|
| Status |
Public on Dec 03, 2014 |
| Title |
WT DMSO: alpha1 (replicate 1) |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Embryonic Fibroblasts Wild Type
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Mouse Embryonic Fibroblasts
genotype: wild type
treatment: DMSO
|
| 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 wild-type Mouse embryonic fibroblasts treated with DMSO.
|
| 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 |
SAMN03248437 |
| SRA |
SRX793488 |
