|
| Status |
Public on Apr 28, 2023 |
| Title |
set_1_d3_RNA_S2 |
| Sample type |
SRA |
| |
|
| Source name |
In vitro differentiated Th9 (d3)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: In vitro differentiated Th9 (d3)
|
| 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.
|
| Growth protocol |
Complete IMDM (10% FBS, 100 IU/mL penicillin, 0.1 mg/mL streptomycin, 55 μM 2-Mercaptoethanol
|
| 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.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
mouse_FPKM_all_samples_RSEM.txt
|
| 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
|
| |
|
| Submission date |
Jan 14, 2023 |
| Last update date |
Apr 28, 2023 |
| Contact name |
Daniella Schwartz |
| E-mail(s) |
Daniella.Schwartz@pitt.edu
|
| Organization name |
University of Pittsburgh
|
| Street address |
200 Lothrop St
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15216 |
| Country |
USA |
| |
|
| 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 |
|
| Relations |
| BioSample |
SAMN32739981 |
| SRA |
SRX19035320 |
