{"database": "metadata", "table": "run_metadata", "rows": [[74303, "SRR23635712", "SRX19518745", "SRS16906106", "SRP424834", "PRJNA939182", "The Effects of Rif1 Loss on Gene Expression During Early Zebrafish Development [SLAM seq]", "GSE226222", "Transcriptome Analysis", "Deregulated DNA replication is a major contributor to human developmental disorders and cancer  yet our understanding of how replication is coordinated with changes in transcription and chromatin structure is limited. Our lab has employed the zebrafish model to investigate the mechanisms driving changes in the replication timing program during development. Previous studies have identified changes in replication timing patterns from the onset of zygotic transcription through gastrulation in zebrafish embryos. The protein Rif1 is crucial for replication timing in a wide range of eukaryotes  yet its role in establishing the replication timing program and chromatin structure during early vertebrate development is not well understood. Using Rif1 mutant zebrafish and performing RNA sequencing and whole genome replication timing analysis  we found that Rif1 mutants were viable but had a defect in female sex determination. Interestingly  Rif1 loss primarily affected DNA replication timing post gastrulation  while its impact on transcription was more pronounced during zygotic genome activation. Our results indicate that Rif1 has distinct roles in regulating DNA replication and transcription at different stages of development. Overall design: SlamSeq three prime mRNA sequencing data was generated for wild type and rif1 mutant zebrafish embryos at different developmental stages 256 cell and Dome.", null, null, null, "SLAM seq 256Cell  omf201  replicate3", "GSM7068342", null, "source name:whole organism|strain:Tab5|tissue:whole organism|developmental stage:Blastula:256 cell|time:2 2.5 hpf|genotype:rif1 omf201/omf201|cell cycle phase:Asynchronous|geo loc name:missing|collection date:missing", "SLAM seq 256Cell  omf201  replicate3", "T to C conversion rates in three primeUTRs were calculated using the SLAM DUNK package with default settings. The 4.3.2 transcript annotation by Lawson et al doi: 10.7554/eLife.55792 was used. Assembly: GRCz11 Supplementary files format and content: slamDunkResults.tar.gz has Tab separated tcount files containing the SLAMSeq statistics per Ensembl gene UTR. Library strategy: SLAM seq", "whole organism", "Zebrafish embryos were spawned and staged within 10 minutes of fertilization and were subsequently incubated at 28.5\u00b0C. 2 cell embryos were injected with 50 pmoles of 4 Thiouridine S4U. Embryos were incubated at 28.5. Prior to collection  all clutches were visually examined to ensure synchronous development  and any unfertilized or morphologically abnormal embryos were removed. Batches of whole embryos were rapidly frozen and stored at  80\u00b0C for later processing for mRNA.", "The mRNA was prepared from whole embryo pools using the RNeasy Mini Kit 493 74104; Qiagen. The QuantSeq libraries were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit for Illumina Lexogen. RNA sequencing was conducted using custom primers on an Illumina Nextseq 500 with High Output chemistry and 75bp single ended reads.", "Adult breeding fish were housed in an aquatic animal facility in tanks of \u223c30 fish per tank and maintained at 26.5\u00b0C with 10 hour light and 14 hour dark cycles.", "strain:Tab5|tissue:whole organism|developmental stage:Blastula:256 cell|time:2 2.5 hpf|genotype:rif1 omf201/omf201|cell cycle phase:Asynchronous", "GSM7068342", "GSM7068342: SLAM seq 256Cell  omf201  replicate3; Danio rerio; OTHER", "GSM7068342 r1", "GSM7068342", "1", "The mRNA was prepared from whole embryo pools using the RNeasy Mini Kit 493 74104; Qiagen. The QuantSeq libraries were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit for Illumina Lexogen. RNA sequencing was conducted using custom primers on an Illumina Nextseq 500 with High Output chemistry and 75bp single ended reads.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "NextSeq 500", null, "SRP424834", null, null, "10-Mutant_256-cell_7-13-18__S10_R1_001.fastq.gz", "fastq", 2284290352.0, 30056452.0, "GSM7068342 r1", "0:76 1:0", "A:670367077;C:393468195;G:556663242;T:663782162;N:9676", 76, 0, null, null, 670367077, 393468195, 556663242, 663782162, 9676, "SRX19518745", "SRS16906106", "SRA1596763", "Sansam Lab, Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation", "Sansam Lab, Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation", 1, 0.83754, null, 0.04615, null, 0.81095, null, 0.65969, null, 76, null, "B", null, "usable mapping rate", "illumina", "nextseq", "3prime", "random_priming", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2023-02-27", "Blastula", "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": ["74303"], "units": {}, "query_ms": 10.217100993031636}