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Sample GSM1557535 Query DataSets for GSM1557535
Status Public on Dec 03, 2014
Title IFNAR1 KO QVDOPH: alpha17 (replicate 1)
Sample type SRA
 
Source name Mouse Embryonic Fibroblasts IFNAR1-KO
Organism Mus musculus
Characteristics cell type: Mouse Embryonic Fibroblasts
genotype: IFNAR1-KO
treatment: Q-VD-OPh
Treatment protocol Q-VD-OPH (MP Biomedicals) was used at 10 μg/ml.
Growth protocol Primary MEFs were generated from IFNAR1 KO mice and respective littermate control embryos (E16.5-18.5). All primary MEFs used for experiments were from passage 4 or less. Control immortalized MEFs were provided by Dr. C. Thompson (University of Pennsylvania) (Wei et al., 2001)
Extracted molecule polyA RNA
Extraction protocol RNA was extracted from duplicate samples and libraries generated for sequencing using the directional RNA-Seq library prep at the Yale Center for Genome Analysis.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description cDNA from Poly(A) selected RNA from Interferon-alpha receptor 1 (IFNAR1) Knockout Mouse embryonic fibroblasts treated with the broad spectrum caspase inhibitor Q-VD-OPh.
Data processing Illumina Casava1.8.2 software used for basecalling.
Fragments were mapped to the mouse genome (mm9) with Tophat2 (Kim et al., 2013), using default parameters.
A reference transcriptome consisting of UCSC known genes (Hsu et al., 2006) was used for isoform-level quantification and differential analysis using Cuffdiff2 (Trapnell et al., 2013).
Quality control analysis and visualization were done using the CummeRbund package (Trapnell et al., 2012), which is part of the R/Bioconductor suite of utilities (Gentleman et al., 2004).
Differentially expressed genes between samples were selected with a Benjamini-Hochberg corrected q-value <0.05, deemed by the Cuffdiff2 program as significant, with the additional parameter of at least a 5-fold difference being used.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files including RPKM values for each sample.
Supplementary_files_format_and_content: gene_exp.diff: Gene differential FPKM. Tests differences in the summed FPKM of transcripts sharing each gene_id
Supplementary_files_format_and_content: genes.count_tracking: Gene counts. Tracks the summed counts of transcripts sharing each gene_id
Supplementary_files_format_and_content: genes.fpkm_tracking: Gene FPKMs. Tracks the summed FPKM of transcripts sharing each gene_id
Supplementary_files_format_and_content: genes.read_group_tracking: Gene read group tracking. Tracks the summed expression and counts of transcripts sharing each gene_id in each replicate
Supplementary_files_format_and_content: run.info: Tab delimited text file listing information about Cuffdiff run.
Supplementary_files_format_and_content: geneIDs_sig_5fold.txt: Processed list of significantly differentially expressed genes (Benjamini-Hochberg corrected q-value <0.05) with at least a 5-fold difference
 
Submission date Dec 02, 2014
Last update date May 15, 2019
Contact name Christian Harman
Organization name Yale University
Department Genetics/Immunobiology
Lab Flavell Lab
Street address 300 Cedar Street, The Anlyan Center
City New Haven
State/province Connecticut
ZIP/Postal code 06520
Country USA
 
Platform ID GPL17021
Series (1)
GSE63794 Apoptotic caspases prevent the induction of type I interferons by mitochondrial DNA
Relations
Reanalyzed by GSE80797
BioSample SAMN03248444
SRA SRX793494

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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