run_metadata: 64987

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
64987	SRR14867729	SRX11185277	SRS9242604	SRP324746	PRJNA739457	Investigation of mettl4 mediated alterative splicing variation	GSE178511	Other	We compare mettl4 KO and WT samples from different species to understand how mettl4 affects the alterative splicing Overall design: mRNA profiles of mettl4 KO and WT				ZEBARFISH WT AB9 Sample 21	GSM5393115		tissue:ZEBARFISH\|genotype:WT\|cell line:AB9	ZEBARFISH WT AB9 Sample 21	Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to mm8 whole genome using bowtie v0.12.2 with parameters q p 4 e 100 y a m 10 best strata Reads Per Kilobase of exon per Megabase of library size RPKM were calculated. In short exons from all isoforms of a gene were merged to create one meta transcript. The number of reads falling in the exons of this meta transcript were counted and normalized by the size of the meta transcript and by the size of the library. Genome build: hg19 mm10 dm6 sacCer1 GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample	ZEBARFISH		RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols		genotype:WT\|cell line:AB9	GSM5393115	GSM5393115: ZEBARFISH WT AB9 Sample 21; Danio rerio; RNA Seq	GSM5393115		1	RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5393115	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP324746			ZEBARFISH-WT-2_R1_001.fastq.gz ZEBARFISH-WT-2_R2_001.fastq.gz	fastq fastq	10653778500.0	35512595.0	GSM5393115 r1	0:150 1:150	A:2472673652;C:2874537502;G:2838089387;T:2467827251;N:650708	150	150			2472673652	2874537502	2838089387	2467827251	650708	SRX11185277	SRS9242604	SRA1248203	GEO	Max Planck Institute for heart and lung research	2	0.03862	0.04475	0.0091	0.00761	0.99799	0.99797	0.57868	0.65107	150	150	T	T	mates < 9% mapping rate	illumina	hiseq_era	unknown	random_priming	trueseq	bulk	unknown	unknown		Germany	2021-06-20	Undetermined	Undetermined	Cell Line	Cell Line