run_metadata: 53032

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
53032	SRR9669988	SRX6430475	SRS5085635	SRP214202	PRJNA554016	Expression of telomerase prevents ALT and maintains telomeric heterochromatin in juvenile brain tumors.	GSE134135	Transcriptome Analysis	The up regulation of a telomere maintenance mechanism TMM is an essential step in cancer progression to escape dysfunctional telomeres senescence and apoptosis. Paediatric brain tumors frequently exhibit Alternative Lengthening of Telomere ALT as active TMM but the mechanisms involved in the induction of ALT in brain tumor cells are not clear. Here we report a model of juvenile zebrafish brain tumor that progressively develops ALT. We discovered that reduced expression of tert and increase in Terra expression precedes ALT development. Additionally tumors show persistent telomeric DNA damage and loss of heterochromatin marks. Comparative analysis of gene expression post the rescue of ALT with telomerase and analysis of telomerase positive paediatric brain cancers showed normalization of telomeric heterochromatin and maintenance of telomere length with reduced expression of genes of the pre replicative complex as hallmark. Thus our study identifies telomere maintenance mechanisms as major drivers of DNA replication and chromatin status at telomeres in brain cancers. Overall design: In order to identify the genes involved in the development of alternative lenghtening of telomeres in juvenile brain cancer we performed RNA sequencing analysis RNA Seq of the transcriptome of two zebrafish models of brain cancer one ALT+ and the other telomerase+.				Sample1 zic ras rep1	GSM3937761		tissue:Adult brain tumor\|treatment:zic inj ras	Sample1 zic ras rep1	Basecalls performed using CASAVA Illumina Inc. The reads were mapped to the reference genome ENSEMBL GRCz11 using STAR Dobin et al. 2013 version 2.5.3a HTSeq count version 0.9.1 was used to generate gene counts. Differential gene expression analysis was performed using DESeq2 version 1.22.2 Genome build: Zebrafish Danio rerio GRCz11 from ENSEMBL database. Supplementary files format and content: tab delimited text files include COUNTS values for each Sample	Adult brain tumor	One of the two groups of samples overexpress also telomerase through the Gal4/UAS system	RNA extracts were collected from tumors developing in adult zebrafish. Total RNA was isolated TRIzol reagent Thermo Fisher Scientific following manufacturer’s instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Lexogen Quant Seq three prime mRNA Seq library prep kit Fwd.	Brain tumors were induced in developing zebrafish through the Gal4/UAS system using the zic:Gal4 driver line and the injection of a UAS:HRASV12G plasmid	treatment:zic inj ras	GSM3937761	GSM3937761: Sample1 zic ras rep1; Danio rerio; RNA Seq	GSM3937761		1	RNA extracts were collected from tumors developing in adult zebrafish. Total RNA was isolated TRIzol reagent Thermo Fisher Scientific following manufacturer's instructions subjected to DNase I Thermo Fisher Scientific treatment and subsequently purified using phenol chloroform Libraries were constructed using Lexogen Quant Seq three prime mRNA Seq library prep kit Fwd.	GEO Accession:GSM3937761	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2500		SRP214202			N1_AI_1_zic_ras_1_S1_R1.fastq.gz	fastq	1840262925.0	18220425.0	GSM3937761 r1	0:101 1:0	A:541527209;C:334145158;G:434769924;T:529718084;N:102550	101	0			541527209	334145158	434769924	529718084	102550	SRX6430475	SRS5085635	SRA919726	GEO	Computational Biology, ICGEB	1	0.83576		0.15359		0.79555		0.59782		101		B		usable mapping rate	illumina	hiseq_era	3prime	cdna_unspecified	lexogen	bulk	unknown	unknown		Unknown	2019-07-11	Adult	Adult	Multi-tissue	Multi-system