{"database": "metadata", "table": "run_metadata", "rows": [[69755, "SRR19155794", "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", null, "pubmed:37968389", null, "Zebrafish perturbation atlas plates4 6", "GSM6127483", null, "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", null, "Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75\u03bcL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30\u2103 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", null, "1", "Embryos were transferred  one by one  into separate wells of a 96 well V bottom plate containing 75\u03bcL of 1X TrypLE + 2 mg/mL Collagenase P. Embryos were then dissociated by manual trituration at 30\u2103 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", null, "SRP374541", null, null, "GAP16_run2.6.fq.part2-L002.fastq.gz", "fastq", 10735063100.0, 107350631.0, "GSM6127483 r66", "0:100", "A:3654454897;C:2064631585;G:2191485525;T:2824048671;N:442422", 100, null, null, null, 3654454897, 2064631585, 2191485525, 2824048671, 442422, "SRX15222308", "SRS12956194", "SRA1418000", "GEO", "Genome Sciences, University of Washington", 1, 0.78506, null, 0.46729, null, 0.82175, null, 0.51332, null, 100, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "3prime", "random_priming", "unknown", "sc", "single_cell_plate", "scirnaseq", null, "United States", "2022-05-10", "Larval", "Larval", "Whole Organism", "All anatomical structures"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["69755"], "units": {}, "query_ms": 7.083663993398659}