|
| Status |
Public on Jul 03, 2024 |
| Title |
10220_Pre-Infection_TCRgd |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMC
cell line: NA
cell type: gamma delta T cells
genotype: NA
treatment: none
|
| Treatment protocol |
Cells were not treated other than staining and sorting
|
| Growth protocol |
Cryopreserved PBMC were thawed, stained, and sorted directly without any culture
|
| Extracted molecule |
total RNA |
| Extraction protocol |
200 cells were directly sorted into 1x lysis buffer supplemented with 6U RNase inhibitor (both Takara Bio). Post sort, sample tubes were vortexed, incubated at RT for 2 minutes, and snap frozen on dry ice prior to storage at -80˚ C.
Upon thawing, cDNA synthesis was performed using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio) as per the manufacturer’s instructions. A total of 150-300pg amplified cDNA was used as input for library preparation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
Broad neutralizer
|
| Data processing |
Quality control was performed on raw FASTQ files using FastQC to assess the quality of the sequencing data.
Adapters and low-quality bases were trimmed using Trimmomatic.
Cleaned reads were aligned to the reference genome using STAR aligner(ver. 2.6.1d) with default parameters.
Aligned reads were quantified to gene-level expression using RSEM(ver. 1.3.1).
Raw read counts and TPM (Transcripts Per Million) were generated for each sample.
Differential expression analysis was carried out using edgeR.
Assembly: hg38
Supplementary files format and content: The processed data files are in tab-delimited text format and include gene expression matrices (TPM and raw counts) and differential expression results (gene IDs, log2 fold changes, p-values, and FDR).
|
| |
|
| Submission date |
Jul 03, 2024 |
| Last update date |
Jul 04, 2024 |
| Contact name |
Dohoon Kim |
| E-mail(s) |
dkim@hivresearch.org
|
| Organization name |
Henry M Jackson Foundation
|
| Street address |
503 BLDG, Walter Reed Army institute of research
|
| City |
silver spring |
| ZIP/Postal code |
20910 |
| Country |
USA |
| |
|
| Platform ID |
GPL15520 |
| Series (1) |
| GSE271442 |
CD16 and CD57 Expressing Gamma Delta T Cells in Acute HIV-1 Infection are Associated with the Development of Neutralization Breadth |
|
| Relations |
| BioSample |
SAMN42305996 |
| SRA |
SRX25204473 |
