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Sample GSM1958362 Query DataSets for GSM1958362
Status Public on Dec 31, 2018
Title 4moC57CS3
Sample type SRA
 
Source name Alveolar macrophages
Organism Mus musculus
Characteristics strain: C57BL6
genotype: Wild-type
exposure: cigarette smoke
time point: 4month
Extracted molecule total RNA
Extraction protocol Qiagen RNAeasy mini kit
Illumina TruSeq RNA sample prep with oligo dT selection
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Fastq data files were aligned to the mouse Mm10 Ensembl genome with Novoalign read aligner version 2.08.02
Novoaligned SAM files were parsed into binary BAM files and differentially expressed genes identified using the RNASeq application from USeq software version 8.7.4
RNASeq application calculates fraction of reads that are exonic, intronic and intergenic and makes normalized read data tracks (FPKM) for visualization in the Integrated Genome Browser
RNASeq application runs DefinedRegionsDifferentialSeq for calculating differential expression using Anders DESeq2 negative binomial statistics and Benjamini and Hochberg mulitple testing correction
Genome_build: Ensembl Mus musculus Mm10
Supplementary_files_format_and_content: Excel file with Ensembl IDs, chromosome coordinates, individual sample raw read counts, FPKM counts, Log2 ratio and false discovery rate
 
Submission date Nov 30, 2015
Last update date May 15, 2019
Contact name Don Delker
E-mail(s) don.delker@hsc.utah.edu
Organization name University of Utah
Department School of Medicine
Street address 30 North 1900 East
City Salt Lake City
State/province Utah
ZIP/Postal code 84132
Country USA
 
Platform ID GPL13112
Series (1)
GSE75513 Rage null mice exposed to cigarette smoke demonstrate attenuated inflammatory, oxidative and ER stress responses in alveolar macrophages
Relations
BioSample SAMN04302147
SRA SRX1456254

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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