run_metadata: 41617
This data as json
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| 41617 | SRR5099112 | SRX2415890 | SRS1853478 | SRP094947 | PRJNA357051 | Development of zebrafish medulloblastoma model by TALENs induced somatic gene inactivation methods | GSE92260 | Transcriptome Analysis | we developed the zebrafish cancer models by TALENs mediated somatic inactivation of tumor suppressor genes rb1 induced brain tumors in tp53 mutation background. Using RNA sequencing analysis in addition to histopathology and immunohistochemistry we demonstrated that the brain tumors induced by rb1 gene somatic inactivation have a molecular feature of MB like PNETs Overall design: QuantSeq three prime mRNA sequencing with whole brain tissue wild type WT zebrafish and tumors induced by rb1 TALENs injected zebrafish at xxx mpf | pubmed:28903419 | FFPE 1 | GSM2424729 | source name:tumor 1 induced by rb1 TALENs|strain:p53M214K|tissue:tumor tissues 1 induced by rb1 TALENs|developmental stage:5 mpf | FFPE 1 | Illumina Casava1.8 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequenceusing fastx trimmer then mapped to danRer10 whole genome using Bowtie2 Read count extraction and nomalization were performed using edgeR. Genome build: danRer10 Supplementary files format and content: FFPE 1.txt and FFPE 2.txt report quantile normalized abundance measurements. Supplementary files format and content: WT.txt report quantile normalized abundance measurements. Column WT1 reports quantile normalized abundance measurements post quantile normalization had done between WT and FFPE 1. Column WT2 reports quantile normalized abundance measurements post quantile normalization had done between WT and FFPE 2. | tumor 1 induced by rb1 TALENs | RNA was harvested using Trizol reagent Invitrogen. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using LEXOGEN Quant Seq Library Prep Kit Cat#001.24 standard protocols. | strain:p53M214K|tissue:tumor tissues 1 induced by rb1 TALENs|developmental stage:5 mpf | GSM2424729 | GSM2424729: FFPE 1; Danio rerio; RNA Seq | GSM2424729 | 1 | RNA was harvested using Trizol reagent Invitrogen. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using LEXOGEN Quant Seq Library Prep Kit Cat#001.24 standard protocols. | GEO Accession:GSM2424729 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP094947 | FFPE-1_fastq.gz | fastq | 985654556.0 | 9758956.0 | GSM2424729 r1 | 0:101 | A:642158389;C:109642019;G:103170689;T:130633868;N:49591 | 101 | 642158389 | 109642019 | 103170689 | 130633868 | 49591 | SRX2415890 | SRS1853478 | SRA502460 | GEO | Research Institute, National Cancer Center | 1 | 0.71847 | 0.59813 | 0.9376 | 0.57167 | 101 | B | usable mapping rate | illumina | nextseq | 3prime | cdna_unspecified | lexogen | bulk | unknown | unknown | Unknown | 2016-12-12 | Adult | Adult | Cancer or Tumor | Cancer or Tumor |