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Sample GSM3768989 Query DataSets for GSM3768989
Status Public on Feb 04, 2021
Title MYCN_gas7mut_1
Sample type SRA
Source name zebrafish tumor
Organism Danio rerio
Characteristics tissue: peripheral sympathetic nervous system
genotype: MYCN overexpression + gas7 knockout
Extracted molecule total RNA
Extraction protocol RNA was extracted from zebrafish tumors overexpressing MYCN alone or MYCN with knokcout of gas7. Total RNA was extracted using the Trizol reagent, as per manufacturer’s instructions. RNA integrity (RIN) was verified on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and 100-200 ng of RNA (RIN ≥ 7.0) in a 5 μl volume was used for library preparation and RNA sequencing (RNAseq).
Paired-end sequencing libraries were prepared using the TruSeq Stranded Total Sample Preparation kit (Illumina) by the Mayo Clinic sequencing core facilities (Rochester, MN) followed by quality control, cluster generation and sequencing on the Illumina HiSeq 2000 platform. The reads were de-multiplexed and converted to FASTQ format using CASAVA software from Illumina (by the Mayo Clinic core).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing Fastq files of pair-end RNA-Seq reads were aligned with Tophat 2.0.14 to the reference genome UCSC danRer10 using Bowtie2 2.2.6 with default parameters.
Gene level counts were obtained using featureCounts 1.4.6 from the subRead package with gene models from corresponding UCSC annotation packages.
Genome_build: danRer10
Supplementary_files_format_and_content: tab-delimited gene counts
Submission date May 16, 2019
Last update date Feb 04, 2021
Contact name Hu Li
Organization name Mayo Clinic
Department Molecular Pharmacology & Experimental Therapeutics
Lab Systems Biology and Pharmacology
Street address 200 First Street, Gonda Building G19-408
City Rochester
State/province MN
ZIP/Postal code 55904
Country USA
Platform ID GPL14875
Series (1)
GSE131307 GAS7 Deficiency Promotes Metastasis of MYCN-driven Neuroblastoma
BioSample SAMN11658384
SRA SRX5843740

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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