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Sample GSM4819708 Query DataSets for GSM4819708
Status Public on Jun 28, 2021
Title LH M1-rep3
Sample type SRA
 
Source name in vitro induced cells
Organism Homo sapiens
Characteristics cell type: THP-1 derived macrophage
treatment: Maintained in growth medium with extra lipid mixture (0.25%) and treated with LPS 100ng/ml+IFNγ 25ng/ml
Treatment protocol For M1 activation, add LPS(100ng/ml) and IFNγ(25ng/ml) to M0 cells.For M2 activation, add IL-4(20ng/ml)and IL-13(20ng/ml)to M0 cells.For extra lipid, add lipid mixture (Sigma Aldrich,0.25%) to growth medium during LPS+IFNγ or IL-4+IL-13 treating.
Growth protocol THP-1 derived macrophage were routinely generated by incubating THP-1(at 2*10e6/well) with PMA (in growth medium) for 48h.Then remove PMA and repace with growth medium without PMA and rest for 24h, collect cells for M0.
Extracted molecule total RNA
Extraction protocol After treatment, cells were collected and flash frozen liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit 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 HiSeq X Ten
 
Description gene_fpkm.txt
Data processing Illumina HiSeq sequencer and software used for sequencing and basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome of hg19 using HISTA2. Transcript assembly were performed using Cufflink. DEG analyses were performed using DESeq2.
Genome_build: UCSC_hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
 
Submission date Oct 06, 2020
Last update date Jun 28, 2021
Contact name Miao Xu
Organization name West China hospital of Sichuan university
Department Clinical Nutrition
Street address 37#,Guoxue alley, Wuhou district
City Chengdu
ZIP/Postal code 610041
Country China
 
Platform ID GPL20795
Series (1)
GSE159112 RNA Sequencing of human THP-1 derived macrophages transcriptomes
Relations
BioSample SAMN16380638
SRA SRX9250919

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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