{"database": "metadata", "table": "run_metadata", "rows": [[73913, "SRR23284054", "SRX19227385", "SRS16633552", "SRP420237", "PRJNA929924", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [SLAM seq]", "GSE224113", "Other", "During early embryogenesis  embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal to zygotic transition requires a tight interplay of mRNA transcription and degradation  but distinguishing their unique contributions remains a challenge. Here  we dissect gene regulation during the zebrafish maternal to zygotic transition by combining single cell RNA sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single cell transcriptomes into their new zygotic and old maternal mRNA components  and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell type restricted expression arises by zygotic transcription  but distinguish a specific role for maternal transcripts in defining germ cell and enveloping layer identity  two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level  and associate a fast replacement with genes that has a restricted zygotic expression in either cell type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post transcriptional events that control gene regulation during early embryogenesis. Overall design: SLAM seq  zebrafish embryos  1hpf and 6hpf  2 technical replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo  6hpf  rep2", "GSM7012036", null, "source name:whole embryo|tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:6hpf|geo loc name:missing|collection date:missing", "zebrafish embryo  6hpf  rep2", "Sequence reads were trimmed for adaptor sequence using cutadapt Trimmed sequence reads were mapped to GRCz11 using STAR Read count extraction and NTR calculation were performed using GRAND SLAM Assembly: GRCz11/102 Supplementary files format and content: tab delimited text file includes readcount and NTR %new RNA for each Sample Library strategy: SLAM seq", "whole embryo", "20mM 4sU injection at 1 cell stage RNA was treated with Iodoacetamide to induce T to C conversions", "Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems  Inc. according to the manufacturer\u2019s protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300\u2009bp was determined by TapeStation Agilent Technologies  USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer\u2019s instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.", null, "tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:6hpf", "GSM7012036", "GSM7012036: zebrafish embryo  6hpf  rep2; Danio rerio; RNA Seq", "GSM7012036 r1", "GSM7012036", "1", "Total RNA was isolated using tri reagent Sigma T9424 and quantified using nanodrop polyA+RNA: Indexed RNA Seq libraries were prepared from 500 ng total RNA using the KAPA Stranded mRNA Seq Kit Kapa Biosystems  Inc. according to the manufacturer's protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300\u2009bp was determined by TapeStation Agilent Technologies  USA. Libraries are then sequenced using an Illumina Nextseq500 sequencer. total RNA: indexed RNA Seq libraries for each sample were generated from total RNA using the Illumina RiboZeroHuman/Mouse/Rat kit following the manufacturer's instructions. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Libraries are then sequenced using an Illumina Novaseq sequencer.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP420237", null, "loader:fastq load.py", "nextseq_20220515_slam_120122_6hr_S20_R1_001.fastq.gz", "fastq", 1231038044.0, 16197869.0, "GSM7012036 r1", "0:76", "A:287858332;C:300689662;G:294179125;T:348288250;N:22675", 76, null, null, null, 287858332, 300689662, 294179125, 348288250, 22675, "SRX19227385", "SRS16633552", "SRA1587567", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.91125, null, 0.06969, null, 0.75538, null, 0.55355, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "poly_a", "ribozero", "sc_generic", "single_cell_generic", "generic-scrnaseq-only", null, "Israel", "2023-01-31", "Gastrula", "Embryo", "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": ["73913"], "units": {}, "query_ms": 15.5707980011357}