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Status |
Public on Aug 08, 2016 |
Title |
ski mac p21_2 |
Sample type |
SRA |
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Source name |
skin Mac, P21
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Organism |
Mus musculus |
Characteristics |
cell type: Mac tissue: skin tissue group: Caudal / skin time: P21
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Extracted molecule |
polyA RNA |
Extraction protocol |
SMART-Seq2 SMART-Seq2
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
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Description |
mouse Macs from skin at day P21
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Data processing |
After de-multiplexing and adapter removal, we aligned reads using Bowtie v 1.1.1 (parameters: -q -p 6 -a -m 100 --minins 0 --maxins 5000 --fr --sam --chunkmbs 200) to the Ensembl cDNA reference. We used BitSeq (v 1.12.0) to quantify transcript levels. Raw read counts were loaded into R and all transcripts that were detected with at least 50 reads in at least four samples (n = 37,521), were processed with DESeq2's variance stabilizing transformation to output normalized read counts, which we subsequently further adjusted by accounting for batch effect with ComBat. Genome_build: mm10 Supplementary_files_format_and_content: Comma-separated text file
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Submission date |
May 20, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Christoph Bock |
E-mail(s) |
cbock@cemm.oeaw.ac.at
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Organization name |
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
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Street address |
Lazarettgasse 14
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City |
Vienna |
ZIP/Postal code |
1090 |
Country |
Austria |
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Platform ID |
GPL17021 |
Series (2) |
GSE81686 |
Differentiation and specification of resident tissue macrophages [SMART-Seq2] |
GSE81774 |
Differentiation and specification of resident tissue macrophages |
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Relations |
BioSample |
SAMN05151670 |
SRA |
SRX1782901 |
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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