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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 28, 2023 |
| Title |
d8_4028_RNA_S9 |
| Sample type |
SRA |
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| Source name |
In vitro differentiated Th9 (d8)
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| Organism |
Homo sapiens |
| Characteristics |
cell type: In vitro differentiated Th9 (d8)
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| Treatment protocol |
Human peripheral blood mononuclear cells (PBMC) were isolated by density centrifugation (Ficoll-Paque). Naïve human CD4+ T cells were magnetically enriched to >95% purity (StemCell) and plated at a density of 1 x10^6 on plate-bound aCD3 (1 μg/mL, OKT3), in the presence of cytokines and antibodies to promote the differentiation of Th9 (1 μg/mL aCD28, 2.5 μg/mL aIFN-γ, 5 ng/mL hTGFβ, 10 ng/mL hIL-2, 30 ng/mL hIL-4, 10 ng/mL hIL-1β) for 5 days. After 5 days, cells were washed and cultured without aCD3 or aCD28 but with all polarizing cytokines and antibodies for an additional 3 days (media, cytokines, and antibodies changed every 2 days, total 8 days of culture)
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| Growth protocol |
Complete RPMI-1640 with glutamine (10% FBS, 100 IU/mL penicillin, 0.1 mg/mL streptomycin)
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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 |
human_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 |
GPL24676 |
| 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 |
SAMN32739960 |
| SRA |
SRX19035341 |
| 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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