NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1602681 Query DataSets for GSM1602681
Status Public on Mar 07, 2015
Title siYap_rep3
Sample type SRA
 
Source name Mst1-/-; Mst2Flox/Flox mouse HCC model
Organism Mus musculus
Characteristics genotype: Mst1-/-; Mst2Flox/Flox
background strain: mixed (C57BL/6; 129Sv)
treatment: siYap-LNPs
treatment time: 9 days
Treatment protocol Animals were then randomized to be treated by intravenous injection of siRNA-lipid nanoparticles (siRNA-LNPs) (either siYap-LNPs or siLuciferase-LNPs) for a period of 9 days.
Growth protocol Mice with liver-specific Mst1/Mst2 double-knockout (Adeno-Cre injected Mst1-/-; Mst2Flox/Flox mice) were monitored for the formation of HCC by ultrasound imaging. The Mst1-/-; Mst2Flox/Flox mice were maintained in a mixed genetic background (C57BL/6; 129Sv). (See Zhou et al., Cancer Cell 2009 "Mst1 and Mst2 maintain hepatocyte quiescence and suppress hepatocellular carcinoma development through inactivation of the Yap1 oncogene.")
Extracted molecule total RNA
Extraction protocol Tumor RNA was isolated. RNA quality was measured using an Agilent Bioanalyzer and RNA was quantified using a Qubit Fluorometer (Life Technologies) before sequencing library generation.
RNAseq libraries were prepared using the ScriptSeq Complete Gold Kit (Epicentre). RNAseq libraries were uniquely indexed with custom primers (SriptSeq) and run on MiSeq (Illumina) to confirm quality of the library before sequencing to deeper coverage using a HiSeq2500 (Illumina). Approximately 50 million reads per sample were obtained.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Reads trimmed with Trimmomatic version 0.30 in single end mode and trimming steps set to ILLUMINACLIP:illuminaAdapters.fa: 2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35
Reads aligned to human genome with tophat version 2.0.8 using UCSC mm10 gene annotation and default settings.
Aligned reads processed to Fragments Per Kilobase of exon per Million fragments mapped (FPKM) using cuffdiff version 2.1.1 (http://cufflinks.cbcb.umd.edu/index.html) with the flag '--max-bundle-frags' set to 4 million to avoid HIDATA error for 43 very high expression genes, the flag '--frag-bias-correct' set to use the UCSC mm10 reference whole genome fasta, and the mm10 genes.gtf transcript file from UCSC.
Split apart the cuffdiff output file genes.read_group_tracking file into sample specific files.
Genome_build: mm10
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
 
Submission date Feb 05, 2015
Last update date May 15, 2019
Contact name Kenneth N Ross
E-mail(s) Kenneth.Ross@dfci.harvard.edu
Organization name Dana-Farber Cancer Institute
Department Pediatric Oncology
Street address 450 Brookline Ave., Rm M640
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL17021
Series (1)
GSE65665 Gene expression profiling of effect of Yap inhibition in a genetically engineered mouse model of hepatocellular carcinoma
Relations
BioSample SAMN03329779
SRA SRX866627

Supplementary file Size Download File type/resource
GSM1602681_JF_7N_siYAP_99_D9.read_group_tracking.txt.gz 268.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap