run_metadata: 68502

This data as json

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
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.		pubmed:36725932		Zebrafish CapQuant seq 2	GSM5907184		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		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.		OTHER	TRANSCRIPTOMIC	other	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP358067			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			158463141	142984303	213148834	143656235	7496	SRX14226378	SRS12047703	SRA1545466	Pharmacology, Weill Cornell Medicine	Pharmacology, Weill Cornell Medicine	1	0.0		0.0		1.0				51		T		under 1.2% mapping rate	illumina	hiseq_era	5prime	poly_a	unknown	bulk	bulk	bulk		United States	2022-02-18	Hatching	Embryo	Embryo Imprecise	All anatomical structures