|
| Status |
Public on Sep 15, 2016 |
| Title |
Ripk3_LPS.6hr_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Ripk3, LPS.6hr
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
genotype/variation: Ripk3-/-
treatment: LPS stimulation for 6hr
cell type: bone marrow-derived macrophages
|
| Treatment protocol |
BMDMs were either left unstimulated, or stimulated with LPS (100 ng/mL) for 6 hrs.
|
| Growth protocol |
1x106 BMDMs/well were plated in 6-well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator for 16 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
fastq files were aligned to version 79 of mouse reference genome GRCm38 using the Subread aligner in the RSubread package.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: version 79 of mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...
|
| |
|
| Submission date |
Sep 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
daniel beiting |
| E-mail(s) |
beiting@vet.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Department |
Pathobiology
|
| Lab |
Beiting
|
| Street address |
380 S. University Ave
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE86922 |
Activity of uncleaved caspase-8 controls anti-bacterial immune defense and TLR-induced cytokine production independent of cell death |
|
| Relations |
| BioSample |
SAMN05773316 |
| SRA |
SRX2164758 |
