|
| Status |
Public on Apr 15, 2024 |
| Title |
lib77916 |
| Sample type |
SRA |
| |
|
| Source name |
treg
|
| Organism |
Homo sapiens |
| Characteristics |
study group: T1D
donor id: TG02-17-099
cell type: treg
sample id: S104344
timepoint: Infusion
|
| Growth protocol |
PBMCs were stained with an antibody cocktail (Supplemental Table 3B), 500 Tregs were sorted into SMARTseq buffer, and stored at -80C until sequencing. Sorting was performed on FACSAria II (BD Biosceinces) cell sorter machine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To avoid batch effects, all samples underwent lysis, RT, and PCR on the same day. The double-stranded cDNA quality was tested on the Agilent Tapestation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were processed using workflows managed on the Galaxy platform; reads were trimmed by 1 base at the 3' end, and then trimmed from both ends until base calls had a minimum quality score of at least 30 (Galaxy FASTQ Trimmer tool v1.0.0) (44).
FastqMcf (v1.1.2, https://benthamopen.com/ ABSTRACT/TOBIOIJ-7-1) was used to remove any remaining adapter sequence.
Reads were aligned using the STAR aligner (v2.4.2a) (45) with the GRCh38 reference genome and gene annotations from ensembl release 77.
Gene counts were generated using HTSeq-count (v0.4.1) (46).
Assembly: GRCh38
Supplementary files format and content: gene count matrix in .csv format
|
| |
|
| 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 |
GPL16791 |
| Series (2) |
| GSE243270 |
Response to Treg therapy is linked to rate of 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 |
SAMN37397973 |
| SRA |
SRX21779512 |
