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Sample GSM5924221 Query DataSets for GSM5924221
Status Public on Feb 20, 2024
Title B2_LV-Mφ_rep2
Sample type SRA
 
Source name RAW264.7 cell line
Organism Mus musculus
Characteristics cell type: mouse leukemia cell of monocyte macrophage
cell line: RAW264.7
treatment: LV-Mφ
Treatment protocol RAW264.7 cells were stimulated for 24 h with lipopolysaccharide (LPS, 50 ng/ml, Sigma) and IFN-γ (20 ng/ml), namely LPS/IFNγ-Mφ.
Growth protocol cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal calf serum (FCS).
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
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 software used for basecalling.
Sequenced reads with low-quality and adapters were trimmed by Trimmomatic-0.39 softeware, then mapped to mm10 whole genome using STAR-2.7.2b with defalt parameters
The unique reads were used to calculate the fragments per kilobase of exon per million fragments mapped (FPKM) with Cufflinks-2.2.1.
Find differential expression genes between stages, HOMER software command getDiffExpression.pl with DESeq2 was employed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
 
Submission date Mar 01, 2022
Last update date Feb 20, 2024
Contact name Ying Chen
E-mail(s) cy.juice@aliyun.com
Phone 13966667603
Organization name Anhui Medical University
Street address No. 81 Meishan Road, Hefei
City Anhui
State/province China
ZIP/Postal code 230032
Country China
 
Platform ID GPL24247
Series (1)
GSE197639 Protozoan-Derived Cytokine-Transgenic Macrophages Reverse Hepatic Fibrosis. 
Relations
BioSample SAMN26332232
SRA SRX14327085

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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