|
| Status |
Public on Nov 25, 2022 |
| Title |
HCC mRNA, sample tag and AbSeq library, J12 |
| Sample type |
SRA |
| |
|
| Source name |
PBMCs
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: PBMCs
disease: HCC
treatment: untreated patients
molecule: mRNA, sample tag, AbSeq tag
|
| Extracted molecule |
total RNA |
| Extraction protocol |
isolated Δ42PD-1+, PD-1+ T and Δ42PD-1-PD-1- T cells were labeled with sample tag and Ab tag before loaded into BD Phapsody for RNA exraction, RNA was extracted according to BD Rhapsody protocol
library was prepared according to BD Rhapsody protocol
single-cell RNA-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Average high-quality (> Q30) base calls of 84%
Sequenced reads were trimmed to 75 bp
Raw reads were process with BD Rhapsody SBG cloud pipeline
Matrix table with raw gene counts for every gene and every T cell subset
Supplementary_files_format_and_content:
J12_Sample_Tag_Metrics.csv (sample tag metrics)
J12_SampleTag06_hs_neg_DBEC_MolsPerCell.csv (Δ42PD-1-PD-1- T cell subsets)
J12_SampleTag04_hs_d42_DBEC_MolsPerCell.csv (Δ42PD-1+ T cell subsets)
J12_SampleTag05_hs_pd1_DBEC_MolsPerCell.csv (PD-1+ T cell subsets)
|
| |
|
| Submission date |
Jan 11, 2022 |
| Last update date |
Nov 25, 2022 |
| Contact name |
Zhiwu Tan |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Hong Kong
|
| Department |
Microbiology
|
| Lab |
AIDS Institute
|
| Street address |
21 Sassoon Road, Pokfulam
|
| City |
Hong Kong |
| ZIP/Postal code |
000000 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE155736 |
Isoformic PD-1 is tumorigenic in hepatocellular carcinoma through seemingly exhausted αβ T cells |
|
| Relations |
| BioSample |
SAMN24839081 |
| SRA |
SRX13722937 |
