{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"PAIRED\", experiment.library_selection = \"PolyA\" and experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\"", "rows": [[10166, "ERR5762357", "ERX5471113", "ERS6291553", "ERP128548", "PRJEB44492", "scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "E-MTAB-10370", "Transcriptome Analysis", "GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice  its role during adult hematopoiesis is incompletely understood. In zebrafish  mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs  whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation  but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells  we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population  we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.", "wt2 gata2b", "SAMEA8606934", "Erasmus Medical Center", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606934|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:wt2 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:wt2 gata2b|sampling site:kidney marrow|sex:female|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "E MTAB 10370:wt2 gata2b p", "wt2 gata2b p", "scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using  FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells.  cDNA was prepared using the manufacturers  protocol 10x Chromium V2. Library was prepared using the manufacturers  protocol 10x Chromium V2.", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP128548", "Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09", "wt2_gata2b.bam", "bam", 25266437196.0, 277653156.0, "E MTAB 10370:wt2 gata2b", "0:91", "A:7555470312;C:5144518052;G:5682746714;T:6882396490;N:1305628", 91, null, null, null, 7555470312, 5144518052, 5682746714, 6882396490, 1305628, "ERX5471113", "ERS6291553", "ERA4089475", "Erasmus Medical Center|European Nucleotide Archive", "Erasmus Medical Center|European Nucleotide Archive", 1, 0.90876, null, 0.18424, null, 0.84017, null, 0.55508, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Netherlands", "2022-04-09", "Adult", "Adult", "Kidney", "Renal System"], [10167, "ERR5762356", "ERX5471112", "ERS6291552", "ERP128548", "PRJEB44492", "scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "E-MTAB-10370", "Transcriptome Analysis", "GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice  its role during adult hematopoiesis is incompletely understood. In zebrafish  mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs  whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation  but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells  we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population  we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.", "wt1 gata2b", "SAMEA8606933", "Erasmus Medical Center", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606933|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:wt1 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:wt1 gata2b|sampling site:kidney marrow|sex:female|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "E MTAB 10370:wt1 gata2b p", "wt1 gata2b p", "scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using  FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells.  cDNA was prepared using the manufacturers  protocol 10x Chromium V2. Library was prepared using the manufacturers  protocol 10x Chromium V2.", "Experimental Factor: genotype:wild type genotype", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP128548", "Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09", "wt1_gata2b.bam", "bam", 36376708095.0, 399744045.0, "E MTAB 10370:wt1 gata2b", "0:91", "A:10397161431;C:8128518427;G:8799445454;T:9049686061;N:1896722", 91, null, null, null, 10397161431, 8128518427, 8799445454, 9049686061, 1896722, "ERX5471112", "ERS6291552", "ERA4089475", "Erasmus Medical Center|European Nucleotide Archive", "Erasmus Medical Center|European Nucleotide Archive", 1, 0.94708, null, 0.08938, null, 0.85449, null, 0.52917, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Netherlands", "2022-04-09", "Adult", "Adult", "Kidney", "Renal System"], [10168, "ERR5762355", "ERX5471111", "ERS6291551", "ERP128548", "PRJEB44492", "scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "E-MTAB-10370", "Transcriptome Analysis", "GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice  its role during adult hematopoiesis is incompletely understood. In zebrafish  mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs  whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation  but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells  we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population  we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.", "hom2 gata2b", "SAMEA8606932", "Erasmus Medical Center", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606932|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:hom2 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:gata2b / |isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:hom2 gata2b|sampling site:kidney marrow|sex:female|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "E MTAB 10370:hom2 gata2b p", "hom2 gata2b p", "scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using  FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells.  cDNA was prepared using the manufacturers  protocol 10x Chromium V2. Library was prepared using the manufacturers  protocol 10x Chromium V2.", "Experimental Factor: genotype:gata2b / ", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP128548", "Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09", "hom2_gata2b.bam", "bam", 22416887402.0, 246339422.0, "E MTAB 10370:hom2 gata2b", "0:91", "A:6732382430;C:4540586585;G:4933684272;T:6209137814;N:1096301", 91, null, null, null, 6732382430, 4540586585, 4933684272, 6209137814, 1096301, "ERX5471111", "ERS6291551", "ERA4089475", "Erasmus Medical Center|European Nucleotide Archive", "Erasmus Medical Center|European Nucleotide Archive", 1, 0.91306, null, 0.21566, null, 0.83469, null, 0.53782, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Netherlands", "2022-04-09", "Adult", "Adult", "Kidney", "Renal System"], [10169, "ERR5762354", "ERX5471110", "ERS6291550", "ERP128548", "PRJEB44492", "scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "E-MTAB-10370", "Transcriptome Analysis", "GATA2 is a pivotal hematopoietic transcription factor required for generation and maintenance of hematopoietic stem cells HSCs. Due to early embryonic lethality of Gata2 deficiency in mice  its role during adult hematopoiesis is incompletely understood. In zebrafish  mammalian functions of Gata2 are split between two orthologues: Gata2a and Gata2b. Previous studies have shown that Gata2b is prominently expressed in hematopoietic stem and progenitor cells HSPCs  whereas Gata2a is mainly expressed in the vasculature. We found that Gata2b deficient zebrafish have a reduction in embryonic definitive HSPC numbers and have impaired myeloid lineage differentiation  but are viable. This allowed us to study the role of Gata2b in adult hematopoiesis. To assess the impact of Gata2b deficiency on the transcriptional profile of HSPCs and differentiated cells  we sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow KM of WT and germline Gata2b deficient zebrafish based on scatter profiles and processed for single cell RNA sequencing. To enrich the scarce HSC population  we used pooled KM from two WT and Gata2b deficient TgCD41:GFP zebrafish per sample and included all CD41:GFPlow expressing cells present in the kidney marrow pool as these cells were shown to contain transplantable HSCs.", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09", null, "Protocols: Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells. cDNA was prepared using the manufacturers protocol 10x Chromium V2. Library was prepared using the manufacturers protocol 10x Chromium V2.", "hom1 gata2b", "SAMEA8606931", "Erasmus Medical Center", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09|External Id:SAMEA8606931|INSDC center alias:Erasmus Medical Center|INSDC center name:Erasmus Medical Center|INSDC first public:2022 04 09T00:20:19Z|INSDC last update:2022 04 09T00:20:19Z|INSDC status:public|Submitter Id:E MTAB 10370:hom1 gata2b|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:adult|genotype:gata2b / |isolate:not applicable|organism part:kidney|sample name:E MTAB 10370:hom1 gata2b|sampling site:kidney marrow|sex:female|strain:AB", null, null, null, null, null, null, null, null, "Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "E MTAB 10370:hom1 gata2b p", "hom1 gata2b p", "scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "Adult zebrafish were euthanized  kidney marrow was isolated and dissociated by pipetting in PBS/10% FCS. 7 AAD 7 amino actinomycin D 0.5mg/L BD biosciences was used for live/dead discrimination. Sorting was performed using  FACSAriaIII BD. 70.000 single viable cells were sorted from 2 pooled kidney marrow of female TgCD41:GFP zebrafish and supplemented with 114 1607 CD41:GFPlow expressing cells.  cDNA was prepared using the manufacturers  protocol 10x Chromium V2. Library was prepared using the manufacturers  protocol 10x Chromium V2.", "Experimental Factor: genotype:gata2b / ", "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "ERP128548", "Illumina NovaSeq 6000 paired end sequencing; scRNA seq of kidney marrow cells from Gata2b deficient and wild type zebrafish", "ENA FIRST PUBLIC:2022 04 09|ENA LAST UPDATE:2022 04 09", "hom1_gata2b.bam", "bam", 18004290759.0, 197849349.0, "E MTAB 10370:hom1 gata2b", "0:91", "A:5232521408;C:3876317502;G:4287902596;T:4606191653;N:1357600", 91, null, null, null, 5232521408, 3876317502, 4287902596, 4606191653, 1357600, "ERX5471110", "ERS6291550", "ERA4089475", "Erasmus Medical Center|European Nucleotide Archive", "Erasmus Medical Center|European Nucleotide Archive", 