|
| Status |
Public on Nov 02, 2017 |
| Title |
KO_CTR_3 |
| Sample type |
SRA |
| |
|
| Source name |
Splenic NK cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: spleen
cell type: NK cells
age: 8 weeks old
genotype: il-1r8-/-
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Splenic NK cells were MACS enriched according to manufacturer’s instructions (Miltenyi Biotec). Purity of NK cells was about 90% as determined by FACS NK cells were stained (CD45-BV650, NK1.1-PE, CD3e-APC, CD11b-BV421, CD27-FITC) and sorted on a FACSAria cell sorter (BD Bioscience). Purity of was ≥ 99%. Splenic NK cells from 6 mice per genotype were pooled in pairs and stimulated with IL-18 (MBL) (20 ng/ml for 4 h). RNA was prepared using standard Qiagen protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
SZ2_15_15_KO_CTR_S15
|
| Data processing |
Basecalling was performed using Illumina bcl2fastq2 Conversion Software v2.16
Single-end sequencing reads were first trimmed using bbduk to remove the first 12 bases. A contaminant kmer discovery length of 13 was used for contaminant removal. Regions of length 20 or above with average quality of less than 10 were trimmed from the end of each read. Finally, trailing polyG and polyA were removed from the reads using cut adapt.
Trimmed reads were aligned to reference genome mm10 and assigned to features in the mm10 gene annotation using the STAR program.
Read Counts were read into R and processed using the edgeR package features were filtered to remove features with no counts
Library Sizes were normalised using the TMM normalisation in the edgeR package to produce normalised counts per million reads
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Comma separated text files include raw counts or normalized counts.
|
| |
|
| Submission date |
Nov 01, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Santiago Zelenay |
| E-mail(s) |
santiago.zelenay@cruk.manchester.ac.uk
|
| Organization name |
CRUK Manchester Institute
|
| Lab |
Cancer Inflammation and Immunity
|
| Street address |
Alderley Park
|
| City |
Manchester |
| State/province |
UK |
| ZIP/Postal code |
SK10 4TG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE105043 |
IL-1R8 is a checkpoint in NK cells regulating anti-tumor and anti-viral activity |
|
| Relations |
| BioSample |
SAMN07964769 |
| SRA |
SRX3350509 |
