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Sample GSM4056807 Query DataSets for GSM4056807
Status Public on Sep 23, 2019
Title PurβKD
Sample type SRA
Source name primary hepatocytes
Organism Mus musculus
Characteristics tissue: primary hepatocytes
genotype: pur-beta knockdown
strain: C57BL/6
Treatment protocol For Purβ-overexpressing experiments, the cells were infected with βgal and Purβ adenoviruses overnight. For Purβ-knocking down experiments, the cells were infected with Scramble and shPurβ1 or shPurβ2 adenoviruses for 30 h.
Growth protocol Primary hepatocytes were isolated from C57BL/6 mice by liver-perfusion with type II collagenase (Worthington Biochem, Lakewood, NJ) and cultured at 37°C and 5% CO2 in DMEM medium supplemented with 5% FBS.
Extracted molecule total RNA
Extraction protocol Total RNAs were extracted using TriPure Isolation Reagent (Roche, Mannheim, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensemble_GRCm38.96 whole genome using tophat2 with parameters -p 8 -N 2 --read-edit-dist 2
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then F PKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. F PKM, expected number of Fragment s Per Kilobase of transcript sequence per Millions base pairs sequenced , considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels ( Tr apnell, Cole, et al., 2010 )
Genome_build: Ensemble_GRCm38.96
Submission date Sep 02, 2019
Last update date Sep 23, 2019
Contact name Zheng Chen
Phone +8645186402029
Organization name Harbin Institute of Technology
Street address 92 Xidazhijie Harbin Institute of Technology
City Harbin
State/province Heilongjiang
ZIP/Postal code 150001
Country China
Platform ID GPL24247
Series (1)
GSE136728 RNA-seq Analysis of mRNA profiles in Purβ-overexpressing and Purβ-knocking down hepatocytes
BioSample SAMN12672758
SRA SRX6790164

Supplementary file Size Download File type/resource
GSM4056807_PurbetaKD_fpkm.xlsx 5.7 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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