|
| Status |
Public on Jul 09, 2023 |
| Title |
tdLN_IL10 |
| Sample type |
SRA |
| |
|
| Source name |
Lymph node
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lymph node
cell line: CD8 T cells
cell type: CD8 T cells
genotype: WT
treatment: IL10-Fc
|
| Treatment protocol |
Tumor-bearing mice were treated the equivalent dose (30 mg/kg) of all components with 3 days interval for total 3 doses, followed by CD8 T cell isolation for TCR sequencing.
|
| Growth protocol |
Primary CD8 T cells were isolated by MACS CD8 T cell microbeads from tumor, spleen, and LN.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol protocol for tissue RNA extraction. Extracted RNA were quantificated by using Qubit fluorometer with Qubit RNA BR Assay Kit
Libraries were prepared using QIAseq Immune Repertoire RNA Library Kit (GeneGlobe configuration no. IMMM-001Z-12) following the directions of the manufacturer.
QIASeqTargeted enrichment & sequencing
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
All data processing steps are using QIAseq TCR Panel Immune Repertoire RNA Library Kit (version 2.01).
Trim reads: First trim from the reads the constant regions generated by the enrichment protocol, and move the UMI sequence to the read indentifier line.
Down-sample reads: Randomly discard the reads until the remaining reads contain about 8 reads per UMI.
Build consensus reas: Error corrected consensus reads are generated by grouping multiple reads that putatively came from the same input simple molecule, based on three factors: (1) the UMI tag sequence; (2) the endogenous sequence near the random fragmentation and UMI ligation site; and (3) the full read sequence.
Merge overlapping R1 and R2 reads: R1 being entirely VDJ sequence, and R2 being V-only.
Split reads by genes (TRAC, TRBC, TRDC, TRGC).
Align the reads to the V-region models and trim overhang regions.
Run IMSEQ to generate clonotype calls and quantities. (parameters: -ev 0.15 -ma -sfb)
Compute diversity metrics. (Total clonotype count, Clonotypes within the top 50% of UMIs, Shannon-Wiener diversity index, Inverse Simpson diversity index)
Assembly: mm10
Supplementary files format and content: QIAseqRNA-immune-repertoire-TCR.clonotypes file in .txt format for three sample groups.
|
| |
|
| Submission date |
Oct 19, 2022 |
| Last update date |
Jul 09, 2023 |
| Contact name |
JuPei Chen |
| E-mail(s) |
pei03231987@nycu.edu.tw
|
| Organization name |
National Yang Ming Chiao Tung University
|
| Street address |
No. 155, Sec. 2, Linong St. Beitou Dist.
|
| City |
Taipei |
| ZIP/Postal code |
112 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE216119 |
A CSF-1R-blocking antibody/IL-10 fusion protein increases anti-tumor immunity by effectuating tumor-resident CD8+ T cells |
|
| Relations |
| BioSample |
SAMN31367962 |
| SRA |
SRX17956888 |
