|
| Status |
Public on Mar 27, 2023 |
| Title |
TF_Stim_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Stimulated Tetramer- TF CD4+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: NOD
cell type: T cell
treatment: pMHCII-NPs + Ex vivo a-CD3/CD28 stimulation
|
| Treatment protocol |
Samples are obtained from mice that have received intravenously 10 doses of pMHCII-NPs. Stimulated cells have been cultured with aCD3/CD28 beads previous to RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA purification using Rneasy Mini kit (QIAGEN)
TruSeq Stranded mRNA Sample Prep Kit v2 according to the manufacturer's protocol (Illumina, San Diego, CA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
aCD3/CD28-stimulated Tetramer- T follicular (CXCR5+/PD-1+) CD4+ T cells from pMHCII-NP-treated NOD mice
Tet_TF_Basal_Stim_Raw_counts.xlsx
|
| Data processing |
Contaminant rRNA filtering with Bowtie2 (2.2.5)
Mouse samples: Alignment with STAR 2.5.3a to the GENCODE release 16 of the Mus musculus genome (mm10 assembly)
Human samples: Alignment with STAR 2.5.3a to the GENCODE release 29 of the Homo sapiens genome (hg38 assembly)
Raw count of reads per gene was obtained with Partek “Quantify to annotation model (Partek E/M)” tool
Counts were normalized by CPM
Differential expression analysis was performed using DESeq2
Genome_build: mm10
Genome_build: hg38
Supplementary_files_format_and_content: Excel sheets (xlsx) containing raw counts
|
| |
|
| Submission date |
Apr 30, 2021 |
| Last update date |
Mar 27, 2023 |
| Contact name |
Pere Santamaria |
| E-mail(s) |
pesantam@clinic.cat
|
| Organization name |
IDIBAPS
|
| Street address |
C/Rosselló 149-153
|
| City |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE173681 |
Transcriptional profiline of murine and human T cell populations |
|
| Relations |
| BioSample |
SAMN18942998 |
| SRA |
SRX10724531 |
