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Sample GSM4073921 Query DataSets for GSM4073921
Status Public on Sep 11, 2022
Title BRL-3A NC-1
Sample type SRA
 
Source name BRL-3A cell line
Organism Rattus norvegicus
Characteristics strain: Sprague-Dawley
tissue: Liver
age: 48h
cell line: BRL-3A
disease state: hypertriglyceridemia
Treatment protocol All of siRNAs were transfected into cells applying lipofectamine 2000 (Life Technologies, Carlsbad, CA) according to manufacture's protocol for 48h then haverst cells. The cultured BRL-3A cells were collected and added to trizol for lysis after storage at -80.
Growth protocol The BRL-3A rat liver cell line (ATCC) were cultured in glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% Fetal bovine serum (FBS) (Life Technologies, Carlsbad, CA) at 37°C with humidified air and 5% CO2
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIZOL Reagent (Cat#15596-018,Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing The main steps of applying Seqtk for filtering are as follows:1、Remove the sequence of joints contained in reads;2、Remove bases with 3 'end mass Q less than 20, that is, the base error rate is less than 0.01,among,Q=-10logerror_ratio;3、Remove reads with length less than 25;4、Remove ribosome RNA reads of the species。
Spliced mapping algorithm of Hisat2 (version:2.0.4) was applied to Genome mapping of preprocessed reads,Take default parameters. The alignment result generated by Mapping is BAM file
Application Stringtie (version: 1.3.0)in Hisat2 than after each gene Fragments could count to count, and then use TMM (trimmed mean of M values) normalization method, finally calculated using perl script FPKM value of each gene.
In order to make gene expression levels between different genes and samples comparable, reads were transformed into FPKM (Fragments Per Kilobase of exon model Per Million mapped reads) to standardize gene expression
EdgeR was used for gene analysis of differences between samples, and multiple hypothesis test and correction were carried out after p-value was obtained. The threshold value of p-value was determined by controlling FDR (False Discovery Rate), and the p-value after correction was q-value.Meanwhile, we calculate Fold-change according to FPKM.
Genome_build: Rnor_6.0
 
Submission date Sep 11, 2019
Last update date Sep 11, 2022
Contact name dongsheng xiao
E-mail(s) dongsheng_xiao@shbio.com
Phone 13871224320
Organization name Shanghai Biotechnology Corporation
Street address No.151 Libing Road, Zhangjiang Hi-Tech Park Pudong, Shanghai 201203, P.R. China
City Shanghai
ZIP/Postal code 201203
Country China
 
Platform ID GPL24688
Series (1)
GSE137252 The novel long noncoding RNA Lnc19959.2 modulating triglyceride metabolism associated genes through interaction with Purb and hnRNPA2B1 (RNA-seq data set)
Relations
BioSample SAMN12726873
SRA SRX6829566

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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