|
| Status |
Public on Apr 16, 2024 |
| Title |
lib87645 |
| Sample type |
SRA |
| |
|
| Source name |
Islet TMR+ CD8 T cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Islet TMR+ CD8 T cells
treatment: 20mer GAD/ IGRP/ ZnT8+PPI library peptides
donorid: CerosalettiLab982935
project number: P474-30
study group: >1 Aab+ any age
|
| Treatment protocol |
After 14h cutlture CD154+ activated T cells were enriched by magnetic bead enrichment and single cell sorted to isolate CD4+CD154+CD69+ T cells. Cells were sorted directly into wells of a 96 w plate containing SMART-seq v1 Ultra Low Input RNA buffer and then processed for library preparation.
|
| Growth protocol |
Cryopreserved PBMC were thawed and rested at 37C for 3h in RPMI with 10% commercial human serum. After resting PBMC were cultures with overlapping peptide libraries (20 aa in length, 12 aa overlap) from the islet proteins GAD65, IGRP, ZnT8, and preproinsulin in the presence of anti-CD40 antibody for 14h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sorted cells were lysed, followed by reverse transcription (SMART-Seq v1 Ultra Low Input RNA Kit; Takara, Mountain View, CA).
Sequencing libraries were prepared using Nextera XT DNA kits (Illumina, San Diego, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. The FASTQs were aligned to the human GRCh38 release 91 reference genome, using STAR v.2.4.2a and gene counts were generated using htseq-count (v0.4.1). Quality control and metrics analysis was performed using the Picard family of tools (v1.134).
Assembly: GRCh38 release 91
Supplementary files format and content: counts.csv: Gene count matrix in text file
|
| |
|
| Submission date |
Feb 23, 2024 |
| Last update date |
Apr 16, 2024 |
| Contact name |
Stephanie Osmond |
| E-mail(s) |
sosmond@benaroyaresearch.org
|
| Organization name |
Benaroya Research Institute
|
| Street address |
1201 9th Ave
|
| City |
Seattle, |
| State/province |
WA |
| ZIP/Postal code |
98101 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE256479 |
Germline-like TCR alpha chains shared between autoreactive T cells in blood and pancreas [dataset2] |
| GSE256481 |
Germline-like TCR alpha chains shared between autoreactive T cells in blood and pancreas |
|
| Relations |
| BioSample |
SAMN40079480 |
| SRA |
SRX23721559 |
