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Sample GSM1611443 Query DataSets for GSM1611443
Status Public on Feb 14, 2015
Title DKOR_MEF2
Sample type SRA
 
Source name Mouse embryo fibroblast 
Organism Mus musculus
Characteristics cell type: Mouse embryo fibroblast 
genotype: Bak−/− Bax−/− (C12 responsive)
Growth protocol Cells were grown in a humidified 95/5% air/CO2 incubator at 37°C. The cells were passaged at 1:5–1:10 dilutions and the remaining cell suspension was seeded directly onto a 12-well tissue culture plate.
Extracted molecule total RNA
Extraction protocol Cells were grown to confluency in 12-well plates. Two wells of each cell line were used for library construction. Total RNA was isolated using Trizol reagent.
1 microgram of total RNA was used for library construction following standard Illumina protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Illumina Casava v1.8.0 software was used for basecalling.
Sequnced reads were mapped to mm9 whole genome using TopHat v2.0.9 with parameters -g 1 --no-novel-juncs --no-novel-indels
Gene level counts were measured using htseq-counts with parameters -m intersection-strict
Gene level counts were normalized across samples using DESeq package for R.
Differential expression between individual samples were measured using DESeq package for R, with padj < 0.01 as threshold.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each sample
Supplementary_files_format_and_content: normalized_readcounts.txt: abundance measurements
Supplementary_files_format_and_content: raw_readcounts.txt: abundance measurements
Supplementary_files_format_and_content: WTvsDKOr_diffexp.txt: DESeq output
Supplementary_files_format_and_content: WTvsDKOnr_diffexp.txt: DESeq output
Supplementary_files_format_and_content: DKOrvsDKOnr_diffexp.txt: DESeq output
 
Submission date Feb 13, 2015
Last update date May 15, 2019
Contact name Terry E Machen
E-mail(s) tmachen@berkeley.edu
Phone 510-642-2983
Organization name Univ California-Berkeley
Department Molec/Cell Bio
Street address 231 LSA
City Berkeley
State/province CA
ZIP/Postal code 94720-3200
Country USA
 
Platform ID GPL17021
Series (1)
GSE65935 Paraoxonase 2 Serves a Proapopotic Function in Mouse and Human Cells in Response to the Pseudomonas aeruginosa Quorum-Sensing Molecule N-(3-oxododecanoyl)-Homoserine Lactone.
Relations
BioSample SAMN03344771
SRA SRX877991

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

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