GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3538853 Query DataSets for GSM3538853
Status Public on Jul 01, 2019
Title B2
Sample type SRA
Source name CD4 T cells (PM2.5 treated)
Organism Mus musculus
Characteristics strain background: C57BL/6
mouse age: 6 weeks
mouse sex: female
tissue: spleen
cell type source: CD4 naïve T cells
stimulation: CD3/CD28 antibodies and TH17 polarization for 4 days
treatment: 100ug/ml of PM2.5 suspensions
Treatment protocol For PM2.5 group, 100ug/ml of PM2.5 suspensions were added to culture medium 6 hours after stimulation. Otherwise, PBS was used as mock in control group.
Growth protocol CD4 naïve T cells were isolated from spleen C57BL/6 mice (6 weeks old female mice were used unless specified) of by CD4+ T Cell Isolation Kit (130-104-453, Miltenyi). About 4×10^5 cells were seeded into the plates which were pre-coated with Anti-CD28 (BD,553295) and Anti-CD3e(BD,553058) in Invitrogen RPMI 1640 (#12633) with 10% FBS and 55 μM 2-mercaptoethanol. The differentiation conditions are as followed: Th17 Differentiation: 5ug/ml Anti-IFNγ(BD,557530), 5 ug/ml Anti-IL4 (BD,554432), 20ng/ml IL-6 (R&D, 7666-MB-005), 10ng/ml IL-23 (R&D,1686-MR-050), 2ng/ml TGFβ (R&D,406-ML-025) and 5ng/ml IL-2(R&D,402-ML-020).
Extracted molecule total RNA
Extraction protocol Cells were cultrued for 4 days, and washed by PBS for 2 times. The total RNA was extracted using the TRIzol reagent (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina Xten at Shanghai Biotechnology Corporation)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
Description mRNA-seq
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 mm10 whole genome using tophat 2.0.6.
Fragments Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using cufflink 2.0.2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts and FPKM values for each Sample .
Submission date Jan 04, 2019
Last update date Jul 01, 2019
Contact name Sun Licheng
Organization name Fudan University
Street address No. 399, wanyuan road
City Shanghai
ZIP/Postal code 201102
Country China
Platform ID GPL21273
Series (1)
GSE124660 mRNA expression profile of mouse CD4 T cells (treated vs. untreated with PM2.5 suspension)
BioSample SAMN10691319
SRA SRX5203101

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap