|
| Status |
Public on May 28, 2024 |
| Title |
(CD4+ CD25- CD200+) 2 |
| Sample type |
SRA |
| |
|
| Source name |
Tumor/spleen
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Tumor/spleen
cell line: T3 Sarcoma
cell type: Tumor antigen specific CD4 T cells
genotype: WT mice
treatment: vaccines containing high doses (15 ug) of mItgb1 SLP
condition: non Cluster-3/5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed, and mRNA was extracted using Nucleospin RNA Plus (Cat#; 740990.50, TaKaRa)
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Data was processed by GTAC@MGI
The downstream analysis was performed using the R programming language.
Assembly: GRCm38.101
Supplementary files format and content: tab-separated values file includes raw counts for each sample
|
| |
|
| Submission date |
May 24, 2024 |
| Last update date |
May 28, 2024 |
| Contact name |
Vladimir Sukhov |
| E-mail(s) |
sukhov@wustl.edu
|
| Organization name |
Washington University in St. Louis
|
| Department |
Immunology
|
| Street address |
660. S Euclid Ave.
|
| City |
St. Louis |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE268300 |
Gene expresion profile of different clusters of antigen specific CD4+ T cells induced by vaccines containing high doses of MHC-II restricted neoantigens |
| GSE268302 |
RNA sequencing of antigen specific CD4+ T cells induced by high vs low doses of MHC-II restricted neoantigens |
|
| Relations |
| BioSample |
SAMN41524099 |
| SRA |
SRX24683552 |
