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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