{"database": "metadata", "table": "run_metadata", "rows": [[53027, "SRR9669993", "SRX6430480", "SRS5085640", "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+.", null, null, null, "Sample6 zic ras tert TR rep3", "GSM3937766", null, "tissue:Adult brain tumor|treatment:zic UAS:tert;UAS:TR inj ras", "Sample6 zic ras tert TR rep3", "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\u2019s 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 UAS:tert;UAS:TR inj ras", "GSM3937766", "GSM3937766: Sample6 zic ras tert TR rep3; Danio rerio; RNA Seq", "GSM3937766", null, "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:GSM3937766", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP214202", null, null, "N6_AI_6_zic_ras_tert_TR_3_S6_R1.fastq.gz", "fastq", 1779340129.0, 17617229.0, "GSM3937766 r1", "0:101 1:0", "A:530371091;C:316769511;G:405002707;T:527096600;N:100220", 101, 0, null, null, 530371091, 316769511, 405002707, 527096600, 100220, "SRX6430480", "SRS5085640", "SRA919726", "GEO", "Computational Biology, ICGEB", 1, 0.81386, null, 0.19286, null, 0.79066, null, 0.58782, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "3prime", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "Unknown", "2019-07-11", "Adult", "Adult", "Multi-tissue", "Multi-system"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["53027"], "units": {}, "query_ms": 14.385392001713626}