{"database": "metadata", "table": "run_metadata", "rows": [[74110, "SRR23380805", "SRX19321394", "SRS16719693", "SRP422528", "PRJNA934545", "A single cell map of maternal and zygotic mRNA dynamics during cell type specification in zebrafish embryos [scSLAM seq]", "GSE224918", "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: single cell  SLAM seq  3 developmental stages  with treated and untreated samples  and biological replicates", "parent bioproject:PRJNA933118", "pubmed:37131717;pubmed:38600066", null, "zebrafish embryo  zfs:0000015  IAA  replicate B  scRNAseq", "GSM7035739", null, "source name:zebrafish embryo|tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:IAA|geo loc name:missing|collection date:missing", "zebrafish embryo  zfs:0000015  IAA  replicate B  scRNAseq", "Alignment of sequencing reads and generation of digital expression matrices was performed essentially as described in Farrell et. al.  Science  2018  using Drop seq tools v1.12. Two modified versions of the genome were produced: one where all T residues were replaced with C and one where all A residues were replaced with G. Prior to alignment  original sequencing reads were preserved and then all A residues were replaced with G. These converted reads were aligned to both modified genomes using Bowtie2 as previously described  then filtered based on which strand the read was aligned to. These two outputs were combined and then processed through the remainder of the Drop seq tools pipeline to produce processed BAM files and digital gene expression matrices. Converted reads were then replaced with the original reads and CIGAR strings were recalculated using Samtools in the final output BAM files. Assembly: GRCz11/102 Supplementary files format and content: Tab separated values files and matrix files", "zebrafish embryo", "20mM 4sUTP injection at 1 cell stage", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "tissue:zebrafish embryo|developmental stage:zfs:0000015|strain:AB/TL|treatment:IAA", "GSM7035739", "GSM7035739: zebrafish embryo  zfs:0000015  IAA  replicate B  scRNAseq; Danio rerio; RNA Seq", "GSM7035739 r1", "GSM7035739", "1", "Drop seq droplet encapsulation of cells. Libraries were built according to the Drop seq protocol version 3.1 12/28/2015  available http://www.dropseq.org/ with the following modifications. Iodoacetamide IAA  Sigma Aldrich was diluted in ethanol to a 100mM working concentration. Following breakage of droplets  beads were washed once with 300uL of 5x IAA buffer 250mM NaPO4 pH8  and incubated in IAA solution 50mM NaPO4 pH8  10mM IAA  20% DMSO  6% Ficoll PM 400 for 15min at 32\u00b0C with rotation. DTT was added to a final concentration of 20mM to stop the reaction  and beads were washed twice with 6x SSC solution before continuing with reverse transcription. An estimated 50\u2013100 STAMPs were included in each 50uL PCR reaction  and 12\u201313 cycles of PCR amplification were performed. Libraries were sequenced using Illumina Nextseq v2.2 Mid or High Output 150bp chemistry.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP422528", null, "loader:fastq load.py", "B08_S8_R2_001.fastq.gz B08_S8_R1_001.fastq.gz B08_S8_I1_001.fastq.gz", "fastq fastq fastq", 6618266424.0, 39394443.0, "GSM7035739 r1", "0:8 1:20 2:140", "A:1772472371;C:1058335373;G:1382074511;T:1301941080;N:398685", 8, 20, 140, null, 1772472371, 1058335373, 1382074511, 1301941080, 398685, "SRX19321394", "SRS16719693", "SRA1590430", "Hebrew University of Jerusalem", "Hebrew University of Jerusalem", 1, 0.66052, null, 0.03428, null, 0.84902, null, 0.4999, null, 140, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "dropseq", null, "Israel", "2023-02-09", "Blastula", "Embryo", "Embryo Imprecise", "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": ["74110"], "units": {}, "query_ms": 10.570054997515399}