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Status |
Public on Apr 28, 2023 |
Title |
set_1_d8_RNA_S4 |
Sample type |
SRA |
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Source name |
In vitro differentiated Th9 (d8)
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Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 cell type: In vitro differentiated Th9 (d8)
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Treatment protocol |
Murine naïve CD4+CD62L+ cells were isolated from spleen and lymph nodes using negative selection (Miltenyi) followed by flow cytometric sorting to >95% purity. Cells were cultured at a density of 0.5 x10^6 per mL and activated with plate bound aCD3Ɛ (10 µg/mL) and aCD28 (10 µg/mL) for 3 days with polarizing cytokine and antibodies to promote the differentiation of Th9 (10 µg/mLaIFN-g, 20 ng/mL mIL-4, 10ng/mL hIL-2, 5 ng/mL hTGF-β) for 3 days. After 3 days, cells were washed and cultured without aCD3 or aCD28 but with polarizing cytokines and antibodies, and with 10 ng/mL hIL-2, in fresh media. Media, cytokines, and antibodies were changed every 2 days. Cells were collected 5 days later (on d8) for analysis
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Growth protocol |
Complete IMDM (10% FBS, 100 IU/mL penicillin, 0.1 mg/mL streptomycin, 55 μM 2-Mercaptoethanol
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Extracted molecule |
total RNA |
Extraction protocol |
Cells were suspended in Trizol LS (Invitrogen), and total RNA extracted according to the manufacturer instruction. Libraries for mRNA-sequencing were prepared using the NEBNext Ultra II Directional RNAseq Library preparation kit, per the manufacturer’s instructions.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
mouse_FPKM_all_samples_RSEM.txt
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Data processing |
Basecalls were performed using bcl2fastq v2.20.0.422 Reads of 50 bases were processed using the rna-seek pipeline (https://ccbr.github.io/RNA-seek/): adapter sequences were trimmed with cutadapt 1.18 Reads were mapped to the mouse transcriptome and genome mm10 or human transcriptome and genome GRCh38 (hg38) using STAR. Gene expression values (FPKM: Fragments Per Kilobase exon Per Million mapped reads; TPM, Tags Per Million mapped reads; counts) were generated using RSEM. Differential gene expression was calculated using DESeq2. Assembly: mm10 (mouse), hg38 (human) Supplementary files format and content: FPKM_all_samples_RSEM
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Submission date |
Jan 14, 2023 |
Last update date |
Apr 28, 2023 |
Contact name |
Daniella Schwartz |
E-mail(s) |
Daniella.Schwartz@pitt.edu
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Organization name |
University of Pittsburgh
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Street address |
200 Lothrop St
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City |
Pittsburgh |
State/province |
PA |
ZIP/Postal code |
15216 |
Country |
USA |
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Platform ID |
GPL24247 |
Series (2) |
GSE222909 |
RNA-seq of in vitro differentiated naïve and Th9 cells |
GSE222910 |
ATAC-seq, ChIP-seq and RNA-seq of in vitro differentiated naïve, Th1, and Th9 cells |
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Relations |
BioSample |
SAMN32739979 |
SRA |
SRX19035322 |
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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