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20 rows where experiment.library_layout = "PAIRED", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and technology = "unknown"

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devstage_curation 5

devstage_curation_coarse 4

tissue_curation 3

experiment.platform 3

experiment.library_selection 3

technology 1

  • unknown · 20 ✖

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC SINGLE CELL · 20 ✖

experiment.library_layout 1

  • PAIRED · 20 ✖
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
11238 11238 ERR10782555 ERX10233132 ERS14439197 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 6 E MTAB 12503:Sample 6   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 6|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 6 p Sample 6 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-6_R1.fastq.gz 20170530.A-6_R2.fastq.gz fastq fastq 14809693138.0 49038719.0 E MTAB 12503:20170530.A 6 R 0:151 1:151 A:4069749497;C:3367864217;G:3430269434;T:3928390721;N:13419269 151 151     4069749497 3367864217 3430269434 3928390721 13419269 ERX10233132 ERS14439197 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.83945 0.69977 0.27269 0.22488 0.74523 0.77654 0.4899 0.4358 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Multi-stage Embryo Whole Organism All anatomical structures
11239 11239 ERR10782554 ERX10233131 ERS14439196 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 5 E MTAB 12503:Sample 5   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 5|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 5 p Sample 5 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:bud|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-5_R1.fastq.gz 20170530.A-5_R2.fastq.gz fastq fastq 14954968728.0 49519764.0 E MTAB 12503:20170530.A 5 R 0:151 1:151 A:4063340262;C:3440933120;G:3455723079;T:3981396987;N:13575280 151 151     4063340262 3440933120 3455723079 3981396987 13575280 ERX10233131 ERS14439196 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.85891 0.86859 0.28842 0.28866 0.7349 0.75051 0.45532 0.49145 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Multi-stage Embryo Whole Organism All anatomical structures
11240 11240 ERR10782553 ERX10233130 ERS14439195 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 2 E MTAB 12503:Sample 2   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 2|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 2 p Sample 2 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-2_R1.fastq.gz 20170530.A-2_R2.fastq.gz fastq fastq 16267571562.0 53866131.0 E MTAB 12503:20170530.A 2 R 0:151 1:151 A:4395815325;C:3765428574;G:3780844712;T:4310729283;N:14753668 151 151     4395815325 3765428574 3780844712 4310729283 14753668 ERX10233130 ERS14439195 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.86977 0.8727 0.28497 0.28427 0.70763 0.72301 0.47478 0.47986 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Pharyngula Embryo Whole Organism All anatomical structures
11241 11241 ERR10782552 ERX10233129 ERS14439194 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 1 E MTAB 12503:Sample 1   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 1|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:wild type genotype|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 1 p Sample 1 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:wild type genotype RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-1_R1.fastq.gz 20170530.A-1_R2.fastq.gz fastq fastq 15446599662.0 51147681.0 E MTAB 12503:20170530.A 1 R 0:151 1:151 A:4289931639;C:3451135010;G:3474244788;T:4217248893;N:14039332 151 151     4289931639 3451135010 3474244788 4217248893 14039332 ERX10233129 ERS14439194 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.90114 0.90507 0.32128 0.32127 0.70232 0.71956 0.47336 0.47528 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Pharyngula Embryo Whole Organism All anatomical structures
11242 11242 ERR10782551 ERX10233128 ERS14439193 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 7 E MTAB 12503:Sample 7   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 7|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:10|developmental stage:bud|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 7 p Sample 7 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:bud|Experimental Factor: genotype:rbm8a d5/d5 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-7_R1.fastq.gz 20170530.A-7_R2.fastq.gz fastq fastq 12726557236.0 42140918.0 E MTAB 12503:20170530.A 7 R 0:151 1:151 A:3510176970;C:2879679978;G:2932244172;T:3392911734;N:11544382 151 151     3510176970 2879679978 2932244172 3392911734 11544382 ERX10233128 ERS14439193 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.88531 0.88678 0.33279 0.3329 0.73545 0.74992 0.52548 0.52864 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Multi-stage Embryo Whole Organism All anatomical structures
