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Sample GSM1026904 Query DataSets for GSM1026904
Status Public on Mar 31, 2013
Title KO macrophages (S1056 to S1075) #7
Sample type SRA
 
Source name mouse peritoneal macrophages
Organism Mus musculus
Characteristics strain: C57BL/6
age: 21 weeks
Sex: male
genotype: SAMHD1 KO
cell type: peritoneal macrophages
Extracted molecule total RNA
Extraction protocol Cells were lysed immediately in µMACS™™ mRNA Isolation Kit lysis buffer and cleaned with with LysateClear Columns (Miltenyi Biotec). mRNA was enriched using Oligo(dT) beads.
Poly-dT-enrichment, DNAse treatment, chemical fragmentation, ss-Synthesis, strand specific library prep according to: Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 2009 Jul 20. doi:10.1093/nar/gkp596
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing pBWA version 0.5.9-r32-MPI-patch2 against mm9
Reads per exon were computed using bedtools version 2.11, summarized per gene based on Ensembl Gene 61 annotation.
The raw counts (absolute number of reads) were normalized with the DESeq R package (v.1.8.1) and sample to sample correlation (Pearson's correlation coefficient) was computed based on the normalized counts.
Genome_build: mm9 (UCSC)
Supplementary_files_format_and_content: tab delimited file with sample size normalized counts per gene (rows) and sample (columns)
 
Submission date Oct 26, 2012
Last update date May 15, 2019
Contact name Tina Schumann
E-mail(s) Tina.Schumann@tu-dresden.de
Organization name Institute of Immunology
Department Medical Faculty "Carl Gustav Carus"
Street address Fetscherstraße 74
City Dresden
ZIP/Postal code 01307
Country Germany
 
Platform ID GPL13112
Series (1)
GSE41879 Gene expression analysis of murine SAMHD1 deficient peritoneal macrophages (S1056 to S1075)
Relations
SRA SRX201666
BioSample SAMN01796052

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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