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Sample GSM7971757 Query DataSets for GSM7971757
Status Public on Dec 19, 2023
Title subject MS5 PBMC, ex vivo
Sample type SRA
 
Source name multiple sclerosis
Organism Homo sapiens
Characteristics tissue: multiple sclerosis
cell line: PBMC
treatment: none
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 SAMN38792345
SRA SRX22870213

Supplementary file Size Download File type/resource
GSM7971757_BF93-P_AT_alignments_clones.xlsx 28.3 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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