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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 15, 2022 |
| Title |
CD4+ T cells, KO-Th0_2 |
| Sample type |
SRA |
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| Source name |
CD4+ T cells
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: spleen
cell type: CD4+ Th0 cells
genotype: Stat4-/-
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| Treatment protocol |
CD4+ T cells were primed in different condition.
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| Growth protocol |
Spleens and lymph nodes were collected from mice of different genotypes, and single-cell suspensions were prepared by mechanical disruption in PBS. Naïve CD4+ T cells were isolated by magnetic sorting with a Miltenyi Biotec CD4+ CD62L+ T Cell Isolation kit, according to the manufacturer’s directions (Miltenyi Biotec, 130-106-643). CD4+ T cells were cultured in IMDM (Hyclone) supplemented with 10% FBS (Genmini), 100 units/ml penicillin, 100 μg/ml streptomycin (Shenggong), 4 mM L-glutamine, and 50μM β-mercaptoethanol, and activated with 5μg/ml precoated anti-CD3 (eBioscience) and 2μg/ml anti-CD28 (eBioscience). Th1 cells were differentiated by the addition of recombinant IL-12 (1 ng/ml, R&D Systems) and anti-IL-4 (10μg/ml, BD Pharmingen). Th17 cells were differentiated by the addition of recombinant IL-6 (20 ng/ml, R&D Systems), recombinant TGF-β (1 ng/ml, R&D Systems), anti-IFNγ (10μg/ml, BD Pharmingen) and anti-IL-4 (10μg/ml, BD Pharmingen), followed by recombinant IL-23 (30 ng/ml, R&D Systems) on day3. Treg cells were differentiated by the addition of TGF-β (5 ng/ml,R&D Systems) and recombinant IL-2 (40 ng/ml, PeproTech). CD4+ T cell cultures were split at ratio of 1:2 on day3 after activation.
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| Extracted molecule |
total RNA |
| Extraction protocol |
CD4+ T cells were collected, flash frozen on dry ice. RNA was harvested using Trizol reagent and cleanup with the RNeasy MiniElute kit. 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
KO_Th0_2
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| Data processing |
Bowtie2 was used to map clean reads to reference gene. Bowtie2 parameters forPE reads:-q--phred64--sensitive--dpad0--gbar99999999--mp1,1--np1--score-minL,0,-0.1-I1-X1000--no-mixed--no-discordant -p 16-k 200 Bowtie2 parameters forSE reads:-q--phred64--sensitive--dpad0--gbar99999999--mp1,1--np1--score-minL,0,-0.1-p16-k 200
HISAT was used to map clean reads to reference genome.HISAT parameters forPE reads:-p8--phred64--sensitive--no-discordant--no-mixed-I1-X1000 HISTAparameters forSE reads:-p8--phred64--sensitive-I1-X 1000
FPKM method is used in calculated expression level.
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs
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| Submission date |
Mar 02, 2020 |
| Last update date |
Dec 15, 2022 |
| Contact name |
Yanan S Zhang |
| E-mail(s) |
yananzhang1031@hotmail.com
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| Phone |
86-18817575525
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| Organization name |
Soochow University
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| Department |
Institutes of Biology and Medical Sciences
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| Lab |
Institutes of Biology and Medical Sciences
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| Street address |
199 Renai Road
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| City |
Suzhou |
| State/province |
Jiangsu |
| ZIP/Postal code |
215123 |
| Country |
China |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE146253 |
Targeting HDAC6-Mediated Deacetylation of STAT4 Is Critical for T helper Type 1 Cell Differentiation and Capability |
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| Relations |
| BioSample |
SAMN14259936 |
| SRA |
SRX7828416 |
| 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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