GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1103012 Query DataSets for GSM1103012
Status Public on Jul 01, 2013
Title macrophages control (IFNAR wt/ko) #1
Sample type SRA
Source name mouse peritoneal macrophages
Organism Mus musculus
Characteristics strain: C57BL/6
age: 18 weeks
gender: male
cell type: peritoneal macrophage
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
Description S1895_mp_Kontrolle_1
Strand specific RNA-Seq
Data processing Read Alignment: pBWA version 0.5.9-r32-MPI-patch2 against mm9 (UCSC)
Counts per feature: Reads per exon were computed using bedtools version 2.11, summarized per gene based on Ensembl Gene 61 annotation.
Normalization of reads per gene: 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
Supplementary_files_format_and_content: Tab-delimited 'counts' file with sample size normalized counts per gene (rows) and sample (columns)
Submission date Mar 20, 2013
Last update date May 15, 2019
Contact name Tina Schumann
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)
GSE45358 Gene expression analysis of murine peritoneal macrophages deficient for SAMHD1 and IFNAR
SRA SRX253175
BioSample SAMN01985470

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap