 2 | 0.02176 | 0.94163 | 0.00286 | 0.02347 | 0.99703 | 0.92991 | 0.46265 | 0.45574 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Hatching | Embryo | Blood | Hematopoietic System | ||||||||||||
| 65664 | 65664 | SRR15483585 | SRX11783410 | SRS9786606 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | draculin:mCherry+;gata1:GFP at 52 hpf #1 | GSM5525115 | tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | draculin:mCherry+;gata1:GFP at 52 hpf #1 | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | GSM5525115 | GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq | GSM5525115 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525115 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | DG2-1_S1_L004_R1_001.fastq.gz DG2-1_S1_L004_R2_001.fastq.gz | fastq fastq | 33634915800.0 | 112116386.0 | GSM5525115 r4 | 0:150 1:150 | A:7645827173;C:6494042604;G:6493405590;T:12974094595;N:27545838 | 150 | 150 | 7645827173 | 6494042604 | 6493405590 | 12974094595 | 27545838 | SRX11783410 | SRS9786606 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 2 | 0.02104 | 0.9407 | 0.00263 | 0.02247 | 0.99701 | 0.93257 | 0.49246 | 0.4561 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Hatching | Embryo | Blood | Hematopoietic System | ||||||||||||
| 65665 | 65665 | SRR15483586 | SRX11783410 | SRS9786606 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | draculin:mCherry+;gata1:GFP at 52 hpf #1 | GSM5525115 | tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | draculin:mCherry+;gata1:GFP at 52 hpf #1 | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | GSM5525115 | GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq | GSM5525115 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525115 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | DG2-1_S1_L005_R1_001.fastq.gz DG2-1_S1_L005_R2_001.fastq.gz | fastq fastq | 34113860700.0 | 113712869.0 | GSM5525115 r5 | 0:150 1:150 | A:7749471214;C:6598363925;G:6596788535;T:13141319294;N:27917732 | 150 | 150 | 7749471214 | 6598363925 | 6596788535 | 13141319294 | 27917732 | SRX11783410 | SRS9786606 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 2 | 0.02131 | 0.94056 | 0.0023 | 0.02334 | 0.99719 | 0.93164 | 0.50985 | 0.45474 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Hatching | Embryo | Blood | Hematopoietic System | ||||||||||||
| 65666 | 65666 | SRR15483587 | SRX11783410 | SRS9786606 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | draculin:mCherry+;gata1:GFP at 52 hpf #1 | GSM5525115 | tissue:hematopoietic cells|developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | draculin:mCherry+;gata1:GFP at 52 hpf #1 | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:52 hpf line:draculin:mCherry;gata1:GFP | GSM5525115 | GSM5525115: draculin:mCherry+;gata1:GFP at 52 hpf #1; Danio rerio; RNA Seq | GSM5525115 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525115 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | DG2-1_S1_L006_R1_001.fastq.gz DG2-1_S1_L006_R2_001.fastq.gz | fastq fastq | 34597356600.0 | 115324522.0 | GSM5525115 r6 | 0:150 1:150 | A:7866654210;C:6690644103;G:6695640643;T:13316020558;N:28397086 | 150 | 150 | 7866654210 | 6690644103 | 6695640643 | 13316020558 | 28397086 | SRX11783410 | SRS9786606 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 2 | 0.02131 | 0.94082 | 0.00235 | 0.02244 | 0.99665 | 0.93089 | 0.53827 | 0.45518 | 150 | 150 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Hatching | Embryo | Blood | Hematopoietic System | ||||||||||||
| 65667 | 65667 | SRR15483581 | SRX11783409 | SRS9786607 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | draculin:mCherry+;gata1:GFP at 30 hpf #2 replicate | GSM5525114 | tissue:hematopoietic cells|developmental stage:30 hpf line:draculin:mCherry;gata1:GFP | draculin:mCherry+;gata1:GFP at 30 hpf #2 replicate | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:30 hpf line:draculin:mCherry;gata1:GFP | GSM5525114 | GSM5525114: draculin:mCherry+;gata1:GFP at 30 hpf #2 replicate; Danio rerio; RNA Seq | GSM5525114 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525114 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=DG1 3 S1 L001 R1 001.fastq.gz read2PairFiles=DG1 3 S1 L001 R2 001.fastq.gz read3PairFiles=DG1 3 S1 L001 I1 001.fastq.gz | DG1-3_S1_L001_I1_001.fastq.gz DG1-3_S1_L001_R1_001.fastq.gz DG1-3_S1_L001_R2_001.fastq.gz | fastq fastq fastq | 53654080172.0 | 174201559.0 | GSM5525114 r1 | 0:150 1:150 2:8 | A:6842604916;C:6327854414;G:6203934909;T:6755061460;N:778151 | 150 | 150 | 8 | 6842604916 | 6327854414 | 6203934909 | 6755061460 | 778151 | SRX11783409 | SRS9786607 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 1 | 0.92988 | 0.06632 | 0.84691 | 0.45741 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Pharyngula | Embryo | Blood | Hematopoietic System | ||||||||||||||||