11243 11243 ERR10782550 ERX10233127 ERS14439192 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 4 E MTAB 12503:Sample 4   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 4|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 4 p Sample 4 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:rbm8a d5/d5 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-4_R1.fastq.gz 20170530.A-4_R2.fastq.gz fastq fastq 15697575554.0 51978727.0 E MTAB 12503:20170530.A 4 R 0:151 1:151 A:4256444510;C:3622485921;G:3650190489;T:4154211501;N:14243133 151 151     4256444510 3622485921 3650190489 4154211501 14243133 ERX10233127 ERS14439192 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.87714 0.88071 0.29319 0.29235 0.69844 0.7164 0.47594 0.47385 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Pharyngula Embryo Whole Organism All anatomical structures
11244 11244 ERR10782549 ERX10233126 ERS14439191 ERP144048 PRJEB58983 RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E-MTAB-12503 Transcriptome Analysis Defects in blood development are a major contributor to complex congenital anomalies. Thrombocytopenia Absent Radius TAR Syndrome is a rare congenital disease presenting with reduced blood platelets megakaryocytic thrombocytopenia and forelimb anomalies concurrent with variable heart and kidney defects caused by hypomorphic RBM8A/Y14 gene function. RBM8A encodes a component of the ubiquitous exon junction complex involved in mRNA splicing transport and nonsense mediated decay. How perturbing a general mRNA processing factor causes the distinct phenotypes of TAR Syndrome remains unknown. Here we connect zebrafish rbm8a perturbation to early hematopoiesis defects via attenuated planar cell polarity PCP signaling involved in controlling developmental cell arrangements. Combining different genetic means to reduce rbm8a function we find a significant reduction of cd41 positive thrombocytes in hypomorphic rbm8a larvae. Transcriptomics analysis documents rbm8a mutant zebrafish embryos already post gastrulation accumulate mRNAs with erroneously included introns a hallmark of defective nonsense mediated decay. Affected mRNAs include transcripts encoding components of the non canonical Wnt pathway involved in PCP signaling and rbm8a mutant embryos show hallmarks of Wnt/PCP dependent early convergent extension defects. We establish that reduced rbm8a function synergizes with perturbations in Wnt/PCP pathway genes including wnt5b wnt11f2 fzd7a and vangl2. Following axis formation rbm8a perturbation impairs the migration and architecture of the lateral plate mesoderm LPM that forms the hematopoietic cardiovascular kidney and forelimb skeleton progenitors. Subsequently rbm8a perturbation impairs expression of early hematopoietic/endothelial genes including runx1a kdrl sox7 and the megakaryocyte regulator gfi1aa. Lastly we document similar hematopoietic defects upon loss of vangl2. Together our data link reduced rbm8a function to LPM migration and hematopoietic defects via attenuated Wnt/PCP signaling. Our… ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31   Protocols: Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Sample 3 E MTAB 12503:Sample 3   strain:mixed AB and Tubingen|ENA FIRST PUBLIC:2023 03 31|individual:20170530.A 3|organism:Danio rerio|organism:Danio rerio|ENA LAST UPDATE:2023 03 31|scientific name:Danio rerio|common name:zebrafish|organism part:embryo|age:24|developmental stage:pharyngula prim 5|genotype:rbm8a d5/d5|ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31                 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling E MTAB 12503:Sample 3 p Sample 3 p RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling Zebrafish embryos were collected at indicated developmental stages tailbud stage and 24 hpf. Total RNA was isolated from genotype defined pooled embryos by Trizol LS extraction as per manufacturer’s guidelines Invitrogen with final precipitation using 70% Ethanol. Libraries for sequencing were generated with the TruSeq RNA Sample Preparation kit Illumina. Experimental Factor: developmental stage:pharyngula prim 5|Experimental Factor: genotype:rbm8a d5/d5 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   ERP144048 Illumina HiSeq 4000 paired end sequencing; RNA seq of zebrafish embryos to investigate how Rbm8a deficiency akin to TAR Syndrome causes hematopoietic defects by modulating Wnt/PCP signaling ENA FIRST PUBLIC:2023 03 31|ENA LAST UPDATE:2023 03 31 20170530.A-3_R1.fastq.gz 20170530.A-3_R2.fastq.gz fastq fastq 13839085674.0 45824787.0 E MTAB 12503:20170530.A 3 R 0:151 1:151 A:3812423011;C:3120168590;G:3163957945;T:3729983766;N:12552362 151 151     3812423011 3120168590 3163957945 3729983766 12552362 ERX10233126 ERS14439191 ERA20162442 University of Zurich|European Nucleotide Archive University of Zurich|European Nucleotide Archive 2 0.88987 0.74432 0.33651 0.27875 0.69229 0.72934 0.46981 0.46116 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq sc unknown unknown   Switzerland 2023-03-31 Pharyngula Embryo Whole Organism All anatomical structures
