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Sample GSM2334713 Query DataSets for GSM2334713
Status Public on Oct 28, 2016
Title KO heptatocyte rep1
Sample type SRA
 
Source name hepatocyte
Organism Mus musculus
Characteristics strain: B6.129S6-Myctm2FwaXB6.Cg-Tg(Alb-cre)
tissue: Liver
cell type: hepatocyte
genotype: Myc-/-
Extracted molecule total RNA
Extraction protocol Total RNAs were extracted using Qiagen RNeasy columns (Valencia, CA). Each RNA sample was assessed for quality and quantity using a Qubit 2.0 fluorometer and Agilent Bioanalyzer TapeStation 2200. The Sample preparation was replicated using Illumina TruSeq Stranded mRNA kit (San Diego, CA). mRNA was used to generate poly-A+ libraries using oligo-dT beads following 2 rounds of poly-A selection.
mRNA was fragmented to an average length of 260 nt by magnesium-catalyzed hydrolysis at 940C and then converted into cDNA by random priming. cDNA 3’ ends were adenylated, followed by adaptor ligation and a 9-cycle PCR to enrich DNA fragments. cDNA libraries were then validated using KAPA Biosystems (Wilmington, MA) primer premix kit with Illumina-compatible DNA primers on the Qubit 2.0 fluorometer and Tapestation 2200 systems described above. Libraries were diluted in 0.1% Tween 20 to concentrations of 2 nM for stabilization. The cDNA libraries were then pooled to final concentrations of 2.5 pM.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description 10b-134-KO
Data processing Raw sequencing reads were quality checked for potential sequencing issues and contaminants using FastQC (Babraham Bioinformatics, Inc, Cambridge, UK.). Adapter sequences, primers, Ns, and reads with quality score below 28 were trimmed using fastq-mcf of ea-utils and PRINSEQ (http://prinseq.sourceforge. net/manual.html). Reads with a remaining length of less than 20 bp after trimming were discarded. Paired end reads were mapped to the mouse genome (m10) using TopHat (http://ccb.jhu.edu/software/tophat/index.shtml) in a strand specific manner. Read coverage on forward and reverse strands for genome browser visualization was computed using SAMtools, BEDtools, and UCSC Genome Browser utilities. Pairwise differential expression was quantified using Cuffdiff and DESeq [4, 5]. Cufflinks was used to determine FPKM levels for each gene from the TopHat alignment and was used as input for Cuffdiff. Significant differentially expressed genes were determined by adjusted P-value with a threshold of 0.05. DESeq was utilized
for raw read counts, which were calculated by HTSeq based on the TopHat alignment (http://www-huber.embl.de/users /anders/HTSeq/doc/count.html). Read counts were then normalized across all samples and significant differentially expressed genes were determined by adjusted P-value with a threshold of 0.05
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
 
Submission date Oct 03, 2016
Last update date May 15, 2019
Contact name Edward V Prochownik
E-mail(s) edward.prochownik@chp.edu
Phone 412-692-6795
Organization name Children’s Hospital of Pittsburgh of UPMC
Department Division of Hematology/Oncology
Street address 4401 Penn Ave.
City Pittsburgh
State/province PA
ZIP/Postal code 15224
Country USA
 
Platform ID GPL19057
Series (1)
GSE87578 Coordinated Activities of Multiple Myc-Dependent and Myc-Independent Biosynthetic Pathways in Hepatoblastoma
Relations
BioSample SAMN05859810
SRA SRX2208279

Supplementary file Size Download File type/resource
GSM2334713_KO_Hepa_replicate1_cufflinks_genes.fpkm_tracking.gz 693.8 Kb (ftp)(http) FPKM_TRACKING
GSM2334713_KO_Hepa_replicate1_cufflinks_isoforms.fpkm_tracking.gz 1017.9 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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