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Sample GSM3770600 Query DataSets for GSM3770600
Status Public on Apr 21, 2023
Title EGFP_oe_R162
Sample type SRA
 
Source name Melanoma
Organism Danio rerio
Characteristics tissue: Melanoma
cdk13 status: Wild-type
Growth protocol p53-/-; mitfa:BRAFV600E;Na-/- one-cell embryos were injected with either 20ng/uL control or experimental MiniCoopR (MCR) DNA along with tol2 in vitro transcribed RNA for integration. In all experiments, 20 zebrafish were raised per tank to control for density effects. Zebrafish were scored for the emergence of raised melanoma lesions as published. Zebrafish were sacrificed on ice and the tumors were dissected.
Extracted molecule total RNA
Extraction protocol Library prepped with random priming (NEBNext Ultra RNA Library Prep Kit for Illumina, E7530), fragmentation time of 15min, 12 PCR cycles, and sequenced on an Illumina HiSeq 2000 (100bp paired end reads).
Melanomas were homogenized in RLT buffer, subjected to QIAshredder columns (Qiagen, 79656), and then RNA was isolated with a column based method with genomic DNA column removal (Qiagen, 74134). RNA was ribodepleted (Illumina Ribozero Gold, MRZG12324). Ribodepletion was confirmed with Agilent 4200 Tapestation.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Reads were aligned to a custom version of the danRer10 genome that also contained the human CDK13 gene sequence using bowtie with parameters --library-type fr-unstranded --no-novel-juncs and -G set revision 90 of the Ensembl GRCz10 genes
Expression of revision 90 GRCz10 genes was quantified using htseq-count with parameters -r name -I gene_name --stranded=no -m intersection-strict
Supplementary_files_format_and_content: Counts files contain gene names and htseq-determined read counts
 
Submission date May 16, 2019
Last update date Apr 21, 2023
Contact name Richard A Young
E-mail(s) young_computation@wi.mit.edu
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL14875
Series (2)
GSE131333 Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance (zfRNAseq)
GSE131334 Oncogenic CDK13 Mutations Impede Nuclear RNA Surveillance
Relations
BioSample SAMN11659659
SRA SRX5846417

Supplementary file Size Download File type/resource
GSM3770600_EGFP_oe_R162.htseq.txt.gz 120.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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