| 65668 | 65668 | SRR15483580 | SRX11783408 | SRS9786605 | SRP332734 | PRJNA755310 | Single cell RNA sequencing analysis of transgenic zebrafish embryo/larvae | GSE182213 | Transcriptome Analysis | The purpose of the experiment was to define the heterogeneity of hematopoietic stem and progenitor cells HSPC at emergence and initial maturation using scRNA Seq of enriched blood populations from transgenic fluorescent zebrafish 30 hpf and 52 hpf. Results provide insight into the different HSPC populations in heamtopoietic development. Overall design: 10X Single cell RNA sequencing from sorted hematopoeitic stem and progenitor cells from transgenic fluorescent zebrafish at 30 hpf and 52 hpf using Illumina HiSeq. Samples conducted in replicate. | pubmed:34525360 | draculin:mCherry+;gata1:GFP at 30 hpf #1 | GSM5525113 | tissue:hematopoietic cells|developmental stage:30 hpf line:draculin:mCherry;gata1:GFP | draculin:mCherry+;gata1:GFP at 30 hpf #1 | Illumina BCL output files were generated to FASTQ files using cellranger mkfastq Custom reference used for alignment was generated using cellranger mkref 10X genomics on GRcz11 FASTA and GTF that included GFP and mCherry mRNA sequences. cellranger count was used on FASTQ files to perform alignment filtering barcode counting and unique molecular identifier counting. Filtered outputs from cell ranger features barcodes and matrix were analyzed using Seurat V4 Hao et al. 2020 and Monocle 3 Trapnell et al. 2014; Cao et al. 2019 Loom files were generated using cellranger output and velocyto pipelines Gioele La Manno et al. 2018. scVelo Bergen et al. 2020 was used for downstream loom file analysis. Genome build: GRCz11/danRer11 Supplementary files format and content: tab separated value text files were generated using cell ranger and loom files were generate using velocyto RNA velocities | hematopoietic cells | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | developmental stage:30 hpf line:draculin:mCherry;gata1:GFP | GSM5525113 | GSM5525113: draculin:mCherry+;gata1:GFP at 30 hpf #1; Danio rerio; RNA Seq | GSM5525113 | 1 | draculin:mCherry+;gata1:GFP or runx1:mCherry+ cells were isolated from transgenic fluorescent zebrafish embryos/larvae using FACS Aria. Sorted Cell populations were loaded on a Chromium Single Cell Controller 10X Genomics to generate single cell gel beads in emulsion GEMs by using Single Cell three prime Reagents Kits v3.1 10X Genomics. Captured cells were lysed and the released RNA wer barcoded through reverse transcription in individual GEMs Zheng et al. 2017. ScRNA Seq libraries were prepared using Single Cell three prime library Gel Bead Kit v3.1 10X Genomics following the manufacture's instructions. | GEO Accession:GSM5525113 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 4000 | SRP332734 | loader:fastq load.py|options: platform=Illumina readTypes=TBT read1PairFiles=DG1 2 S1 L001 R1 001.fastq.gz read2PairFiles=DG1 2 S1 L001 R2 001.fastq.gz read3PairFiles=DG1 2 S1 L001 I1 001.fastq.gz | DG1-2_S1_L001_I1_001.fastq.gz DG1-2_S1_L001_R1_001.fastq.gz DG1-2_S1_L001_R2_001.fastq.gz | fastq fastq fastq | 65514487192.0 | 212709374.0 | GSM5525113 r1 | 0:150 1:150 2:8 | A:8050271487;C:8057897221;G:7684156435;T:8113136954;N:944003 | 150 | 150 | 8 | 8050271487 | 8057897221 | 7684156435 | 8113136954 | 944003 | SRX11783408 | SRS9786605 | SRA1278863 | GEO | Chanin 501, Developmental and Molecular Biology, Albert Einstein College of Medicine | 1 | 0.94401 | 0.03521 | 0.88339 | 0.35428 | 150 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | United States | 2021-08-16 | Pharyngula | Embryo | Blood | Hematopoietic 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");;