|
| Status |
Public on Dec 05, 2023 |
| Title |
NK Pt03 Ex Vivo [RNA_S03] |
| Sample type |
SRA |
| |
|
| Source name |
PBMC
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: PBMC
cell type: CD56dim CD16+ NK cells
treatment: Ex vivo
participant id: Pt03
paticipant phenotype: HIVN
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the NK cell populations using a commercial PicoPure RNA Isolation Kit
RNA-Seq libraries were generated as described in a previous study. Briefly, whole transcriptome amplification (WTA) and tagmentation-based library preparation was performed using SMART-seq2, followed by sequencing with a 75-cycle kit on a NextSeq 500 instrument (Illumina, CA). The quantification of transcript abundance was conducted using RSEM software (v1.2.22) supported by the STAR aligner software (STAR_2.4.2a). The raw reads were aligned to the Hg38 human genome database.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
raw_counts.csv.gz
TPM.csv.gz
|
| Data processing |
FASTQ files were obtained by Illumina bcl2fastq2.
STAR and RSEM were used to align to GRCh38 and to calculate the raw counts for genes, respectively.
Assembly: GRCh38
Supplementary files format and content: raw counts and TPM in csv
|
| |
|
| Submission date |
May 19, 2023 |
| Last update date |
Dec 05, 2023 |
| Contact name |
Ce Gao |
| E-mail(s) |
CGAO4@MGH.HARVARD.EDU
|
| Organization name |
Ragon Institute of MGH, MIT and Harvard
|
| Lab |
Yu/Lichterfeld Labs
|
| Street address |
400 Technology Square
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE232914 |
IL-15-DEPENDENT IMMUNE CROSS-TALK BETWEEN NK CELLS AND DENDRITIC CELLS IN HIV-1 ELITE CONTROLLERS [RNA-seq] |
| GSE232916 |
IL-15-DEPENDENT IMMUNE CROSS-TALK BETWEEN NK CELLS AND DENDRITIC CELLS IN HIV-1 ELITE CONTROLLERS |
|
| Relations |
| BioSample |
SAMN35215968 |
| SRA |
SRX20439571 |
