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Sample GSM6752800 Query DataSets for GSM6752800
Status Public on Jun 28, 2023
Title EOMA _Empty- pLC5-ciR_rep2
Sample type SRA
 
Source name EOMA
Organism Mus musculus
Characteristics cell line: EOMA
treatment: Empty- pLC5-ciR
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from EOMA cells using TRIzol reagent (Thermo Fisher Scientific, USA).
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
 
Description C2
Data processing Raw data were firstly processed through in-house perl scripts to remove reads containing adapter, reads containing ploy-N and low quality reads, and were then filtered by Q20, Q30 and GC contents.
The acquired clean data were mapped to the mouse reference genome (mm10) using HISAT2 (v2.0.4).
For each sample, read counts for each gene were obtained with HTSeq(v0.6.1) and were standardized as fragments per kilobase million (FPKM).
Differential expression analysis of two groups was performed using the DESeq R package (1.10.1). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.
Assembly: mm10
Supplementary files format and content: Matrix table with mRNA FPKM for each sample
 
Submission date Nov 22, 2022
Last update date Jun 28, 2023
Contact name shuaijie qian
E-mail(s) qsjbxh1997@outlook.com
Phone 13540675514
Organization name West China Hospital, Sichuan University
Lab Lab of Gastroenterology and Hepatology
Street address NO. 1, 4th Keyuan Road, Chengdu,
City chengdu
State/province sichuan
ZIP/Postal code 610041
Country China
 
Platform ID GPL24247
Series (2)
GSE218578 The angiogenic role of circRNA-007371 in liver fibrosis [RNA-Seq]
GSE218581 The angiogenic role of circRNA-007371 in liver fibrosis
Relations
BioSample SAMN31840443
SRA SRX18352756

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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