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Status |
Public on Apr 28, 2023 |
Title |
set_3_naive_RNA_S13 |
Sample type |
SRA |
|
|
Source name |
naive T cells
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 cell type: naive T cells
|
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.
|
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
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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
|
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 |
SAMN32739974 |
SRA |
SRX19035327 |