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Sample GSM5750706 Query DataSets for GSM5750706
Status Public on Oct 06, 2023
Title siNC-3
Sample type SRA
 
Source name human macrophages
Organism Homo sapiens
Characteristics tissue: peripheral blood
cell type: THP1 monocyte cell line -derived macrophages
treatment: THP1-derived macrophages were transfected with control siRNA for 48 h.
Treatment protocol THP1-derived macrophages were transfected with METTL3 siRNA pools or control siRNA for 48 h. Then, macrophages were stimulated with IL-4 (20 ng/ml) for 24 h.
Growth protocol Human THP1 cell lines (purchased from the American Type Culture Collection (ATCC), USA) were maintained in RPMI-1640 medium, 10% heat-inactivated FBS. To generate macrophage-like cells, THP-1 cell were seeded along with 200 nM PMA for 48 h. Cells were incubated at 37 °C with 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using RNeasy Micro Kit (Cat#74004, Qiagen)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)
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide
 
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 mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Differentially expressed genes were identified using Cuffdiff. The p-value significance threshold in multiple tests was set by the false discovery rate (FDR). The fold-changes were also estimated according to the FPKM in each sample.
Genome_build: GRCh38.91
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .
 
Submission date Dec 23, 2021
Last update date Oct 06, 2023
Contact name Xiao Han
E-mail(s) sqhx12@126.com
Phone 02164932897
Organization name Children’s Hospital of Fudan University
Street address 399 Wanyuan Rd, Minhang, Shanghai, China
City Shanghai
State/province Select state...
ZIP/Postal code 201102
Country China
 
Platform ID GPL24676
Series (1)
GSE192533 Differenatiation of mRNA expression in METTL3-depleted macrophages
Relations
BioSample SAMN24365689
SRA SRX13496391

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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