|
| Status |
Public on Oct 15, 2020 |
| Title |
RNA-Seq LIver40_CD49a_pos_unstim |
| Sample type |
SRA |
| |
|
| Source name |
NK cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Liver
cell type: Liver CD49a+ NK cells
treatment: Unstimulated
|
| Treatment protocol |
protocol below every subset section
|
| Growth protocol |
freshly isolated cells from human Liver tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Human liver tissue was passed through 70-μm mesh filters and rinsed with 10% FBS in PBS. Leukocytes were isolated using Ficoll gradients.
Illumina
SMART-seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Bulk RNA-seq
|
| Data processing |
Single-end reads were trimmed for low quality bases and removal of low-quality reads using ReadTools
Trimmed reads were mapped to the Homo sapiens genome (GRCh38.92 assembly) using STAR (v2.5.3a) mapper
The reads mapped in multiple genomic locations were eliminated by using Samtools (v1.4)
Read counts for features (exons) were generated using the featureCounts function from the Subread package (v 1.22.1)
For ATAC-seq low quality peaks such as blacklisted peaks were eliminated.
Genome_build: hg38
Supplementary_files_format_and_content: Raw gene count matrix was generated using featureCounts function from the Subread package (v 1.22.1) with Ensembl Known Gene models (version GRCh38.92) as reference annotations
Supplementary_files_format_and_content: ATAC-seq peaks were identified by using the HOMER tool
|
| |
|
| Submission date |
Sep 24, 2020 |
| Last update date |
Oct 05, 2020 |
| Contact name |
Georg Stary |
| Organization name |
Medical University of Vienna
|
| Department |
Dermatology
|
| Street address |
Spitalgasse 23
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE158485 |
A discrete subset of epigenetically primed human NK cells mediates antigen-specific immune responses |
|
| Relations |
| BioSample |
SAMN16253760 |
| SRA |
SRX9183025 |
