|
| Status |
Public on Jun 28, 2024 |
| Title |
invitroNK_Donor9792_control_GEX |
| Sample type |
SRA |
| |
|
| Source name |
human natural killer cells
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
donor: Donor9792
cell type: human natural killer cells
library type: GEX
|
| Growth protocol |
NK cells were isolated from LRS chambers from normal human donors, and cultured in vitro in 1 ng/mL IL-15 or activated with IL-12/15/18 overnight and then cultured in low-dose IL-15.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Single-cell suspensions of samples were processed according to manufacturer's instructions for 10x Genomics 5' droplet-based scRNA-seq, including staining of CITE-seq and hashtagging antibodies for pooling and demultiplexing for 30 minutes.
cDNA was prepared after 10x Genomics GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps. Purified cDNA was amplified before being cleaned up using SPRIselect beads. The supernatant was then collected for the Cell Surface Protein Library. Samples were then run on a Bioanalyzer to determine the cDNA concentration for the GEX library preparation. GEX (Gene Expression) and TotalSeqC Feature libraries were prepared as recommended by 10x Genomics for Feature Barcode technology for Cell Surface Protein(v1/v2 Chemistry) user guides with appropriate modifications to the PCR cycles based on the calculated cDNA concentration. The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer's protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the IlluminaNovaSeq6000instrument.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
9792_LD_HTO_GEXbarcodes.tsv.gz
9792_LD_HTO_GEXfeatures.tsv.gz
9792_LD_HTO_GEXmatrix.mtx.gz
|
| Data processing |
CellRanger 6.1.2 was used to align the fastq files to the genome, including determing antibody derived tag and hashtag counts. CellRanger was run separately for ADT and HTO reads.
Assembly: GRCh38; mm10 for human/mouse experiments
Supplementary files format and content: filtered_feature_bc_matrix from cellranger outs. CellRanger was run separately for ADT and HTO libraries
Supplementary files format and content: The feature reference csv files for hashtag demultiplexing and ADT assignments.
Library strategy: CITE-seq
|
| |
|
| Submission date |
Apr 23, 2024 |
| Last update date |
Jun 28, 2024 |
| Contact name |
Todd Fehniger |
| Organization name |
Washington University School of Medicine
|
| Department |
Medicine
|
| Street address |
660 South Euclid Avenue, Campus Box 8007
|
| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL25526 |
| Series (1) |
| GSE264696 |
Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional mechanisms [CITE-seq] |
|
| Relations |
| BioSample |
SAMN41063547 |
| SRA |
SRX24349647 |
