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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
69748 SRR19155787 SRX15222308 SRS12956194 SRP374541 PRJNA836866 Embryo scale reverse genetics at single cell resolution GSE202639 Transcriptome Analysis The maturation of single cell transcriptomic technologies has facilitated the generation of comprehensive cellular atlases from whole embryos. A majority of this data however has been collected from wild type embryos without xxx appreciation for latent variation present in development. Here we present single cell transcriptomic data from 1812 individually resolved developing zebrafish embryos encompassing 19 time points 23 genetic perturbations and totaling 3.2M cells. The high degree of replication in our study 8 or more embryos per condition allows us to estimate the variance in cell type abundance organism wide and to detect perturbation dependent deviance in cell type composition relative to wild type embryos. Our approach is sensitive to rare cell types resolving developmental trajectories and genetic dependencies in the cranial ganglia neurons a cell population that comprises less than 1% of the embryo. Additionally time series profiling of individual mutants identified a group of brachyury independent cells with strikingly similar transcriptomes to notochord sheath cells leading to new hypotheses about the origins of the skull. We anticipate that standardized collection of high resolution organism scale single cell data from large numbers of individual embryos will enable mapping the genetic dependencies of zebrafish cell types while also addressing long standing challenges in developmental genetics including the cellular and transcriptional plasticity underlying phenotypic diversity across individuals. Overall design: Whole zebrafish embryos were collected across multiple timepoints or in response to genetic perturbations with sci RNA seq3. Please note that the following processed data files have been updated on Mar 7 2023: zperturb full cell metadata.csv zperturb full gene metadata.csv zperturb full raw counts.RDS   pubmed:37968389   Zebrafish perturbation atlas plates4 6 GSM6127483   tissue:Whole embryo|cell type:Whole embryo|developmental stage:18 24 36 48 72 hpf|strain:AB|genotype:ctrl cr tbx16 tbx16 tbx16l tbx16 msgn1 cdx4 cdx4 cdx1a tbxta tbx16 tbx16l msgn1 wnt3a wnt8a noto smo tbx1 hand2 egr2b epha4a hoxb1a mafba zc4h2 phox2a foxi1 hgfa met foxd3 tfap2a tfap2a foxd3 Zebrafish perturbation atlas plates4 6 The demultiplexing barcoded processing gene counting and aggregation were performed using the Brotman Baty sci RNA seq demultiplexing and processing pipelines https://github.com/bbi lab/bbi dmux; https://github.com/bbi lab/bbi sci. Count matrix was loaded into Monocle3 for further analysis Assembly: GRCz11 Supplementary files format and content: Count Matrix RDS file Cell Metadata comma separated values .csv Gene Metadata comma separated values .csv Supplementary files format and content: zperturb pilot cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb pilot raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb pilot cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb pilot gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb pilot hashTable.txt hash oligo count table Supplementary files format and content: reference cds.RDS monocle3 cell data set object Supplementary files format and content: reference raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: reference cell metadata.csv cell metadata table comma separated Supplementary files format and content: reference gene metadata.csv gene metadata table comma separated Supplementary files format and content: reference expt1 hashTable.txt hash oligo count table Supplementary files format and content: reference expt2 hashTable.txt hash oligo count table Supplementary files format and content: reference expt3 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full cds.RDS monocle3 cell data set object Supplementary files format and content: zperturb full raw counts.RDS dgCMatrix with raw counts Supplementary files format and content: zperturb full cell metadata.csv cell metadata table comma separated Supplementary files format and content: zperturb full gene metadata.csv gene metadata table comma separated Supplementary files format and content: zperturb full run1 hashTable.txt hash oligo count table Supplementary files format and content: zperturb full run2 hashTable.txt hash oligo count table Whole embryo   Embryos were transferred one by one into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS 5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. Zebrafish embryos were raised in embryo media at 28.5C. cell type:Whole embryo|developmental stage:18 24 36 48 72 hpf|strain:AB|genotype:ctrl cr tbx16 tbx16 tbx16l tbx16 msgn1 cdx4 cdx4 cdx1a tbxta tbx16 tbx16l msgn1 wnt3a wnt8a noto smo tbx1 hand2 egr2b epha4a hoxb1a mafba zc4h2 phox2a foxi1 hgfa met foxd3 tfap2a tfap2a foxd3 GSM6127483 GSM6127483: Zebrafish perturbation atlas plates4 6; Danio rerio; RNA Seq GSM6127483   1 Embryos were transferred one by one into separate wells of a 96 well V bottom plate containing 75μL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30℃ once every 5 minutes. Dissociation continued until no visible chunks were present under a dissecting scope which took between 20 40 minutes depending on embryo stage e.g. 20 minutes for 18hpf and 40 minutes for 72hpf. Stop solution [1x dPBS 5% FBS ] was then added to each well to quench the proteases. three prime end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico. GEO Accession:GSM6127483 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA SINGLE ILLUMINA Illumina NovaSeq 6000   SRP374541     GAP16_run2.1.fq.part2-L002.fastq.gz fastq 10212890200.0 102128902.0 GSM6127483 r6 0:100 A:3482663353;C:1957605793;G:2087822231;T:2684378509;N:420314 100       3482663353 1957605793 2087822231 2684378509 420314 SRX15222308 SRS12956194 SRA1418000 GEO Genome Sciences, University of Washington 1 0.7628   0.45135   0.82294   0.50602   100   B   usable mapping rate illumina novaseq_era 3prime random_priming unknown sc single_cell_plate scirnaseq   United States 2022-05-10 Larval Larval Whole Organism All anatomical structures