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Status |
Public on Dec 31, 2018 |
Title |
4moC57CS0 |
Sample type |
SRA |
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Source name |
Alveolar macrophages
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Organism |
Mus musculus |
Characteristics |
strain: C57BL6 genotype: Wild-type exposure: cigarette smoke time point: 4month
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Extracted molecule |
total RNA |
Extraction protocol |
Qiagen RNAeasy mini kit Illumina TruSeq RNA sample prep with oligo dT selection
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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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
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Submission date |
Nov 30, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Don Delker |
E-mail(s) |
don.delker@hsc.utah.edu
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Organization name |
University of Utah
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Department |
School of Medicine
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Street address |
30 North 1900 East
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City |
Salt Lake City |
State/province |
Utah |
ZIP/Postal code |
84132 |
Country |
USA |
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Platform ID |
GPL13112 |
Series (1) |
GSE75513 |
Rage null mice exposed to cigarette smoke demonstrate attenuated inflammatory, oxidative and ER stress responses in alveolar macrophages |
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Relations |
BioSample |
SAMN04302144 |
SRA |
SRX1456251 |
Supplementary data files not provided |
SRA Run Selector |
Processed data are available on Series record |
Raw data are available in SRA |
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