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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
51024 SRR12429755 SRX8925577 SRS7181811 SRP180876 PRJNA515051 Zebrafish Samples for Loss of ATRX cooperates with p53 Deficiency to promote the Development of Sarcomas and other Malignancies GSE125040 Transcriptome Analysis The SWI/SNF family chromatin remodeling protein ATRX is a tumor suppressor in sarcomas gliomas and other malignancies. Its loss of function facilitates the alternative lengthening of telomeres ALT pathway in tumor cells while it also affects Polycomb repressive complex 2 PRC2 silencing of its target genes. To further define the role of inactivating ATRX mutations in carcinogenesis we knocked out atrx in our previously published p53/nf1 deficient zebrafish line that develops malignant peripheral nerve sheath tumors and gliomas. Complete inactivation of atrx using CRISPR cas9 was lethal in developing fish and resulted in an alpha thalassemia like phenotype including reduced alpha globin expression. In p53/nf1 deficient zebrafish neither peripheral nerve sheath tumors nor gliomas showed accelerated onset in atrx+/ fish but these fish developed various tumors that were not observed in their atrx+/+ siblings including epithelioid sarcoma angiosarcoma undifferentiated pleomorphic sarcoma and rare types of carcinoma. Most of these cancer types are included in the AACR Genie database of human tumors associated with mutant ATRX indicating that our zebrafish model reliably reflects a role for ATRX loss in the early pathogenesis of these types of human cancers. RNA seq of p53/nf1 and p53/nf1/atrx deficient tumors revealed that down regulation of telomerase accompanied ALT mediated lengthening of the telomeres in atrx mutant samples. Moreover inactivating mutations in atrx disturbed PRC2 target gene silencing indicating a connection between ATRX loss and PRC2 dysfunction in cancer development. Overall design: Gene expression values were derived from paired end RNA Seq data that compared zebrafish samples from p53/nf1/atrx deficient tumors to samples from atrx wildtype controls 3 vs. 3 samples.   pubmed:30970016;pubmed:32651197   MPNST suz12 mut Z3 GSM4720869   tissue:Zebrafish malignant peripheral nerve sheath tumors MPNSTs|tp53: / |nf1b: / |nf1a:+/ |atrx:wt|suz12a:+/ |suz12b:+/ MPNST suz12 mut Z3 FastQC was used to evaluate read quality on raw RNA Seq reads and trimmed reads. Trimming of low quality reads and clipping of sequencing adapters was done using the program Trimmomatic version 0.36 and all reads shorter than 36bp post trimming were dropped Trimmomatic was run with settings of ILLUMINACLIP:adapters/TruSeq3 PE 2.fa: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 AVGQUAL:10. Reads were aligned to the zebrafish Danio rerio reference genome with TopHat version 2.1.0 using UCSC danRer10 and settings of x 1 g 1 r 44 mate std dev 223 with values for the flags r and mate std dev coming from the mean fragment size. Bam sorting and indexing was done with SamTools and duplicate reads were removed using Picard tools http://picard.sourceforge.net. Aligned reads processed to Fragments Per Kilobase of exon per Million fragments mapped FPKM using cufflinks version 2.2.1 http://cufflinks.cbcb.umd.edu/index.html with the G flag to use the danRer10 reference annotation to estimate isoform expression and not assemble novel transcripts and the flags max bundle frags 4000000 N compatible hits norm. Gene level counts were obtained with htseq count version 0.9.1. Differential gene expression was evaluated with the R Bioconductor package DESeq2 and normalized expression values for individual samples were obtained from DESeq2 using the variance stabilizing transform on the raw counts. The variance stabilizing transformed data were used for GSEA. Genome build: GRCz10 Supplementary files format and content: genes.fpkm tracking files are tab delimited text files output by cufflinks in a generic FPKM tracking format with estimated gene level expression values in the form of FPKM values and raw count.txt files are tab delimited text files output by htseq count with gene level counts Zebrafish malignant peripheral nerve sheath tumors MPNSTs The zebrafish atrx mutant lines were generated by the CRISPR Cas9 genome editing system using the previous described protocol Hwang et al. Nature Biotechnology 2013. The plasmid constructs pDR274 #42250 and pMLM3613 #42251 were purchased from Addgene. Oligonucleotides 5’ TAG GTC CTG AGT TCC GTA ACA A 3’ and 5’ AAA CTT GTT ACG GAA CTC AGG A 3’ were annealed and cloned into the pDR274 vector to generate single guide RNAs gRNAs targeting atrx exon 4. Each embryo was injected with 1 nl of solution containing 25 ng/μl gRNA and 600 ng/μl Cas9 mRNA at the 1 cell stage. Mosaic F0 fish with germline mutation were identified and stable mutant lines were established by outcrossing. RNA was isolated from one half of p53/nf1/atrx deficient MPNSTs and p53/nf1 deficient control MPNSTs using the AllPrep DNA/RNA Mini Kit from Qiagen Hilden Germany and the other half was set asside for analysis by histopathology. Library preparation quality control and next generation sequencing were conducted by the Molecular Biology Core Facility of the Dana Farber Cancer Institute following standard protocols. Zebrafish were raised and maintained according to standard procedures. They were derived from the p53/nf1 deficient background Shin et al. Disease Models & Mechanisms 2012. All zebrafish studies and maintenance were done in accord with Dana Farber Cancer Institute IACUC approved protocol #02 107. tp53: / |nf1b: / |nf1a:+/ |atrx:wt|suz12a:+/ |suz12b:+/ GSM4720869 GSM4720869: MPNST suz12 mut Z3; Danio rerio; RNA Seq GSM4720869   1 RNA was isolated from one half of p53/nf1/atrx deficient MPNSTs and p53/nf1 deficient control MPNSTs using the AllPrep DNA/RNA Mini Kit from Qiagen Hilden Germany and the other half was set asside for analysis by histopathology. Library preparation quality control and next generation sequencing were conducted by the Molecular Biology Core Facility of the Dana Farber Cancer Institute following standard protocols. GEO Accession:GSM4720869 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA NextSeq 500   SRP180876     20170730_Z3_MWZ4474_S6_R1_001.fastq.gz 20170730_Z3_MWZ4474_S6_R2_001.fastq.gz fastq fastq 7640907450.0 50939383.0 GSM4720869 r1 0:75 1:75 A:2079034539;C:1748735317;G:1754586436;T:2057075691;N:1475467 75 75     2079034539 1748735317 1754586436 2057075691 1475467 SRX8925577 SRS7181811 SRA834478 GEO Pediatric Oncology, Dana-Farber Cancer Institute 2 0.93466 0.93441 0.0777 0.07678 0.7766 0.79368 0.53878 0.53762 75 75 B B biological fallback assumption illumina nextseq unknown cdna_unspecified unknown bulk unknown unknown   United States 2020-08-11 Undetermined Embryo Cancer or Tumor Cancer or Tumor