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Status |
Public on Jul 01, 2019 |
Title |
B3 |
Sample type |
SRA |
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Source name |
CD4 T cells (PM2.5 treated)
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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
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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.
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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).
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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)
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
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Description |
mRNA-seq
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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 .
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Submission date |
Jan 04, 2019 |
Last update date |
Jul 01, 2019 |
Contact name |
Sun Licheng |
E-mail(s) |
16111510037@fudan.edu.cn
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Organization name |
Fudan University
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Street address |
No. 399, wanyuan road
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City |
Shanghai |
ZIP/Postal code |
201102 |
Country |
China |
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Platform ID |
GPL21273 |
Series (1) |
GSE124660 |
mRNA expression profile of mouse CD4 T cells (treated vs. untreated with PM2.5 suspension) |
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Relations |
BioSample |
SAMN10691318 |
SRA |
SRX5203102 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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