|
| Status |
Public on Mar 07, 2015 |
| Title |
siLuc_rep8 |
| 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: siLuciferase-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 |
SAMN03329782 |
| SRA |
SRX866624 |