1, 0.94131, null, 0.08871, null, 0.83465, null, 0.52792, null, 91, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "Netherlands", "2022-04-09", "Adult", "Adult", "Kidney", "Renal System"], [11813, "ERR11788863", "ERX11187331", "ERS16221143", "ERP149944", "PRJEB64780", "A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain", "E-MTAB-13223", "Transcriptome Analysis", "To understand the cellular basis of the immune compartment of the zebrafish brain we have established reliable protocols for dissociation and prospective isolation of brain leukocytes  using fluorescent transgenic lines. By combining this approach with single cell RNA sequencing  we have generated a gene expression atlas composed of the distinct immune cells present in the homeostatic brain. These analyses revealed the presence of subpopulations of mononuclear phagocytes and other leukocytes  including cell types that have not been  or have been poorly  characterized so far. Here  we present the characterization of a new mononuclear phagocyte population that represents an important fraction among all brain leukocytes.  Adult brain single cell suspensions were prepared from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 and a total of 14 000 cd45:DsRed+ cells were processed for single cell profiling using the 10x Genomics platform.", "ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25", null, "Protocols: FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3  were dissected in 0.9X Dulbecco\u2032s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33\u00b0C for 30 45 minutes  fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4\u00baC 10 min and filtered through a 40\u00b5m nylon mesh. Just before flow cytometry analysis  using calcein violet to exclude dead cells 1\u00b5M  Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson. RNA Illumina", "Sample 1", "SAMEA114235870", "Universite Libre de Bruxelles", "ENA FIRST PUBLIC:2023 12 25T01:15:29Z|ENA LAST UPDATE:2023 12 25T01:15:29Z|External Id:SAMEA114235870|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:29Z|INSDC last update:2023 12 25T01:15:29Z|INSDC status:public|Submitter Id:E MTAB 13223:Sample 1|age:5|broker name:ArrayExpress|cell type:leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:pool of 3 fish|isolate:not applicable|organism part:brain|sample name:E MTAB 13223:Sample 1|scientific name:Danio rerio|sex:male and female|strain:AB", null, null, null, null, null, null, null, null, "A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain", "E MTAB 13223:Sample 1 p", "Sample 1 p", "A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain", "FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3  were dissected in 0.9X Dulbecco\u2032s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33\u00b0C for 30 45 minutes  fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4\u00baC 10 min and filtered through a 40\u00b5m nylon mesh. Just before flow cytometry analysis  using calcein violet to exclude dead cells 1\u00b5M  Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson.  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By combining this approach with single cell RNA sequencing  we have generated a gene expression atlas composed of the distinct immune cells present in the homeostatic brain. These analyses revealed the presence of subpopulations of mononuclear phagocytes and other leukocytes  including cell types that have not been  or have been poorly  characterized so far. Here  we present the characterization of a new mononuclear phagocyte population that represents an important fraction among all brain leukocytes.  Adult brain single cell suspensions were prepared from adult Tgp2ry12:GFP; cd45:DsRed fish n=3 and a total of 14 000 cd45:DsRed+ cells were processed for single cell profiling using the 10x Genomics platform.", "ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25", null, "Protocols: FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3  were dissected in 0.9X Dulbecco\u2032s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33\u00b0C for 30 45 minutes  fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4\u00baC 10 min and filtered through a 40\u00b5m nylon mesh. Just before flow cytometry analysis  using calcein violet to exclude dead cells 1\u00b5M  Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson. RNA Illumina", "Sample 1", "SAMEA114235870", "Universite Libre de Bruxelles", "ENA FIRST PUBLIC:2023 12 25T01:15:29Z|ENA LAST UPDATE:2023 12 25T01:15:29Z|External Id:SAMEA114235870|INSDC center name:Universite Libre de Bruxelles|INSDC first public:2023 12 25T01:15:29Z|INSDC last update:2023 12 25T01:15:29Z|INSDC status:public|Submitter Id:E MTAB 13223:Sample 1|age:5|broker name:ArrayExpress|cell type:leukocyte|collection date:not collected|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|geographic location country and/or sea:not collected|individual:pool of 3 fish|isolate:not applicable|organism part:brain|sample name:E MTAB 13223:Sample 1|scientific name:Danio rerio|sex:male and female|strain:AB", null, null, null, null, null, null, null, null, "A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain", "E MTAB 13223:Sample 1 p", "Sample 1 p", "A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain", "FACS sorting of cd45:Dsred cells. Brains from adult Tgp2ry12:GFP; cd45:DsRed fish n=3  were dissected in 0.9X Dulbecco\u2032s Phosphate Buffered Saline DPBS were triturated and treated with Liberase TM at 33\u00b0C for 30 45 minutes  fully dissociated using a syringe with a 26G needle and washed in 2% fetal bovine serum diluted in 0.9X DPBS. Cell suspensions were centrifuged at 290g 4\u00baC 10 min and filtered through a 40\u00b5m nylon mesh. Just before flow cytometry analysis  using calcein violet to exclude dead cells 1\u00b5M  Thermo Fisher. Flow cytometry acquisition and cell sorting was performed on a FACS ARIA II Becton Dickinson.  RNA Illumina", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP149944", "NextSeq 550 paired end sequencing; A single cell transcriptomic atlas reveals a new myeloid parenchymal population in the zebrafish brain", "ENA FIRST PUBLIC:2023 12 25|ENA LAST UPDATE:2023 12 25", "L41805_Track-81377_R1.fastq.gz L41805_Track-81377_R2.fastq.gz", "fastq fastq", 3184137096.0, 37906394.0, "E MTAB 13223:L41805 Track 81377", "0:28 1:56", "A:899943184;C:685571078;G:703849582;T:889228559;N:5544693", 28, 56, null, null, 899943184, 685571078, 703849582, 889228559, 5544693, "ERX11187331", "ERS16221143", "ERA26318932", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", 2, 0.00734, 0.90077, 0.00293, 0.20318, 0.99064, 0.82765, 0.47994, 0.53473, 28, 56, "T", "B", "sc-like readlen", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-12-25", "Adult", "Adult", "Brain", "Nervous System"], [15009, "ERR12306826", "ERX11683773", "ERS17043893", "ERP155237", "PRJEB70303", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E-MTAB-13554", "Transcriptome Analysis", "To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", null, "Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", "Coated", "SAMEA114641726", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641726|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Coated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Coated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1", null, null, null, null, null, null, null, null, "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E MTAB 13554:Coated p", "Coated p", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP155237", "NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", "230324-Coated_S1_L003_I1_001.fastq.gz 230324-Coated_S1_L003_I2_001.fastq.gz 230324-Coated_S1_L003_R1_001.fastq.gz 230324-Coated_S1_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 10050750400.0, 62817190.0, "E MTAB 13554:230324 Coated S1 L003", "0:10 1:10 2:30 3:110", "A:1894211982;C:1556769050;G:1595134885;T:1863244619;N:530364", 10, 10, 30, 110, 1894211982, 1556769050, 1595134885, 1863244619, 530364, "ERX11683773", "ERS17043893", "ERA27417303", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-11-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [15010, "ERR12306829", "ERX11683773", "ERS17043893", "ERP155237", "PRJEB70303", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E-MTAB-13554", "Transcriptome Analysis", "To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", null, "Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", "Coated", "SAMEA114641726", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641726|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Coated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Coated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1", null, null, null, null, null, null, null, null, "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E MTAB 13554:Coated p", "Coated p", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP155237", "NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", "230324-Coated_S1_L004_I1_001.fastq.gz 230324-Coated_S1_L004_I2_001.fastq.gz 230324-Coated_S1_L004_R1_001.fastq.gz 230324-Coated_S1_L004_R2_001.fastq.gz", "fastq fastq fastq fastq", 9780757760.0, 61129736.0, "E MTAB 13554:230324 Coated S1 L004", "0:10 1:10 2:30 3:110", "A:1844808667;C:1516149264;G:1549838165;T:1813091860;N:383004", 10, 10, 30, 110, 1844808667, 1516149264, 1549838165, 1813091860, 383004, "ERX11683773", "ERS17043893", "ERA27417303", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-11-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [15011, "ERR12306828", "ERX11683773", "ERS17043893", "ERP155237", "PRJEB70303", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E-MTAB-13554", "Transcriptome Analysis", "To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", null, "Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", "Coated", "SAMEA114641726", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641726|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Coated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Coated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1", null, null, null, null, null, null, null, null, "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E MTAB 13554:Coated p", "Coated p", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP155237", "NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", "230324-Coated_S1_L002_I1_001.fastq.gz 230324-Coated_S1_L002_I2_001.fastq.gz 230324-Coated_S1_L002_R1_001.fastq.gz 230324-Coated_S1_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 9639368480.0, 60246053.0, "E MTAB 13554:230324 Coated S1 L002", "0:10 1:10 2:30 3:110", "A:1817388578;C:1494319441;G:1527564319;T:1787447672;N:345820", 10, 10, 30, 110, 1817388578, 1494319441, 1527564319, 1787447672, 345820, "ERX11683773", "ERS17043893", "ERA27417303", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-11-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [15012, "ERR12306832", "ERX11683773", "ERS17043893", "ERP155237", "PRJEB70303", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E-MTAB-13554", "Transcriptome Analysis", "To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", null, "Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", "Coated", "SAMEA114641726", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641726|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Coated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Coated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1", null, null, null, null, null, null, null, null, "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E MTAB 13554:Coated p", "Coated p", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP155237", "NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", "230324-Coated_S1_L001_I1_001.fastq.gz 230324-Coated_S1_L001_I2_001.fastq.gz 230324-Coated_S1_L001_R1_001.fastq.gz 230324-Coated_S1_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 9823147840.0, 61394674.0, "E MTAB 13554:230324 Coated S1 L001", "0:10 1:10 2:30 3:110", "A:1851113558;C:1521671335;G:1558230628;T:1822067428;N:331191", 10, 10, 30, 110, 1851113558, 1521671335, 1558230628, 1822067428, 331191, "ERX11683773", "ERS17043893", "ERA27417303", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-11-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [15013, "ERR12306833", "ERX11683774", "ERS17043894", "ERP155237", "PRJEB70303", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E-MTAB-13554", "Transcriptome Analysis", "To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", null, "Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", "Uncoated", "SAMEA114641727", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Uncoated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1", null, null, null, null, null, null, null, null, "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E MTAB 13554:Uncoated p", "Uncoated p", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP155237", "NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", "230324-Uncoated_S2_L001_I1_001.fastq.gz 230324-Uncoated_S2_L001_I2_001.fastq.gz 230324-Uncoated_S2_L001_R1_001.fastq.gz 230324-Uncoated_S2_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 8871716800.0, 55448230.0, "E MTAB 13554:230324 Uncoated S2 L001", "0:10 1:10 2:30 3:110", "A:1718985845;C:1319560520;G:1372197713;T:1688254655;N:306567", 10, 10, 30, 110, 1718985845, 1319560520, 1372197713, 1688254655, 306567, "ERX11683774", "ERS17043894", "ERA27417303", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-11-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [15014, "ERR12306830", "ERX11683774", "ERS17043894", "ERP155237", "PRJEB70303", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E-MTAB-13554", "Transcriptome Analysis", "To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", null, "Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", "Uncoated", "SAMEA114641727", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Uncoated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1", null, null, null, null, null, null, null, null, "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E MTAB 13554:Uncoated p", "Uncoated p", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP155237", "NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", "230324-Uncoated_S2_L003_I1_001.fastq.gz 230324-Uncoated_S2_L003_I2_001.fastq.gz 230324-Uncoated_S2_L003_R1_001.fastq.gz 230324-Uncoated_S2_L003_R2_001.fastq.gz", "fastq fastq fastq fastq", 9075478720.0, 56721742.0, "E MTAB 13554:230324 Uncoated S2 L003", "0:10 1:10 2:30 3:110", "A:1758677834;C:1349774831;G:1404463433;T:1725994897;N:480625", 10, 10, 30, 110, 1758677834, 1349774831, 1404463433, 1725994897, 480625, "ERX11683774", "ERS17043894", "ERA27417303", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-11-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [15015, "ERR12306831", "ERX11683774", "ERS17043894", "ERP155237", "PRJEB70303", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E-MTAB-13554", "Transcriptome