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Sample GSM3537441 Query DataSets for GSM3537441
Status Public on Feb 03, 2019
Title Tumor tissue from HCD mice,number 1
Sample type SRA
Source name hepatocellular carcinoma
Organism Mus musculus
Characteristics cell type: Hep1-6
culture condition: Hep1-6 cells were cultured in DMEM supplemented with 10% FBS,and then subcutaneously injected into C57BL/6J mice fed with high cholesterol diet.
strain: C57BL/6J
diet: high cholesterol diet (HCD)
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Pairedend libraries were synthesized by using the TruSeq® RNA Sample Preparation Kit (Illumina, USA) following TruSeq® RNA Sample Preparation Guide.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
Description Tumor tissue from HCD mice were harvested and total RNA were extracted
Data processing Basecalls performed using CASAVA version 1.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Seqtk.
mRNA-seq reads were aligned to the mm10 genome assembly using TopHat(version:2.0.9)
Gene abundance measurements were generationed and normalized using HTSeq. The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM).
Differential expression were analysed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Submission date Jan 03, 2019
Last update date Feb 03, 2019
Contact name Fu jing
Organization name Eastern Hepatobiliary Surgery Hospital
Department Liver Centre of SMMU
Lab International Cooperation Laboratory on Signal Transduction
Street address No.225 Changhai road
City shanghai
ZIP/Postal code 200438
Country China
Platform ID GPL21273
Series (1)
GSE124599 RNA-seq data for tumor tissues from mice fed with normal diet (ND) or high cholesterol diet (HCD) [Hep1-6]
BioSample SAMN10688921
SRA SRX5197731

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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