|
| Status |
Public on Jul 19, 2019 |
| Title |
B6.naive_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Lung
cell type: NK1.1+ NK cells
genotype: wildtype
|
| Treatment protocol |
Challenged with B16 melanoma cells and lung harvested on day 7 after inoculation. Cells were purified by high speed flow cytometric sorting.
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA purification was performed following the manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the Smart Seq v4 Low RNA v3.0 Sample preparation kit (Clontech) following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
2.B6.naive_S2
|
| Data processing |
Sequence reads were aligned to the GRCm38/mm10 build of the Mus musculus genome using the Subread aligner. Only uniquely mapped read pairs (fragments) were retained.
Genewise counts were obtained using featureCounts. Fragments overlapping exons in annotation build 38.1 of NCBI RefSeq database were included. Genes were filtered from downstream analysis if they failed to achieve a CPM (counts per million mapped fragments) value of 0.5 or greater in at least two libraries.
Counts were converted to log2 counts per million(CPM), quantile normalized and precision weighted with the ‘voom’ function of the limma package. After normalization, the expression levels were converted into log2 reads per kilobase per million(RPKM), and a linear model was fitted to each gene. Empirical Bayes moderated t-statistics were used to assess differences in expression. Genes were called differentially expressed if they achieved a false discovery rate of 0.15 or less.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-RPKM values for each library. The supplementary file 'Supp_Raw_Counts.txt' includes raw read counts for genes in each library.
|
| |
|
| Submission date |
Apr 12, 2018 |
| Last update date |
Jul 19, 2019 |
| Contact name |
Wei Shi |
| E-mail(s) |
Wei.Shi@onjcri.org.au
|
| Organization name |
Olivia Newton John Cancer Research Institute
|
| Department |
Bioinformatics and Cancer Genomics
|
| Street address |
Level 5, ONJ Cancer Centre, 145 Studley Rd
|
| City |
Heidelberg |
| State/province |
VIC |
| ZIP/Postal code |
3084 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE113030 |
NKp46 machinery required for effective NK cell killing |
|
| Relations |
| BioSample |
SAMN08918456 |
| SRA |
SRX3926890 |
