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11 rows where devstage_curation = "Juvenile" and tissue_curation_coarse = "Hematopoietic System"

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tissue_curation 2

technology 2

experiment.platform 2

experiment.library_strategy 2

experiment.library_source 2

experiment.library_selection 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Hematopoietic System · 11 ✖

devstage_curation_coarse 1

devstage_curation 1

  • Juvenile · 11 ✖
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
68297 68297 SRR099352 SRX041562 SRS172412 SRP005640 PRJNA79973 Zebrafish Development 4432-2WA Other Sample from publication: Determinism and Stochasticity during Maturation of the Zebrafish Antibody Repertoire. Authors: Jiang Weinstein Penland White Fish and Quake.   pubmed:21393572 Immunoglobulin heavy chain cDNA from 1 mpf WIK zebrafish Danio rerio leading with MID barcode CTCGCGTGTC 4433 1MA D8 4433 1MA D8                     1 4433 1MA D8 Zebrafish WIK Standard Roche 454 GS Titanium shotgun library protocol was followed.     AMPLICON TRANSCRIPTOMIC PCR SINGLE LS454 454 GS FLX Titanium <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP005640         70233197.0 233302.0 4433 1MA D8 0:4 1:297.04   4 297               SRX041562 SRS172412 SRA029829 Stanford University|Quake Stanford University 1 0.14812   0.01088   0.99969   0.10799   36   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Juvenile Juvenile BCR TCR repertoire Hematopoietic System
68298 68298 SRR099351 SRX041561 SRS172411 SRP005640 PRJNA79973 Zebrafish Development 4432-2WA Other Sample from publication: Determinism and Stochasticity during Maturation of the Zebrafish Antibody Repertoire. Authors: Jiang Weinstein Penland White Fish and Quake.   pubmed:21393572 Immunoglobulin heavy chain cDNA from 1 mpf WIK zebrafish Danio rerio leading with MID barcode CGTGTCTCTA 4433 1MA C7 4433 1MA C7                     1 4433 1MA C7 Zebrafish WIK Standard Roche 454 GS Titanium shotgun library protocol was followed.     AMPLICON TRANSCRIPTOMIC PCR SINGLE LS454 454 GS FLX Titanium <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP005640         109094731.0 316792.0 4433 1MA C7 0:4 1:340.37   4 340               SRX041561 SRS172411 SRA029829 Stanford University|Quake Stanford University 1 0.13409   0.01258   0.99955   0.01535   37   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Juvenile Juvenile BCR TCR repertoire Hematopoietic System
68299 68299 SRR099350 SRX041560 SRS172410 SRP005640 PRJNA79973 Zebrafish Development 4432-2WA Other Sample from publication: Determinism and Stochasticity during Maturation of the Zebrafish Antibody Repertoire. Authors: Jiang Weinstein Penland White Fish and Quake.   pubmed:21393572 Immunoglobulin heavy chain cDNA from 1 mpf WIK zebrafish Danio rerio leading with MID barcode ATATCGCGAG 4433 1MA B6 4433 1MA B6                     1 4433 1MA B6 Zebrafish WIK Standard Roche 454 GS Titanium shotgun library protocol was followed.     AMPLICON TRANSCRIPTOMIC PCR SINGLE LS454 454 GS FLX Titanium <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP005640         110436791.0 353780.0 4433 1MA B6 0:4 1:308.16   4 308               SRX041560 SRS172410 SRA029829 Stanford University|Quake Stanford University 1 0.28629   0.01104   0.99945   0.0273   107   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Juvenile Juvenile BCR TCR repertoire Hematopoietic System
68300 68300 SRR099349 SRX041559 SRS172409 SRP005640 PRJNA79973 Zebrafish Development 4432-2WA Other Sample from publication: Determinism and Stochasticity during Maturation of the Zebrafish Antibody Repertoire. Authors: Jiang Weinstein Penland White Fish and Quake.   pubmed:21393572 Immunoglobulin heavy chain cDNA from 1 mpf WIK zebrafish Danio rerio leading with MID barcode ATCAGACACG 4433 1MA A5 4433 1MA A5                     1 4433 1MA A5 Zebrafish WIK Standard Roche 454 GS Titanium shotgun library protocol was followed.     AMPLICON TRANSCRIPTOMIC PCR SINGLE LS454 454 GS FLX Titanium <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP005640         107336405.0 335816.0 4433 1MA A5 0:4 1:315.63   4 315               SRX041559 SRS172409 SRA029829 Stanford University|Quake Stanford University 1 0.16203   0.01649   0.99935   0.00111   37   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Juvenile Juvenile BCR TCR repertoire Hematopoietic System
