|
| Status |
Public on Jun 28, 2024 |
| Title |
4965_D7_ML_C |
| Sample type |
SRA |
| |
|
| Source name |
human natural killer cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: IL-12/15/18
time: D7
cell type: human natural killer cells
|
| Growth protocol |
NK cells were isolated from LRS chambers from normal human donors, rested overnight in 1 ng/mL IL-15 then 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 for 1 week. For the samples labeled cNK, eML, or effcNK without D7 included, these were sorted for ML subsets after 7 days of culture in 1ng/mL IL-15.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were washed with PBS twice and spun down at 500g for 5 minutes. Nuclei were prepared by lysis cells using lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL) and incubating on ice for 10 minutes. Followed with 500g spin for 10mins at 4C. Supernatant was removed for subsequent library preparation.
After obtaining nuclei, cells were incubated with transpoase from Illumina DNA Prep, (M) Tagmentation kit for 30mins at 37C. Immediately following transposition, purify DNA and remove excess enzyme using Qiagen MinElute PCR purification kit. To amplify tranposed DNA fragments the NEBNext® High-Fidelity 2X PCR Master Mix was used and IDT for Illumina DNA/RNA UD Indexes Set A, Tagmentation to barcode samples. To reduce GC and size bias in PCR, the appropriate number of PCR cycles is determined using qPCR between 5-8 cycles followed with a PCR cleanup using the Qiagen MinElute PCR purification kit.
Bulk ATAC-seq
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Illumina NovaSeq 6000
|
| Data processing |
Fastq files were trimmed of their adapters using CutAdapt. Trimmed sequences were then aligned using Bowtie2 with the hg38 genome. Samtools was then used to convert alignment file to bam and filtered. Picard was used ro remove PCR duplicate reads. Peaks were then called using Genrich.
Assembly: GRCh38
Supplementary files format and content: Peaks were then called using Genrich and to generate processed narrowpeak files
|
| |
|
| 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 |
GPL24676 |
| Series (1) |
| GSE264693 |
Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional mechanisms [ATAC-seq] |
|
| Relations |
| BioSample |
SAMN41062985 |
| SRA |
SRX24349088 |