Analysis", "To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", null, "Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", "Uncoated", "SAMEA114641727", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Uncoated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1", null, null, null, null, null, null, null, null, "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E MTAB 13554:Uncoated p", "Uncoated p", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "PolyA", "PAIRED", "ILLUMINA", "NextSeq 550", null, "ERP155237", "NextSeq 550 paired end sequencing; 10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", "230324-Uncoated_S2_L002_I1_001.fastq.gz 230324-Uncoated_S2_L002_I2_001.fastq.gz 230324-Uncoated_S2_L002_R1_001.fastq.gz 230324-Uncoated_S2_L002_R2_001.fastq.gz", "fastq fastq fastq fastq", 8705210880.0, 54407568.0, "E MTAB 13554:230324 Uncoated S2 L002", "0:10 1:10 2:30 3:110", "A:1687330583;C:1295837902;G:1345522657;T:1655826422;N:314916", 10, 10, 30, 110, 1687330583, 1295837902, 1345522657, 1655826422, 314916, "ERX11683774", "ERS17043894", "ERA27417303", "European Bioinformatics Institute|European Nucleotide Archive", "European Bioinformatics Institute|European Nucleotide Archive", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2023-11-20", "Hatching", "Embryo", "Whole Organism", "All anatomical structures"], [15016, "ERR12306827", "ERX11683774", "ERS17043894", "ERP155237", "PRJEB70303", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E-MTAB-13554", "Transcriptome Analysis", "To study the biodistribution of DNA origami in zebrafish and to determine differences in biodistribution based on the coating of the nanostructure using oligolysine PEG copolymers  zebrafish embryos 2dpf were injected with coated or uncoated DNA origami wireframe nanosheets without xxx targeting molecule  but containing a detection fluorophores. post treatment  the embryos were disassociated into a single cell suspension and sorted through FACS for embryos containing nanostructures fluorophores. 10X sc libraries were generated from the sorted embryos and sequenced to establish cell type predictions for cells with coated and uncoated structures respectively.", "ENA FIRST PUBLIC:2024 09 30|ENA LAST UPDATE:2024 09 30", null, "Protocols: Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences. Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd. Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells. The cDNA libraries were amplified using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 with 14 PCR cycles.", "Uncoated", "SAMEA114641727", "KIS", "ENA first public:2024 09 30|External Id:SAMEA114641727|INSDC center name:KIS|INSDC last update:2023 11 20T16:06:50Z|INSDC status:public|Submitter Id:E MTAB 13554:Uncoated|age:2|broker name:ArrayExpress|collection date:not collected|common name:zebrafish|developmental stage:embryo stage|geographic location country and/or sea:not collected|isolate:not applicable|organism part:whole organism|sample name:E MTAB 13554:Uncoated|scientific name:Danio rerio|sex:not available|strain:transgenic lines Tgfli1:EGFPy1", null, null, null, null, null, null, null, null, "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "E MTAB 13554:Uncoated p", "Uncoated p", "10X genomics libraries for scRNA seq of zebrafish embryos 2dpf treated with uncoated and oligolysine PEG copolymer coated DNA origami wireframe nanosheets", "Embryos 48 hpf were disassociated into a single cell suspension. Four hours post injections  around 200 Tgfli1:EGFP embryos were euthanized in 0.02% tricaine. The tissue was dissociated with harsh pipetting in 0.25% trypsin EDTA GIBCO and 100mg/mL collagenase Sigma Aldrich for 3 min at 30oC  followed by resuspension in DMEM 10% FBS. The cells were then pelleted at 700xg for 5 min  washed once in 1X PBS  filtered through a 40 \u03bcm cell strainer MERCK and stained with 1mM DAPI solution Abcam. TS+ cells were FACS sorted on a FACSARIA III with BD FACSDIVA software v. 9.0.1 BD Biosciences.  Zebrafish D. rerio were maintained and bred in compliance with Swedish legislation on animal welfare regulations approved by Stockholms djurf\u00f6rs\u00f6ksetiska n\u00e4mnd.  Each zebrafish embryo Tgfli1:EGFP was microinjected with 4 nl of the sample. The samples for injections were prepared at a final concentration of 100\u2009nM in 1x PBS effective dose estimated to around 4 6 nM. Embryos at 48 hpf were anesthetized using 0.1% tricaine MS222  transferred onto an agarose surface  placed on their ventral side  and injected into the common cardinal vein Duct of Cuvier. scRNAseq libraries were generated from the sorted cells using 10X Genomics Chromium Single Cell 3\u02b9 Reagent Kits v3.1 per manufacturer's instructions  targeting 8000 cells.  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