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| Status |
Public on Mar 31, 2013 |
| Title |
WT macrophages (S1056 to S1075) #9 |
| Sample type |
SRA |
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| Source name |
mouse peritoneal macrophages
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: 17 weeks
Sex: female
genotype: wild type
cell type: peritoneal macrophages
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| 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
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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 |
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)
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| Submission date |
Oct 26, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Tina Schumann |
| E-mail(s) |
Tina.Schumann@tu-dresden.de
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| Organization name |
Institute of Immunology
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| Department |
Medical Faculty "Carl Gustav Carus"
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| Street address |
Fetscherstraße 74
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| City |
Dresden |
| ZIP/Postal code |
01307 |
| Country |
Germany |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE41879 |
Gene expression analysis of murine SAMHD1 deficient peritoneal macrophages (S1056 to S1075) |
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| Relations |
| SRA |
SRX201658 |
| BioSample |
SAMN01796044 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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