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Sample GSM7371880 Query DataSets for GSM7371880
Status Public on May 18, 2024
Title Liver tumor tissues, Hras12V transgenic mice, female, 15-month
Sample type SRA
 
Source name Liver Tumor (HCC)
Organism Mus musculus
Characteristics tissue: Liver Tumor (HCC)
genotype: Hras12V transgenic
Sex: Female
strain: C57BL/6
age: 15 months
treatment: none
Extracted molecule total RNA
Extraction protocol RNA was harvested using mir VanaTM miRNA Isolation kit (Cat# AM1561, Ambion). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS Stranded mRNA-seq Library Prep Kit following manufacturer's protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description T
Data processing fastx (version:0.0.13)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastx (version:0.0.13) (parameter- Quality limit: 0.01).
Trimmed sequence reads were mapped to GrCM38/mm10 using tophat (version:2.0.9) (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8).
Read count extraction and normalization were performed using cufflink (version:2.1.1).
Differential genes analysis was performed using cuffdiff.
Assembly: mm10
Supplementary files format and content: gene_expression.txt: Tab-delimited text file includes count and FPKM values for each Sample.
 
Submission date May 17, 2023
Last update date May 18, 2024
Contact name aiguo Wang
Organization name Dalian Medical University
Street address DaLian
City DaLian
ZIP/Postal code 116044
Country China
 
Platform ID GPL17021
Series (1)
GSE232694 Transcriptomic Landscape of Hras12V Oncogene-Induced Hepatocarcinogenesis with Gender Disparity
Relations
BioSample SAMN35130993
SRA SRX20414902

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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