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Sample GSM3676391 Query DataSets for GSM3676391
Status Public on Oct 25, 2019
Title Sy12_1B
Sample type SRA
 
Source name SKH-1 Mouse
Organism Mus musculus
Characteristics strain: SKH-1
infection status: Infected
tissue: Skin
Treatment protocol Mice were either infected with MmuPV1 or sham infected then completed a 25 week DMBA-UV skin cancer induction protocol. Three weeks following infection, mice were treated on their back skin with 50 ug of DMBA, rested for one week, then subjected to 3 doses of 100 mJ/cm^2 per week for 25 weeks.
Extracted molecule total RNA
Extraction protocol Tissue was extacted using the Qiagen RNeasy Mini Kit (50) Cat no. 74104
Novogene: "Briefly, mRNA from Eukaryote organisms is purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA is first fragmented randomly by addition of fragmentation buffer. Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization(1). In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads."
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description MmuPV1 infection, completed 25 wk DMBA-UV Protocol
Data processing Novogene: Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Novogene: "The Sequenced Reads/raw reads often contain low quality reads or reads with adaptors. In order to avoid this, it's necessary to filter the raw reads under conditions to get the clean reads. Raw reads filtering conditions are as follows: (1) Remove reads containing adaptors; (2) Remove reads containing N > 10% (N represents base that could not be determined); (3) The Qscore (Quality value) of over 50% bases of the read is <= 5."
Novogene: "Mapping the clean reads to the reference genome or the transcriptome is the basis for the next following analysis. Novogene use STAR to accomplish the mapping. In order to avoid losing a lot of effective junction reads, Novogene use STAR software to alignment for RNA-seq sequencing data analysis, the junction reads can be positioned precisely."
Novogene: "For the samples with biological replicates, differential expression analysis of two conditions/groups was performed using the DESeq2 R package (Anders et al., 2010). It provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. So, if the readcount of the i-th gene in j-th sample is Kij, there is: Kij ~ NB(μij,σij2). And the resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate."
Novogene: "Volcano diagram can visually show the whole distribution of differential expression genes. For the samples with biological replicates, the threshold of differential expression genes is: padj < 0.05. For the samples without biological replicates, the threshold of differential expression genes is: |log2(FoldChange)| > 1 and qvalue < 0.005."
Novogene: "Cluster Analysis of differential expression genes was used to estimate expression pattern of differential expression genes under different experimental conditions. Through clustering genes in similar expression pattern, unknown functions of transcripts were recognized, with the reason that same kind of transcripts have similar functions or participate in the same metabolic processes or cellular pathways. Hierarchical clustering analysis was carried out with the log10(FPKM+1) of union differential expression genes of all comparison groups under different experimental conditions."
Genome_build: mm10
Supplementary_files_format_and_content: readcount_genename.txt - contains read counts for all genes across all samples. Used for subsequent analysis performed by Novogene.
 
Submission date Mar 18, 2019
Last update date Oct 25, 2019
Contact name Jonathan Leigh Messerschmidt
E-mail(s) jmesserschmidt@mgh.harvard.edu
Organization name Massachusetts General Hospital
Department Center for Cancer Immunology, Cutaneous Biology Research Center, Center for Cancer Research
Lab Dr. Shawn Demehri
Street address 149 13th Street
City Boston
State/province MA
ZIP/Postal code 02129
Country USA
 
Platform ID GPL24247
Series (1)
GSE128476 Papillomavirus-Colonized Murine Skin Confers Cancer Resistance
Relations
BioSample SAMN11160504
SRA SRX5537227

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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