|
| Status |
Public on Apr 01, 2019 |
| Title |
IRE1 KO NK at day 7 replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
NK cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: IRE1 KO
sample time: day 7
virus: yes
|
| Treatment protocol |
Mice were infected with 7.5 × 103 PFU of MCMV by i.p. injection and spleens were harvested at day0, 1.5 and 7 after infection.
|
| Growth protocol |
Mice were bred at Dana-Farber Cancer Institute and Weill Cornell Medical Center in accordance with the guidelines of the Institutional Animal Care and Use Committee (IACUC).Host C57BL/6 × B6.SJL animals (CD45.1+CD45.2+) were lethally irradiated with 900 grays of radiation and reconstituted with a 1:1 mixture of bone marrow cells from B6.SJL WT (CD45.1+) and knockout or transgenic donor (CD45.2+) mice, co-injected with anti-NK1.1 (clone PK136) to deplete any residual donor or host mature NK cells. CD45.1+CD45.2+ host NK cells were excluded from all analyses.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from sorting-purified Ly49H+ WT or IRE1NK NK cells was extracted with the RNeasy RNA purification micro kit (Qiagen) according to the manufacturer’s instructions.
poly(A)+ RNA-seq libraries (pair-end 75) were prepared with an Illumina TruSeq RNA Sample Preparation Kit V2 according to the manufacturer's instructions (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Replicates are paired as WT and KO
|
| Data processing |
Sequence data from Illumina's HiSeq4000 sequencer were 'de-multiplexed' to generate FASTQ files for each sample with Illumina's CASAVA pipeline (version 1.8.2).
The reads that passed Illumina's quality and purity filter (> 90%) were aligned to the mouse genome (mm9 build) with tophat2 with default parameters.
The resulting SAM alignment files were then converted to the BAM file format, then were sorted and indexed with SAMtools (version 0.1.14).
The HTSeq was used for summarization of the aligned sequence reads into counts.
Differential gene expression was analyzed with the DESeq2. Transcripts with adjusted P value < 0.01 were considered differentially expressed between genotypes (wild-type and IRE1 KO) and infection times (day 0, 1.5, 7).
Genome_build: mm9
Supplementary_files_format_and_content: Gene count number was generated for each sample by HTseq2 as supplementary files.
|
| |
|
| Submission date |
Apr 16, 2018 |
| Last update date |
Apr 01, 2019 |
| Contact name |
Yichi Xu |
| E-mail(s) |
xuy2@mskcc.org
|
| Organization name |
MSKCC
|
| Street address |
1275 York Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE113214 |
The IRE1-XBP1 pathway promotes natural killer cell responses against viral infection and cancer by regulation of c-Myc |
|
| Relations |
| BioSample |
SAMN08939475 |
| SRA |
SRX3944402 |