35816 35816 SRR33052294 SRX28317427 SRS24656196 SRP577565 PRJNA1248471 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3ß Inhibitors with Anti Neurodegenerative Efficacy GSE294097 Transcriptome Analysis Spatial transcriptome sequencing technology has provided high resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease like pathological changes in zebrafish providing a unique insight into the pathogenesis of tau pathology mediated cell cell interactions in AD. Overall design: This study utilized four Danio rerio lines: wild type WT and three transgenic lines AD3 AD4 AD5 expressing human Tau protein with the P301S mutation Tau P301S. All transgenic lines were generated via stable integration of the human TAU P301S transgene.       WT GSM8898657   source name:Brain|tissue:Brain|geo loc name:missing|collection date:missing WT Reads were processed using the SAW 7.1.0 pipeline with default and recommended parameters. Assembly: GRCz11 Supplementary files format and content: Mask files matrix files and image files. Brain   Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ before Stereo seq library preparation. Where indicated the same sections were stained with nucleic acid dye Thermo fisher Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma P7000 in 0.01 M HCl buffer incubated at 37℃ for 5 minutes and then washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42℃ using SuperScript II Invitrogen 18064 014 10 U/ml reverse transcriptase 1 mM dNTPs 1 M betaine solution PCR reagent 7.5 mM MgCl2 5 mM DTT 2 U/ml RNase inhibitor 2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl 25 mM EDTA 100 mM NaCl 0.5% SDS at 55℃ for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme cDNA Release buffer treatment for over night at 55℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product 1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer 0.3 mM Stereo seq Library R primer…   tissue:Brain GSM8898657 GSM8898657: WT; Danio rerio; RNA Seq GSM8898657 r1 GSM8898657 1 Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ before Stereo seq library preparation. Where indicated the same sections were stained with nucleic acid dye Thermo fisher Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma P7000 in 0.01 M HCl buffer incubated at 37℃ for 5 minutes and then washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42℃ using SuperScript II Invitrogen 18064 014 10 U/ml reverse transcriptase 1 mM dNTPs 1 M betaine solution PCR reagent 7.5 mM MgCl2 5 mM DTT 2 U/ml RNase inhibitor 2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl 25 mM EDTA 100 mM NaCl 0.5% SDS at 55℃ for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme cDNA Release buffer treatment for over night at 55℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product 1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer 0.3 mM Stereo seq Library R primer…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP577565     WT_L01_read_1.fq.gz WT_L01_read_2.fq.gz fastq fastq 74425524705.0 551300183.0 GSM8898657 r1 0:35 1:100 A:19898122181;C:17423066656;G:16942100032;T:20160847006;N:1388830 35 100     19898122181 17423066656 16942100032 20160847006 1388830 SRX28317427 SRS24656196 SRA2109204 ShanTou University ShanTou University                       T B mate1 technical by mapping diff bgi bgi unknown cdna_unspecified unknown sc unknown unknown   China 2025-04-09 Undetermined Undetermined Brain Nervous System
35817 35817 SRR33052295 SRX28317426 SRS24656195 SRP577565 PRJNA1248471 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3ß Inhibitors with Anti Neurodegenerative Efficacy GSE294097 Transcriptome Analysis Spatial transcriptome sequencing technology has provided high resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease like pathological changes in zebrafish providing a unique insight into the pathogenesis of tau pathology mediated cell cell interactions in AD. Overall design: This study utilized four Danio rerio lines: wild type WT and three transgenic lines AD3 AD4 AD5 expressing human Tau protein with the P301S mutation Tau P301S. All transgenic lines were generated via stable integration of the human TAU P301S transgene.       AD5 GSM8898656   source name:Brain|tissue:Brain|geo loc name:missing|collection date:missing AD5 Reads were processed using the SAW 7.1.0 pipeline with default and recommended parameters. Assembly: GRCz11 Supplementary files format and content: Mask files matrix files and image files. Brain   Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ before Stereo seq library preparation. Where indicated the same sections were stained with nucleic acid dye Thermo fisher Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma P7000 in 0.01 M HCl buffer incubated at 37℃ for 5 minutes and then washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42℃ using SuperScript II Invitrogen 18064 014 10 U/ml reverse transcriptase 1 mM dNTPs 1 M betaine solution PCR reagent 7.5 mM MgCl2 5 mM DTT 2 U/ml RNase inhibitor 2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl 25 mM EDTA 100 mM NaCl 0.5% SDS at 55℃ for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme cDNA Release buffer treatment for over night at 55℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product 1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer 0.3 mM Stereo seq Library R primer…   tissue:Brain GSM8898656 GSM8898656: AD5; Danio rerio; RNA Seq GSM8898656 r1 GSM8898656 1 Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ before Stereo seq library preparation. Where indicated the same sections were stained with nucleic acid dye Thermo fisher Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma P7000 in 0.01 M HCl buffer incubated at 37℃ for 5 minutes and then washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42℃ using SuperScript II Invitrogen 18064 014 10 U/ml reverse transcriptase 1 mM dNTPs 1 M betaine solution PCR reagent 7.5 mM MgCl2 5 mM DTT 2 U/ml RNase inhibitor 2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl 25 mM EDTA 100 mM NaCl 0.5% SDS at 55℃ for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme cDNA Release buffer treatment for over night at 55℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product 1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer 0.3 mM Stereo seq Library R primer…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP577565     AD5_L01_read_1.fq.gz AD5_L01_read_2.fq.gz fastq fastq 84955633785.0 629300991.0 GSM8898656 r1 0:35 1:100 A:22736382740;C:20123949961;G:19583698932;T:22509389862;N:2212290 35 100     22736382740 20123949961 19583698932 22509389862 2212290 SRX28317426 SRS24656195 SRA2109204 ShanTou University ShanTou University                       T B mate1 technical by mapping diff bgi bgi unknown cdna_unspecified unknown sc unknown unknown   China 2025-04-09 Undetermined Undetermined Brain Nervous System
35818 35818 SRR33052296 SRX28317425 SRS24656194 SRP577565 PRJNA1248471 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3ß Inhibitors with Anti Neurodegenerative Efficacy GSE294097 Transcriptome Analysis Spatial transcriptome sequencing technology has provided high resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease like pathological changes in zebrafish providing a unique insight into the pathogenesis of tau pathology mediated cell cell interactions in AD. Overall design: This study utilized four Danio rerio lines: wild type WT and three transgenic lines AD3 AD4 AD5 expressing human Tau protein with the P301S mutation Tau P301S. All transgenic lines were generated via stable integration of the human TAU P301S transgene.       AD4 GSM8898655   source name:Brain|tissue:Brain|geo loc name:missing|collection date:missing AD4 Reads were processed using the SAW 7.1.0 pipeline with default and recommended parameters. Assembly: GRCz11 Supplementary files format and content: Mask files matrix files and image files. Brain   Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ before Stereo seq library preparation. Where indicated the same sections were stained with nucleic acid dye Thermo fisher Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma P7000 in 0.01 M HCl buffer incubated at 37℃ for 5 minutes and then washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42℃ using SuperScript II Invitrogen 18064 014 10 U/ml reverse transcriptase 1 mM dNTPs 1 M betaine solution PCR reagent 7.5 mM MgCl2 5 mM DTT 2 U/ml RNase inhibitor 2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl 25 mM EDTA 100 mM NaCl 0.5% SDS at 55℃ for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme cDNA Release buffer treatment for over night at 55℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product 1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer 0.3 mM Stereo seq Library R primer…   tissue:Brain GSM8898655 GSM8898655: AD4; Danio rerio; RNA Seq GSM8898655 r1 GSM8898655 1 Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ before Stereo seq library preparation. Where indicated the same sections were stained with nucleic acid dye Thermo fisher Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma P7000 in 0.01 M HCl buffer incubated at 37℃ for 5 minutes and then washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42℃ using SuperScript II Invitrogen 