run_metadata: 59316

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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
59316	SRR11855602	SRX8405703	SRS6718144	SRP264942	PRJNA635369	Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing	GSE151273	Transcriptome Analysis	Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis especially in neural tissues. Mutations in pre mRNAs processing factor 31 PRPF31 cause autosomal dominant retinitis pigmentosa a progressive retinal degeneration disease. The transcriptome wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here we showed that the differentiation and viability of retinal progenitor cells RPCs are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild type human PRPF31 rather than the disease associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak five prime splicing site. Moreover genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis. Overall design: Head mRNA profiles of 36 hpf sibling wild type and prpf31 / zebrafish were generated by deep sequence in three independent biological replicates.		pubmed:33476374		AB Head sib2	GSM4570138		source name:Head\|strain:AB\|tissue:Head\|age:36 hpf type	AB Head sib2	Illumina Casava1.8 software used for basecalling. RNA seq reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 genome assembly using HISAT version 2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels Trapnell Cole et al. 2010 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Supplementary files format and content: tab delimited text files with raw gene counts for every gene and every sample	Head		Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3’ ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 µl USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system		strain:AB\|tissue:Head\|age:36 hpf type	GSM4570138	GSM4570138: AB Head sib2; Danio rerio; RNA Seq	GSM4570138		1	Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 µl USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system	GEO Accession:GSM4570138	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP264942			sib2_1.fastq.gz sib2_2.fastq.gz	fastq fastq	12076874100.0	40256247.0	GSM4570138 r1	0:150 1:150	A:3116319895;C:2937698203;G:2949917740;T:3072719174;N:219088	150	150			3116319895	2937698203	2949917740	3072719174	219088	SRX8405703	SRS6718144	SRA1080304	GEO	Huazhong University of Science and Technology	2	0.95283	0.95237	0.06658	0.06623	0.69292	0.69365	0.44936	0.45234	150	150	B	B	biological fallback assumption	illumina	hiseq_era	5prime	poly_a	nebnext	bulk	unknown	unknown		China	2020-05-27	Pharyngula	Embryo	Head	Nervous System