run_metadata: 38043

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
38043	SRR1371225	SRX585639	SRS631982	SRP043064	PRJNA252044	Transcriptome Analysis Reveals a Comprehensive Regulatory Network Involved in the Zebrafish Model of Diamond Blackfan Anemia from RPL5 Deficiency [miRNA Seq]	GSE58344	Transcriptome Analysis	In this study we generated a zebrafish model of DBA with RPL5 morphants and implemented high throughput RNA seq and miRNA seq to identify key genes lncRNAs and miRNAs during zebrafish development and hematopoiesis. We found that RPL5 is required for both primitive and definitive hematopoiesis processes that are partially mediated by the P53 pathway. Several genes such as cirh1a noc2l tars and nol6 and miRNAs such as dre miR 10a* dre miR 722 dre miR 737 and dre miR 142a 3p were significantly deregulated and these changes may play a crucial role in hematopoiesis ribosome biogenesis and development process. We also characterized the lncRNome in zebrafish with RPL5 deficiency. By constructing a comprehensive regulatory network we identified central node genes in the network connected to the P53 pathway almost all of which were targeted by the significantly deregulated miRNAs listed above. Our results therefore establish a regulatory network for critical genes and miRNAs involved in the RPL5 deficient zebrafish model and provide a comprehensive basis for the molecular pathogenesis of RPL5 mediated DBA and other ribosomopathies. Overall design: Determine the differences of miRNome between RPL5 deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPL5 mediated human diseases	parent bioproject:PRJNA252043	pubmed:26961822		morpholino control [miRNA]	GSM1408094		tissue:embryo\|genotype/variation:control morpholino\|developmental stage:48hpf	morpholino control [miRNA]	FASTX Toolkit clipper was used to remove sequencing adapters. The .fastq file was converted to a tab delimited file which held only the unique sequence read and its corresponding number of copies. The files were uploaded to DSAP http://dsap.cgu.edu.tw/index.htm for clustering of tags classification of non coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase database respectively. The differential expressed miRNAs were detected by R package DEGseq using the output data of DSAP. Genome build: Zv9	embryo	Zebrafish embryos at the one cell stage were injected with the MOs using an Microinjector WPI SYS PV830. Based on initial injection trials 2 5 ng MO and control MO was chosen as the optimal concentration.	Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions.	Zebrafish embryos were kept in a 28.5℃ incubator to 48hpf	genotype/variation:control morpholino\|developmental stage:48hpf	GSM1408094	GSM1408094: morpholino control [miRNA]; Danio rerio; miRNA Seq	GSM1408094		1	Immediately post harvesting 40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at 80°C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer’s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer’s instructions.	GEO Accession:GSM1408094	miRNA-Seq	TRANSCRIPTOMIC	size fractionation	SINGLE	ILLUMINA	Illumina HiSeq 2000		SRP043064					308681847.0	3810887.0	GSM1408094 r1	0:81	A:63686404;C:75263287;G:80056961;T:89650625;N:24570	81				63686404	75263287	80056961	89650625	24570	SRX585639	SRS631982	SRA169796	GEO	Beijing Institute of Genomics	1	8e-05		2e-05		0.99991		0.42857		81		T		under 1.2% mapping rate	illumina	hiseq_era	unknown	size_fractionation	unknown	bulk	unknown	unknown		China	2014-06-10	Hatching	Embryo	Embryo Imprecise	All anatomical structures