18064 014 10 U/ml reverse transcriptase 1 mM dNTPs 1 M betaine solution PCR reagent 7.5 mM MgCl2 5 mM DTT 2 U/ml RNase inhibitor 2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl 25 mM EDTA 100 mM NaCl 0.5% SDS at 55℃ for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme cDNA Release buffer treatment for over night at 55℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product 1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer 0.3 mM Stereo seq Library R primer…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP577565     AD4_L01_read_1.fq.gz AD4_L01_read_2.fq.gz fastq fastq 44786077200.0 331748720.0 GSM8898655 r1 0:35 1:100 A:11725098079;C:10594300338;G:10327407801;T:12138018161;N:1252821 35 100     11725098079 10594300338 10327407801 12138018161 1252821 SRX28317425 SRS24656194 SRA2109204 ShanTou University ShanTou University                       T B mate1 technical by mapping diff bgi bgi unknown cdna_unspecified unknown sc unknown unknown   China 2025-04-09 Undetermined Undetermined Brain Nervous System
35819 35819 SRR33052297 SRX28317424 SRS24656193 SRP577565 PRJNA1248471 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3ß Inhibitors with Anti Neurodegenerative Efficacy GSE294097 Transcriptome Analysis Spatial transcriptome sequencing technology has provided high resolution transcriptome data for studying the molecular mechanism of Tau P301S mediating Alzheimer's disease like pathological changes in zebrafish providing a unique insight into the pathogenesis of tau pathology mediated cell cell interactions in AD. Overall design: This study utilized four Danio rerio lines: wild type WT and three transgenic lines AD3 AD4 AD5 expressing human Tau protein with the P301S mutation Tau P301S. All transgenic lines were generated via stable integration of the human TAU P301S transgene.       AD3 GSM8898654   source name:Brain|tissue:Brain|geo loc name:missing|collection date:missing AD3 Reads were processed using the SAW 7.1.0 pipeline with default and recommended parameters. Assembly: GRCz11 Supplementary files format and content: Mask files matrix files and image files. Brain   Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ before Stereo seq library preparation. Where indicated the same sections were stained with nucleic acid dye Thermo fisher Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma P7000 in 0.01 M HCl buffer incubated at 37℃ for 5 minutes and then washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42℃ using SuperScript II Invitrogen 18064 014 10 U/ml reverse transcriptase 1 mM dNTPs 1 M betaine solution PCR reagent 7.5 mM MgCl2 5 mM DTT 2 U/ml RNase inhibitor 2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl 25 mM EDTA 100 mM NaCl 0.5% SDS at 55℃ for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme cDNA Release buffer treatment for over night at 55℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product 1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer 0.3 mM Stereo seq Library R primer…   tissue:Brain GSM8898654 GSM8898654: AD3; Danio rerio; RNA Seq GSM8898654 r1 GSM8898654 1 Tissue sections were adhered to the Stereo seq chip generated by BGI China surface and incubated at 37℃ for 3 minutes. Then the sections were fixed in methanol and incubated for 40 minutes at 20℃ before Stereo seq library preparation. Where indicated the same sections were stained with nucleic acid dye Thermo fisher Q10212 and imaging was performed with a Motic Custom PA53 FS6 microscope prior to in situ capture at the channel of FITC. post washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L tissue sections placed on the chip were permeabilized using 0.1% pepsin Sigma P7000 in 0.01 M HCl buffer incubated at 37℃ for 5 minutes and then washed with 0.1x SSC buffer Thermo AM9770 supplemented with 0.05 U/ml RNase inhibitor NEB M0314L. RNA released from the permeabilized tissue and captured by the DNB was reverse transcribed overnight at 42℃ using SuperScript II Invitrogen 18064 014 10 U/ml reverse transcriptase 1 mM dNTPs 1 M betaine solution PCR reagent 7.5 mM MgCl2 5 mM DTT 2 U/ml RNase inhibitor 2.5 mM Stereo seq TSO and 1x First Strand buffer. post reverse transcription tissue sections were washed twice with 0.1x SSC buffer and digested with Tissue Removal buffer 10 mM Tris HCl 25 mM EDTA 100 mM NaCl 0.5% SDS at 55℃ for 10 minutes. cDNA containing chips were then subjected to Prepare cDNA Release Mix cDNA Release Enzyme cDNA Release buffer treatment for over night at 55℃. cDNA were purified using the VAHTSTM DNA Clean Beads 0.8×. The concentrations of the resulting PCR products were quantified by QubitTM dsDNA Assay Kit Thermo Q32854. A total of 20 ng of DNA were then fragmented with in house Tn5 transposase at 55℃ for 10 minutes post which the reactions were stopped by the addition of 0.02% SDS