|
| Status |
Public on Jan 25, 2024 |
| Title |
Untreated biol rep 3 [TCR-2] |
| Sample type |
SRA |
| |
|
| Source name |
brain tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain tumor
time: Day 21 post implantation
cell type: immune cells
genotype: WT
treatment: none
|
| Extracted molecule |
other |
| Extraction protocol |
RNA was extracted using Zymo mini/midi RNA extraction kit.
Celero™ EZ DNA-Seq, 24 reactions kit (Tecan Genomics) was utilized to generate sequencing libraries following the manufacturer’s instructions. RNA-sequencing was performed using Illumina NovaSeq 6000, SP 2 x 50.
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
CD45+ immune cell were selected from GBM tumor microenvironment following tissue dissociation and positive cell selection. SMARTer Mouse TCR a/b Profiling Kit (Takara Bio) was utilized to amplify TCR beta chains using PCR and sequencing libraries were generated following the manufacturers instructions. RNA-sequencing was performed using Illumina MiSeq x 300.
|
| Data processing |
*library strategy: RNA seq of TCR
TCR vb data alignment and analysis were performed using MixCR 4.0
Assembly: mm10
Supplementary files format and content: Processed text files contains count values for each sample
|
| |
|
| Submission date |
Dec 21, 2023 |
| Last update date |
Jan 25, 2024 |
| Contact name |
Duane Mitchell |
| E-mail(s) |
Duane.Mitchell@neurosurgery.ufl.edu
|
| Organization name |
University of Florida
|
| Street address |
1333 Center Drive, BSB B1-150
|
| City |
Gainesville |
| State/province |
Florida |
| ZIP/Postal code |
32610 |
| Country |
USA |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE251800 |
mRNA-based precision targeting of neoantigens and tumor-associated antigens in malignant brain tumors [KR158 RNA-TCR] |
|
| Relations |
| BioSample |
SAMN38931895 |
| SRA |
SRX22969578 |
