run_metadata: 73915
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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 |
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| 73915 | SRR23284056 | SRX19227383 | SRS16633550 | 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 | zebrafish embryo 6hpf rep1 | GSM7012034 | 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 rep1 | 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’s protocol. Libraries were size selected with SPRI beads and quantified by QuBIT Life Technologies. Average size of 300 bp 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. | tissue:whole embryo|genotype:AB/TL|treatment:4sU injection|time:6hpf | GSM7012034 | GSM7012034: zebrafish embryo 6hpf rep1; Danio rerio; RNA Seq | GSM7012034 r1 | GSM7012034 | 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 bp 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. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP420237 | loader:fastq load.py | novaseq_20220630_slam_120122_6h_1.fastq.gz novaseq_20220630_slam_120122_6h_2.fastq.gz | fastq fastq | 7578082116.0 | 37515258.0 | GSM7012034 r1 | 0:101 1:101 | A:1938942537;C:1836634013;G:1866966085;T:1935520946;N:18535 | 101 | 101 | 1938942537 | 1836634013 | 1866966085 | 1935520946 | 18535 | SRX19227383 | SRS16633550 | SRA1587567 | Hebrew University of Jerusalem | Hebrew University of Jerusalem | 2 | 0.86852 | 0.87284 | 0.11981 | 0.11692 | 0.7571 | 0.75702 | 0.63941 | 0.63601 | 101 | 101 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | poly_a | ribozero | sc_generic | single_cell_generic | generic-scrnaseq-only | Israel | 2023-01-31 | Gastrula | Embryo | Whole Organism | All anatomical structures |