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9 rows where experiment.library_selection = "RANDOM", experiment.library_source = "TRANSCRIPTOMIC SINGLE CELL" and tissue_curation = "Whole Organism"

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devstage_curation 3

devstage_curation_coarse 2

tissue_curation_coarse 1

tissue_curation 1

  • Whole Organism · 9 ✖

technology 1

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

  • TRANSCRIPTOMIC SINGLE CELL · 9 ✖

experiment.library_selection 1

  • RANDOM · 9 ✖

experiment.library_layout 1

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