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Sample GSM2310945 Query DataSets for GSM2310945
Status Public on Sep 15, 2016
Title Ripk3Casp8_unstim_rep1
Sample type SRA
 
Source name Ripk3Casp8, unstimulated
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: Ripk3-/-Casp8-/-
treatment: untreated
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
 
Description Only the R1 paired-end reads have been provided; the R2 paired-end reads are unavailable.
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 SAMN05773309
SRA SRX2164753

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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