{"database": "metadata", "table": "run_metadata", "rows": [[68502, "SRR18074848", "SRX14226378", "SRS12047703", "SRP358067", "PRJNA803151", "mRNA aging shapes the Cap2 methylome in mammalian mRNA", "GSE196043", "Other", "The mRNA cap structure is a major site of dynamic mRNA methylation.  mRNA caps exist in either the Cap1 or Cap2 form  depending on the presence of 2' O methylation on the first  or both the first and second transcribed nucleotide  respectively.  However  the identity of Cap2 containing mRNAs and the function of Cap2 are unclear.  Here we describe CLAM Cap Seq  a method for transcriptome wide mapping and quantification of Cap2.  We find that unlike other epitranscriptomic modifications  Cap2 can occur on all mRNAs.  Cap2 is formed through a slow continuous conversion of mRNAs from Cap1 to Cap2 as mRNAs age in the cytosol.  As a result  Cap2 is enriched on long lived mRNAs.  We find that large increases in the abundance of Cap1 leads to activation of RIG I  especially in conditions where RIG I expression is increased.  The methylation of Cap1 to Cap2 markedly reduces the ability of RNAs to bind and activate RIG I.  We find that the slow Cap2 methylation rate allows Cap2 to accumulate on host mRNAs yet ensures that low Cap2 levels occur on newly expressed viral RNAs.  Overall  these results reveal an immunostimulatory role for Cap1  and that Cap2 functions to reduce activation of the innate immune response. Overall design: We developed next generation sequencing methods for quantification of Cap2 methylation in bulk mRNA CapTag seq  as well as in individual mRNAs in a transcriptome wide manner CLAM Cap seq. Furthermore  we developed tools for measuring translation and stability of transcript start nucleotide TSN mRNA isoforms by combining polysome profiling and actinomycin D treatment with TSS seq transcription start site sequencing.", null, "pubmed:36725932", null, "Zebrafish CapQuant seq 2", "GSM5907184", null, "source name:48 hpf embryo|cell line/tissue:whole|genotype:wild type A/B|purification:oligodT25 beads", "Zebrafish CapQuant seq 2", "Removal of low quality reads and three prime end adapter trimming was performed with flexbar v2.5. Removal of duplicated reads was accomplished with pyFastqDuplicateRemover.py within the pyCRAC package v1.3.2. Read trimming was performed using seqtk package v1.3. Read alignement to fly  mouse or human genome was conducted using Bowtie v1.2.3. five prime end read coverage was calculated per each genomic position using BEDTools v2.28.0. Genome build: Drosohila melanogaster; dm6  Mus musculus; mm10  Homo sapiens; hg38.", "48 hpf embryo", null, "CapTag seq Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  PolyA+ RNA was isolated from total RNA using magnetic oligodT25 beads NEB.", "Zebrafish AB line embryos were maintained in E3 medium at 28 degrees and staged as previously described Kimmel et al.  Developmental Dynamics  1995.", "cell line/tissue:whole|genotype:wild type A/B|purification:oligodT25 beads", "GSM5907184", "GSM5907184: Zebrafish CapQuant seq 2; Danio rerio; OTHER", "GSM5907184 r1", "GSM5907184", "1", "CapTag seq Total RNA was extracted using TRIzol reagent according to the manufacturers instructions followed by isopropanol precipitation.  PolyA+ RNA was isolated from total RNA using magnetic oligodT25 beads NEB.", null, "OTHER", "TRANSCRIPTOMIC", "other", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP358067", null, null, "Zebrafish_CQS2_R1.fastq.gz", "fastq", 658260009.0, 12907059.0, "GSM5907184 r1", "0:51 1:0", "A:158463141;C:142984303;G:213148834;T:143656235;N:7496", 51, 0, null, null, 158463141, 142984303, 213148834, 143656235, 7496, "SRX14226378", "SRS12047703", "SRA1545466", "Pharmacology, Weill Cornell Medicine", "Pharmacology, Weill Cornell Medicine", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "5prime", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "United States", "2022-02-18", "Hatching", "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": ["68502"], "units": {}, "query_ms": 10.498149989871308}