|
| Status |
Public on Sep 14, 2021 |
| Title |
Patient2U_TCR |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood mononuclear cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: T cells
diagnosis: PD
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CSF cells were Live cell sorted using an LSRFortessa (BD biosciences). RNA was extracted according to the 10x v2 5' Expression library kit
Libraries were prepared according to the 10x v2 5'V(D)J Kit
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
| |
|
| Data processing |
Library strategy: single cell TCR-seq
Real-Time Analysis (RTA) software called RTA2 used for basecalling
Base call fles were demultiplexed using cellranger mkfastq version 3.0.2
TCR-seq reads were mapped aligned to the GRCh38 2.0.0 vdj genome assembly available from 10X Genomics using cellranger count version 3.0.2
T cell receptor sequences were generated using cellranger vdj version 3.0.2
Genome_build: GRCh38 vdj 2.0.0
Supplementary_files_format_and_content: two files for each sample; one file that indicates clonotypes and one file that has th sequence for each cell barcode
|
| |
|
| Submission date |
Nov 10, 2020 |
| Last update date |
Sep 15, 2021 |
| Contact name |
Emma Tapp |
| E-mail(s) |
etapp@stanford.edu, dgate@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
Neurology
|
| Lab |
Wyss-Coray
|
| Street address |
290 Jane Stanford Way
|
| City |
Stanford |
| State/province |
California (CA) |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL21697 |
| Series (1) |
| GSE161192 |
CD4+ T cells contribute to neurodgeneration in Lewy Body dementia |
|
| Relations |
| BioSample |
SAMN16725372 |
| SRA |
SRX9470007 |