and gently mixing at 37℃ for 5 minutes post fragmentation. Fragmented products were amplified as described below: 25 ml of fragmentation product 1x KAPA HiFi Hotstart Ready Mix and 0.3 mM Stereo seq Library F primer 0.3 mM Stereo seq Library R primer…   RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA PAIRED DNBSEQ DNBSEQ-T7   SRP577565     AD3_L01_read_1.fq.gz AD3_L01_read_2.fq.gz fastq fastq 60591288060.0 448824356.0 GSM8898654 r1 0:35 1:100 A:15920282345;C:14771409856;G:14276809765;T:15621229410;N:1556684 35 100     15920282345 14771409856 14276809765 15621229410 1556684 SRX28317424 SRS24656193 SRA2109204 ShanTou University ShanTou University                       T B mate1 technical by mapping diff bgi bgi unknown cdna_unspecified unknown sc unknown unknown   China 2025-04-09 Undetermined Undetermined Brain Nervous System
35865 35865 SRR33094447 SRX28358130 SRS24687221 SRP578075 PRJNA1249535 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy PRJNA1249535 Other Single cell transcriptome sequencing provides high resolution transcriptome data on the molecular mechanisms by which Tau P301S mediates Alzheimer's disease like pathological changes in zebrafish providing unique insights into the pathogenesis of Tau pathology mediated cell to cell interactions in AD.     TauP301S 4   TauP301S 4   breed:zebrafish|age:4 month|collection date:2024 05 18|geo loc name:China:Shantou|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal                 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy TauP301S 4 TauP301S 4 tissue     RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA PAIRED BGISEQ BGISEQ-500   SRP578075     AD4_S1_L001_R1_001.fastq.gz AD4_S1_L001_R2_001.fastq.gz fastq fastq 129145897746.0 427635423.0 AD4 S1 L001 R1 001.fastq.gz 0:151 1:151 A:37870495722;C:24917123133;G:22536537853;T:43764941649;N:56799389 151 151     37870495722 24917123133 22536537853 43764941649 56799389 SRX28358130 SRS24687221 SRA2110625 Shantou university medical college|Neuroscience Center Shantou university medical college                       T B mate1 technical by mapping diff bgi bgi unknown poly_a unknown sc unknown unknown   China 2025-04-13 Adult Adult Brain Nervous System
35866 35866 SRR33094448 SRX28358129 SRS24687220 SRP578075 PRJNA1249535 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy PRJNA1249535 Other Single cell transcriptome sequencing provides high resolution transcriptome data on the molecular mechanisms by which Tau P301S mediates Alzheimer's disease like pathological changes in zebrafish providing unique insights into the pathogenesis of Tau pathology mediated cell to cell interactions in AD.     TauP301S 3   TauP301S 3   breed:zebrafish|age:4 month|collection date:2024 05 17|geo loc name:China:Shantou|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal                 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy TauP301S 3 TauP301S 3 tissue     RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA PAIRED BGISEQ BGISEQ-500   SRP578075     AD3_S1_L001_R1_001.fastq.gz AD3_S1_L001_R2_001.fastq.gz fastq fastq 130723873718.0 432860509.0 AD3 S1 L001 R1 001.fastq.gz 0:151 1:151 A:38509426012;C:25238065771;G:22586405501;T:44332442791;N:57533643 151 151     38509426012 25238065771 22586405501 44332442791 57533643 SRX28358129 SRS24687220 SRA2110625 Shantou university medical college|Neuroscience Center Shantou university medical college                       T B mate1 technical by mapping diff bgi bgi unknown poly_a unknown sc unknown unknown   China 2025-04-13 Adult Adult Brain Nervous System
35867 35867 SRR33094449 SRX28358128 SRS24687219 SRP578075 PRJNA1249535 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy PRJNA1249535 Other Single cell transcriptome sequencing provides high resolution transcriptome data on the molecular mechanisms by which Tau P301S mediates Alzheimer's disease like pathological changes in zebrafish providing unique insights into the pathogenesis of Tau pathology mediated cell to cell interactions in AD.     TauP301S 2   TauP301S 2   breed:zebrafish|age:4 month|collection date:2024 05 16|geo loc name:China:Shantou|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal                 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy TauP301S 2 TauP301S 2 tissue     RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA PAIRED BGISEQ BGISEQ-500   SRP578075     AD2_S1_L001_R1_001.fastq.gz AD2_S1_L001_R2_001.fastq.gz fastq fastq 130145208498.0 430944399.0 AD2 S1 L001 R1 001.fastq.gz 0:151 1:151 A:37802929660;C:22980541562;G:20982421471;T:48304142442;N:75173363 151 151     37802929660 22980541562 20982421471 48304142442 75173363 SRX28358128 SRS24687219 SRA2110625 Shantou university medical college|Neuroscience Center Shantou university medical college                       T B mate1 technical by mapping diff bgi bgi unknown poly_a unknown sc unknown unknown   China 2025-04-13 Adult Adult Brain Nervous System
