|
| Status |
Public on Feb 04, 2021 |
| Title |
MYCN_gas7mut_2 |
| 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 |
| E-mail(s) |
li.hu@mayo.edu
|
| 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 |
|
| Relations |
| BioSample |
SAMN11658383 |
| SRA |
SRX5843741 |
