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Sample GSM3592214 Query DataSets for GSM3592214
Status Public on Feb 06, 2019
Title Gfp_1
Sample type SRA
 
Source name liver
Organism Mus musculus
Characteristics cell type: primary hepatocytes
strain: db/db
tissue: liver
age: 10 weeks
genotype/variation: infection with adeno-associated virus 8 (AAV8) encoding eGFP
Treatment protocol Hepatocytes were transfected with adenovirus at approximately 10^6 viral particles per million cells for 24hr prior to RNA collection.
Growth protocol Primary murine hepatocytes were equilibrated in regular growth media (See DeBosch et al 2014 J Biol Chem) overnight following collagenase digestion.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol Reagent precisely per manufacturer protocol.
Library preparation was performed with 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in buffer containing 40mM Tris Acetate pH 8.2, 100mM Potassium Acetate and 30mM Magnesium Acetate and heating to 94 degrees for 150 seconds. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-3000 using single reads extending 50 bases.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing RNA-seq reads were aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5. Transcript counts were produced by Sailfish version 0.6.3.
Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation and read distribution over known gene models with RSeQC version 2.3.
To enhance the biological interpretation of the large set of transcripts, grouping of genes/transcripts based on functional similarity was achieved using the R/Bioconductor packages GAGE and Pathview.
GAGE and Path-view were also used to generate pathway maps on known signaling and metabolism pathways curated by KEGG.
Genome_build: NCBI GRCm38.p2 
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
 
Submission date Feb 05, 2019
Last update date Feb 12, 2019
Contact name Brian Jesse DeBosch
E-mail(s) deboschb@wustl.edu
Organization name Washington University School of Medicine
Department Pediatrics and Cell Biology & Physiology
Lab DeBosch
Street address 660 S. Euclid Ave, Box 8208
City St. Louis
State/province MO
ZIP/Postal code 63110
Country USA
 
Platform ID GPL21493
Series (1)
GSE126134 Effect of Arg2 overexpression on murine liver gene expression profiles
Relations
BioSample SAMN10879240
SRA SRX5337891

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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