35868 35868 SRR33094450 SRX28358127 SRS24687218 SRP578075 PRJNA1249535 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy PRJNA1249535 Other Single cell transcriptome sequencing provides high resolution transcriptome data on the molecular mechanisms by which Tau P301S mediates Alzheimer's disease like pathological changes in zebrafish providing unique insights into the pathogenesis of Tau pathology mediated cell to cell interactions in AD.     TauP301S 1   TauP301S 1   breed:zebrafish|age:4 month|collection date:2024 05 15|geo loc name:China:Shantou|sex:not determined|tissue:brain|BioSampleModel:Model organism or animal                 P301S Mutant Tau Driven Zebrafish Platform Enables Systematic Identification of Pharmacological GSK3B Inhibitors with Anti Neurodegenerative Efficacy TauP301S 1 TauP301S 1 tissue     RNA-Seq TRANSCRIPTOMIC SINGLE CELL PolyA PAIRED BGISEQ BGISEQ-500   SRP578075     AD1_S1_L001_R1_001.fastq.gz AD1_S1_L001_R2_001.fastq.gz fastq fastq 151897861402.0 502973051.0 AD1 S1 L001 R1 001.fastq.gz 0:151 1:151 A:44290580650;C:26864167508;G:24611898618;T:56043760812;N:87453814 151 151     44290580650 26864167508 24611898618 56043760812 87453814 SRX28358127 SRS24687218 SRA2110625 Shantou university medical college|Neuroscience Center Shantou university medical college                       T B mate1 technical by mapping diff bgi bgi unknown poly_a unknown sc unknown unknown   China 2025-04-13 Adult Adult Brain Nervous System
71597 71597 SRR21780858 SRX17775679 SRS15301946 SRP400655 PRJNA885906 Cell Type Specific Responses to the Microbiota Across All Tissues of the Larval Zebrafish PRJNA885906 Other The transcriptional responses of the host zebrafish to the presence of the microbiota was assessed across all cell types throughout the larval body at single cell resolution. The goal of this work is to generate a resource for generating new hypotheses about the intricate interactions between animal hosts and their microbiota.       BefA diss BefA 1532   strain:Tgins; eGFP|dev stage:6dpf|sex:not applicable|tissue:dissected digestive systems|BioSampleModel:Model organism or animal                 germ free 6dpf dissected digestive systems treated with protein 1532 1532 the cells are from dissected guts from germ free larvae but were treated with exogenous protein     RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP400655     BefAdiss_S2_L008_R1_001.fastq.gz BefAdiss_S2_L008_R2_001.fastq.gz fastq fastq 62618506720.0 355786970.0 BefAdiss S2 L008 R1 001.fastq.gz 0:26 1:150 A:18434729847;C:13374700052;G:13922149278;T:16789619859;N:97307684 26 150     18434729847 13374700052 13922149278 16789619859 97307684 SRX17775679 SRS15301946 SRA1511285 University of Oregon|Institute of Molecular Biology University of Oregon 2 0.00182 0.89692 0.00064 0.07716 0.9962 0.82798 0.42608 0.6075 26 150 T B sc-like readlen illumina hiseq_era unknown random_priming unknown sc unknown unknown   United States 2022-10-02 Larval Larval Gut Digestive System
71598 71598 SRR21780859 SRX17775678 SRS15301945 SRP400655 PRJNA885906 Cell Type Specific Responses to the Microbiota Across All Tissues of the Larval Zebrafish PRJNA885906 Other The transcriptional responses of the host zebrafish to the presence of the microbiota was assessed across all cell types throughout the larval body at single cell resolution. The goal of this work is to generate a resource for generating new hypotheses about the intricate interactions between animal hosts and their microbiota.       GF diss2 GF 1531   strain:Tgins; eGFP|dev stage:6dpf|sex:not applicable|tissue:dissected digestive systems|BioSampleModel:Model organism or animal                 germ free 6dpf dissected digestive systems lane 2 1531 1531 the cells dissected guts from germ free larvae were split across two lanes library 1530/1531 come from same sample     RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP400655     GFdiss2_S1_L004_R1_001.fastq.gz GFdiss2_S1_L004_R2_001.fastq.gz fastq fastq 66862372720.0 379899845.0 GFdiss2 S1 L004 R1 001.fastq.gz 0:26 1:150 A:10814720171;C:8609009803;G:8785194946;T:9942289999;N:28711157801 26 150     10814720171 8609009803 8785194946 9942289999 28711157801 SRX17775678 SRS15301945 SRA1511285 University of Oregon|Institute of Molecular Biology University of Oregon 2 0.00191 0.92014 0.00074 0.08575 0.99616 0.87793 0.35964 0.58459 26 150 T B sc-like readlen illumina hiseq_era unknown random_priming unknown sc unknown unknown   United States 2022-10-02 Larval Larval Gut Digestive System