68301 68301 SRR099329 SRX041558 SRS172408 SRP005640 PRJNA79973 Zebrafish Development 4432-2WA Other Sample from publication: Determinism and Stochasticity during Maturation of the Zebrafish Antibody Repertoire. Authors: Jiang Weinstein Penland White Fish and Quake.   pubmed:21393572 Immunoglobulin heavy chain cDNA from 1 mpf WIK zebrafish Danio rerio leading with MID barcode AGCACTGTAG 4432 1MA D4 4432 1MA D4                     1 4432 1MA D4 Zebrafish WIK Standard Roche 454 GS Titanium shotgun library protocol was followed.     AMPLICON TRANSCRIPTOMIC PCR SINGLE LS454 454 GS FLX Titanium <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP005640         94113837.0 297721.0 4432 1MA D4 0:4 1:312.11   4 312               SRX041558 SRS172408 SRA029829 Stanford University|Quake Stanford University 1 0.16753   0.02013   0.99979   3e-05   37   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Juvenile Juvenile BCR TCR repertoire Hematopoietic System
68302 68302 SRR099328 SRX041557 SRS172407 SRP005640 PRJNA79973 Zebrafish Development 4432-2WA Other Sample from publication: Determinism and Stochasticity during Maturation of the Zebrafish Antibody Repertoire. Authors: Jiang Weinstein Penland White Fish and Quake.   pubmed:21393572 Immunoglobulin heavy chain cDNA from 1 mpf WIK zebrafish Danio rerio leading with MID barcode AGACGCACTC 4432 1MA C3 4432 1MA C3                     1 4432 1MA C3 Zebrafish WIK Standard Roche 454 GS Titanium shotgun library protocol was followed.     AMPLICON TRANSCRIPTOMIC PCR SINGLE LS454 454 GS FLX Titanium <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP005640         77768777.0 243405.0 4432 1MA C3 0:4 1:315.50   4 315               SRX041557 SRS172407 SRA029829 Stanford University|Quake Stanford University 1 0.16711   0.01816   0.99979   0.0   37   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Juvenile Juvenile BCR TCR repertoire Hematopoietic System
68303 68303 SRR099327 SRX041556 SRS172406 SRP005640 PRJNA79973 Zebrafish Development 4432-2WA Other Sample from publication: Determinism and Stochasticity during Maturation of the Zebrafish Antibody Repertoire. Authors: Jiang Weinstein Penland White Fish and Quake.   pubmed:21393572 Immunoglobulin heavy chain cDNA from 1 mpf WIK zebrafish Danio rerio leading with MID barcode ACGCTCGACA 4432 1MA B2 4432 1MA B2                     1 4432 1MA B2 Zebrafish WIK Standard Roche 454 GS Titanium shotgun library protocol was followed.     AMPLICON TRANSCRIPTOMIC PCR SINGLE LS454 454 GS FLX Titanium <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP005640         120450312.0 390504.0 4432 1MA B2 0:4 1:304.45   4 304               SRX041556 SRS172406 SRA029829 Stanford University|Quake Stanford University 1 0.18757   0.01811   0.99977   0.00024   59   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Juvenile Juvenile BCR TCR repertoire Hematopoietic System
68304 68304 SRR099326 SRX041555 SRS172405 SRP005640 PRJNA79973 Zebrafish Development 4432-2WA Other Sample from publication: Determinism and Stochasticity during Maturation of the Zebrafish Antibody Repertoire. Authors: Jiang Weinstein Penland White Fish and Quake.   pubmed:21393572 Immunoglobulin heavy chain cDNA from 1 mpf WIK zebrafish Danio rerio leading with MID barcode ACGAGTGCGT 4432 1MA A1 4432 1MA A1                     1 4432 1MA A1 Zebrafish WIK Standard Roche 454 GS Titanium shotgun library protocol was followed.     AMPLICON TRANSCRIPTOMIC PCR SINGLE LS454 454 GS FLX Titanium <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Technical Read</READ_CLASS><READ_TYPE>Adapter</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>5</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP005640         145945736.0 457354.0 4432 1MA A1 0:4 1:315.11   4 315               SRX041555 SRS172405 SRA029829 Stanford University|Quake Stanford University 1 0.17607   0.02473   0.99957   0.00036   40   B   usable mapping rate legacy early unknown random_priming unknown bulk other_seq 454   United States 2011-04-07 Juvenile Juvenile BCR TCR repertoire Hematopoietic System
71018 71018 SRR21091734 SRX17106223 SRS14681693 SRP392539 PRJNA870096 Single cell transcriptome profiling reveals diverse immune cell populations and their responses to viral infection in the spleen of zebrafish GSE211396 Transcriptome Analysis Teleost fish are indispensable model organisms for comparative immunology research that should provide fundamental insights into the evolutionary history of vertebrate immunity and eventually lead to an improved understanding of the general principles of immune system design. Although numerous studies on ?sh immunology have been conducted knowledge about the cell types that orchestrate piscine immune systems remains limited. In this study we generated a comprehensive atlas of immune cell types in a zebrafish model on the basis of single cell transcriptome profiling. Overall design: Spleen leukocyte PBS administered control SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated byFicoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.   pubmed:37227178;pubmed:40392591   vaccinated+SVCV scRNAseq GSM6469457   source name:Spleen|cell type:leukocyte|tissue:Spleen|strain:AB|age:5 wpf 7 wpf|geo loc name:missing|collection date:missing vaccinated+SVCV scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files Spleen   Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.   cell type:leukocyte|tissue:Spleen|strain:AB|age:5 wpf 7 wpf GSM6469457 GSM6469457: vaccinated+SVCV scRNAseq; Danio rerio; RNA Seq GSM6469457 r1 GSM6469457 1 Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP392539     vaccinated+SVCV_S1_L001_R1_001.fastq.gz vaccinated+SVCV_S1_L001_R2_001.fastq.gz fastq fastq 54148439576.0 455028904.0 GSM6469457 r1 0:28 1:91 A:15899568894;C:11520113647;G:12620718617;T:14107197313;N:841105 28 91     15899568894 11520113647 12620718617 14107197313 841105 SRX17106223 SRS14681693 SRA1477254 College of Life Sciences, Zhejiang University College of Life Sciences, Zhejiang University 2 0.01082 0.82759 0.00393 0.19284 0.99093 0.82164 0.42631 0.61086 28 91 T B sc-like readlen illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   China 2022-08-16 Juvenile Juvenile Spleen Hematopoietic System
71019 71019 SRR21091735 SRX17106222 SRS14681692 SRP392539 PRJNA870096 Single cell transcriptome profiling reveals diverse immune cell populations and their responses to viral infection in the spleen of zebrafish GSE211396 Transcriptome Analysis Teleost fish are indispensable model organisms for comparative immunology research that should provide fundamental insights into the evolutionary history of vertebrate immunity and eventually lead to an improved understanding of the general principles of immune system design. Although numerous studies on ?sh immunology have been conducted knowledge about the cell types that orchestrate piscine immune systems remains limited. In this study we generated a comprehensive atlas of immune cell types in a zebrafish model on the basis of single cell transcriptome profiling. Overall design: Spleen leukocyte PBS administered control SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated byFicoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.   pubmed:37227178;pubmed:40392591   SVCV scRNAseq GSM6469456   source name:Spleen|cell type:leukocyte|tissue:Spleen|strain:AB|age:5 wpf 7 wpf|geo loc name:missing|collection date:missing SVCV scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files Spleen   Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.   cell type:leukocyte|tissue:Spleen|strain:AB|age:5 wpf 7 wpf GSM6469456 GSM6469456: SVCV scRNAseq; Danio rerio; RNA Seq GSM6469456 r1 GSM6469456 1 Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP392539     SVCV_S1_L001_R1_001.fastq.gz SVCV_S1_L001_R2_001.fastq.gz fastq fastq 52273900644.0 439276476.0 GSM6469456 r1 0:28 1:91 A:15161666574;C:11232538299;G:11962650688;T:13914991728;N:2053355 28 91     15161666574 11232538299 11962650688 13914991728 2053355 SRX17106222 SRS14681692 SRA1477254 College of Life Sciences, Zhejiang University College of Life Sciences, Zhejiang University 2 0.0088 0.86697 0.00319 0.19264 0.99251 0.78289 0.46167 0.59016 28 91 T B sc-like readlen illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   China 2022-08-16 Juvenile Juvenile Spleen Hematopoietic System
