|
| Status |
Public on Apr 15, 2024 |
| Title |
2_102-017_3 |
| Sample type |
SRA |
| |
|
| Source name |
blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
cell type: PBMC
treatment: Treg
library type: GEX, ADT
trex id: 46
day: Day 0
|
| Treatment protocol |
Then they samples were incubated with Total-Seq C (1:6 dilution) for 30min at 4C.
|
| Growth protocol |
PBMCs from three high-dose group subjects were stained with the commercially available TotalSeq-C human universal cocktail V1.0 reagent (Bioloegend Cat. #39905). For each experiment we processed thawed PBMCs from one patient including three different time points (baseline, early timepoint (1 or 2 weeks and an late timepoints (4 or 13 weeks)). PBMCs (1x106/well) were distributed in a 96-well plate and incubated with human TruStain FcX block (BioLegend Cat. #422301) for 10min at 4C
|
| Extracted molecule |
other |
| Extraction protocol |
After two washes approximately 100,000 PBMCs per sample were processed according to the 10X Genomics protocol. A single cell suspension was prepared and loaded onto the 10x Chromium Controller (10X Genomics) according to the manufacturer’s protocol, with a target capture of 5,000 cells per channel.
Sequencing libraries were generated using the NextGEM Single Cell 5' v1.1 kit (10x Genomics).
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
Base-calling was performed automatically with Illumina RTA (v. 1.18.66.3).
For each flowcell, libraries were demultiplexed using Cellranger mkfastq (v 6.1.1; All unambiguously demultiplexed reads for each sample were combined for downstream processing.
Reads were aligned to the genome, collapsed to UMIs, and counts per gene ID were estimated using 10X Cell Ranger count (v. 6.1.1).
Barcodes were called as cells or background using default settings in 10X Cell Ranger (v. 6.1.1).
Assembly: GRCh38
Supplementary files format and content: Sparse matrix HDF5 file with UMI counts per barcode per gene ID, and table of read characteristics for each UMI / barcode combination
Library strategy: CITE-seq
|
| |
|
| Submission date |
Sep 14, 2023 |
| Last update date |
Apr 15, 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) |
| GSE243201 |
Maintenance of beta cell function in adolescent T1D subjects treated with a single dose of polyclonal expanded Treg is linked to lower ex vivo Treg expansion |
| GSE243278 |
A phase II randomized trial with autologous polyclonal expanded regulatory T cells in children with new-onset type 1 diabetes |
|
| Relations |
| BioSample |
SAMN37395390 |
| SRA |
SRX21776561 |
