|
| Status |
Public on Sep 01, 2021 |
| Title |
NK donor 6 NKG2A-KO |
| Sample type |
SRA |
| |
|
| Source name |
expanded NK cells
|
| Organism |
Homo sapiens |
| Characteristics |
nkg2astatus: KO
donorid: 6
|
| Treatment protocol |
NK cells were electroporated with Cas9 RNP with or without KLRC1-targeting gRNA. Culture was continued for 7 days until analysis.
|
| Growth protocol |
NK cells were cultured in RPMI-1640 supplemented with 10% fetal calf serum and 100 U/mL penicillin-streptomycin. NK cells were expanded with K562/mIL-21/4-1BBL feeder cells.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
1E6 NK cells were lysed in TRIzol, stored and shipped at -80C. RNA isoaltion and quality check were performed by BGI on an Agilent 2100 Bioanalyzer, with RIN>7.8 for all samples.
Oligo(dT) primers were used for cDNA library generation
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
| |
|
| Data processing |
Data was analyzed on the Galaxy Europe platform.
Sequenced reads were trimmed using Trimmomatic (HEADCROP, 12), followed by mapping to the hg38 genome using HISAT2 2.1.0 with standard paramters for paired-end reads on the Galaxy Europe platform.
Count tables were generated using FeatureCounts 2.0.1 (unstranded data, hg38 reference genome) with standard settings from the Galaxy Europe platform (featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923–930. https://doi.org/10.1093/bioinformatics/btt656)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files contain read counts for each sample
Supplementary_files_format_and_content: matrix table with gene counts for all samples of all genotypes
|
| |
|
| Submission date |
Jun 21, 2021 |
| Last update date |
Sep 01, 2021 |
| Contact name |
Roel G.J. Klein Wolterink |
| E-mail(s) |
[email protected]
|
| Organization name |
Maastricht University
|
| Department |
Internal Medicine
|
| Lab |
Tumor Immunology
|
| Street address |
Universiteitssingel 50
|
| City |
Maastricht |
| ZIP/Postal code |
6229 ER |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL29480 |
| Series (1) |
| GSE178566 |
RNAseq analysis of NKG2A-knockout versus wildtype expanded human NK cells |
|
| Relations |
| BioSample |
SAMN19796874 |
| SRA |
SRX11188443 |