71020 71020 SRR21091736 SRX17106221 SRS14681691 SRP392539 PRJNA870096 Single cell transcriptome profiling reveals diverse immune cell populations and their responses to viral infection in the spleen of zebrafish GSE211396 Transcriptome Analysis Teleost fish are indispensable model organisms for comparative immunology research that should provide fundamental insights into the evolutionary history of vertebrate immunity and eventually lead to an improved understanding of the general principles of immune system design. Although numerous studies on ?sh immunology have been conducted knowledge about the cell types that orchestrate piscine immune systems remains limited. In this study we generated a comprehensive atlas of immune cell types in a zebrafish model on the basis of single cell transcriptome profiling. Overall design: Spleen leukocyte PBS administered control SVCV infected infected and SVCV vaccinated plus SVCV infected vaccinated+infected groups of the AB zebrafish were isolated byFicoll Hypaque 1.080 g/mL density gradient centrifugation and analyzed using scRNAseq.   pubmed:37227178;pubmed:40392591   PBS scRNAseq GSM6469455   source name:Spleen|cell type:leukocyte|tissue:Spleen|strain:AB|age:5 wpf 7 wpf|geo loc name:missing|collection date:missing PBS scRNAseq The demultiplexing barcoded processing gene counting and aggregation were made using the Cell Ranger software v2.1.1 https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger Assembly: mm10 Supplementary files format and content: Tab separated values files and matrix files Spleen   Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter’s instructions single cell 3’ v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.   cell type:leukocyte|tissue:Spleen|strain:AB|age:5 wpf 7 wpf GSM6469455 GSM6469455: PBS scRNAseq; Danio rerio; RNA Seq GSM6469455 r1 GSM6469455 1 Leukocytes were collected from the spleen samples through Ficoll Hypaque 1.080 g/mL density gradient centrifugation as previously described.[58a 62] Briefly zebrafish were anesthetized by MS222 post 7 days of SVCV challenge. The spleen was carefully excised and transferred through a 40 μm stainless nylon mesh Greiner Bio OneGmbH Germany. The cell suspension was suspended in Leibovitz's L 15 Medium L 15 Gibco supplemented with penicillin 100 U/ml Sigma Aldrich streptomycin 100 μg/ml Sigma Aldrich and heparin sodium 10 U/ml Sigma Aldrich. The cell suspension was slowly added into a Ficoll Hypaque 1.080 g/mL density gradient centrifugation centrifuged at 1 200 g for 25 min and the cell layer of the interface was carefully aspirated and then washed with ice cold PBS at 400 g for 10 min. Cell quantity and viability were determined using 0.4% trypan blue Sigma St. Louis MO USA which showed that more than 95% were living cells. The cells of each group were counted using a cell counting plate. Library was performed according to the manufacter's instructions single cell three prime v2 protocol 10x Genomics. Briefly GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion GEM. The poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA which contains an Ilumina R1 primer sequence Unique Molecular Identifier UMI and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence paired end constructs with P5 and P7 sequences and a sample index were added.   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED ILLUMINA NextSeq 500   SRP392539     PBS_S1_L001_R1_001.fastq.gz PBS_S1_L001_R2_001.fastq.gz fastq fastq 48934762310.0 411216490.0 GSM6469455 r1 0:28 1:91 A:14053810123;C:10679154471;G:11495668034;T:12705747178;N:382504 28 91     14053810123 10679154471 11495668034 12705747178 382504 SRX17106221 SRS14681691 SRA1477254 College of Life Sciences, Zhejiang University College of Life Sciences, Zhejiang University 2 0.00845 0.84491 0.00304 0.17543 0.99212 0.78833 0.45994 0.6033 28 91 T B sc-like readlen illumina nextseq unknown poly_a unknown sc single_cell_droplet 10x   China 2022-08-16 Juvenile Juvenile Spleen 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");;