|
| Status |
Public on Dec 19, 2023 |
| Title |
subject MS5 PBMC, stimulated with candida |
| Sample type |
SRA |
| |
|
| Source name |
multiple sclerosis
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: multiple sclerosis
cell line: PBMC
treatment: candida
|
| Treatment protocol |
antigens used for stimulation were Epstein-Barr virus, autologuous EBV-infected cell lines, varicella zoster virus, influenza A, candida, or no antigen.
|
| Growth protocol |
CSF and PBMC directly ex vivo, antigen specific cells sorted after 6 days in culture
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cells were lysed in Trizol and stored at -80. RNA was extracted from Trizol aqueous phase with Takara Nucleospin RNA XS columns
Takara SMARTer Human TCR a/b Profiling Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
data processing done by MedGenome
Supplementary files format and content: excel files with TCR alpha and beta sequences and number of reads
Supplementary files format and content: excel file with TCR beta CDR3 regions aligned for all antigens and conditions for each subject
|
| |
|
| Submission date |
Dec 12, 2023 |
| Last update date |
Dec 19, 2023 |
| Contact name |
John William Lindsey |
| E-mail(s) |
john.w.lindsey@uth.tmc.edu
|
| Phone |
7135007135
|
| Organization name |
University of Texas Health Science Center At Houston
|
| Street address |
6431 Fannin St, Ste 7.044 MSB, Neurology Dept
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030-1501 |
| Country |
USA |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE250037 |
Expanded T lymphocytes in the cerebrospinal fluid of multiple sclerosis patients are specific for Epstein-Barr virus infected B cells |
|
| Relations |
| BioSample |
SAMN38792339 |
| SRA |
SRX22870219 |