71599 71599 SRR21780860 SRX17775677 SRS15301944 SRP400655 PRJNA885906 Cell Type Specific Responses to the Microbiota Across All Tissues of the Larval Zebrafish PRJNA885906 Other The transcriptional responses of the host zebrafish to the presence of the microbiota was assessed across all cell types throughout the larval body at single cell resolution. The goal of this work is to generate a resource for generating new hypotheses about the intricate interactions between animal hosts and their microbiota.       GF diss1 GF 1530   strain:Tgins; eGFP|dev stage:6dpf|sex:not applicable|tissue:dissected digestive systems|BioSampleModel:Model organism or animal                 germ free 6dpf dissected digestive systems lane 1 1530 1530 the cells dissected guts from germ free larvae were split across two lanes library 1530/1531 come from same sample     RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP400655     GFdiss1_S1_L007_R1_001.fastq.gz GFdiss1_S1_L007_R2_001.fastq.gz fastq fastq 63769716736.0 362327936.0 GFdiss1 S1 L007 R1 001.fastq.gz 0:26 1:150 A:18291156920;C:14095548431;G:14421791117;T:16786925671;N:174294597 26 150     18291156920 14095548431 14421791117 16786925671 174294597 SRX17775677 SRS15301944 SRA1511285 University of Oregon|Institute of Molecular Biology University of Oregon 2 0.00172 0.91725 0.00064 0.08763 0.99648 0.82804 0.39234 0.5982 26 150 T B sc-like readlen illumina hiseq_era unknown random_priming unknown sc unknown unknown   United States 2022-10-02 Larval Larval Gut Digestive System
71600 71600 SRR21780861 SRX17775676 SRS15301943 SRP400655 PRJNA885906 Cell Type Specific Responses to the Microbiota Across All Tissues of the Larval Zebrafish PRJNA885906 Other The transcriptional responses of the host zebrafish to the presence of the microbiota was assessed across all cell types throughout the larval body at single cell resolution. The goal of this work is to generate a resource for generating new hypotheses about the intricate interactions between animal hosts and their microbiota.       GF1 GF1 HWLY5BBXX   strain:Tgnkx2.2a; eGFP|dev stage:6dpf|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal                 germ free no microbiota 6dpf whole larvae HWLY5BBXX GF1 HWLY5BBXX GF1 data is culmination of two HiSeq4000 runs. One run CV/GF samples were both run on the same line and in the second run CV/GF samples were run on individual lanes. Data was demultiplexed and treatment groups combined for total number of reads per group to be above spec.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP400655     GF1_S2_L006_R2_001.fastq.gz GF1_S2_L006_R1_001.fastq.gz fastq fastq 43844549700.0 146148499.0 GF1 S2 L006 R1 001.fastq.gz 0:150 1:150 A:10577324109;C:7388773641;G:8146030296;T:17727050506;N:5371148 150 150     10577324109 7388773641 8146030296 17727050506 5371148 SRX17775676 SRS15301943 SRA1511285 University of Oregon|Institute of Molecular Biology University of Oregon 2 0.02507 0.90549 0.00575 0.09697 0.99348 0.79091 0.53513 0.47471 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown sc unknown unknown   United States 2022-10-02 Larval Larval Whole Organism All anatomical structures
71601 71601 SRR21780862 SRX17775675 SRS15301942 SRP400655 PRJNA885906 Cell Type Specific Responses to the Microbiota Across All Tissues of the Larval Zebrafish PRJNA885906 Other The transcriptional responses of the host zebrafish to the presence of the microbiota was assessed across all cell types throughout the larval body at single cell resolution. The goal of this work is to generate a resource for generating new hypotheses about the intricate interactions between animal hosts and their microbiota.       CV2 CV2 HWLY5BBXX   strain:Tgnkx2.2a; eGFP|dev stage:6dpf|sex:not applicable|tissue:whole larvae|BioSampleModel:Model organism or animal                 conventional 6dpf whole larvae HWLY5BBXX CV2 HWLY5BBXX CV2 data is culmination of two HiSeq4000 runs. One run CV/GF samples were both run on the same line and in the second run CV/GF samples were run on individual lanes. Data was demultiplexed and treatment groups combined for total number of reads per group to be above spec.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM PAIRED ILLUMINA Illumina HiSeq 4000   SRP400655     CV2_S1_L006_R1_001.fastq.gz CV2_S1_L006_R2_001.fastq.gz fastq fastq 42260060400.0 140866868.0 CV2 S1 L006 R1 001.fastq.gz 0:150 1:150 A:10306378433;C:7083604228;G:7794391616;T:17070639212;N:5046911 150 150     10306378433 7083604228 7794391616 17070639212 5046911 SRX17775675 SRS15301942 SRA1511285 University of Oregon|Institute of Molecular Biology University of Oregon 2 0.0311 0.89818 0.0069 0.11191 0.99257 0.78642 0.52164 0.50459 150 150 T B mate1 technical by mapping diff illumina hiseq_era unknown random_priming unknown sc unknown unknown   United States 2022-10-02 Larval Larval Whole Organism All anatomical structures

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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");;