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| Status |
Public on Aug 08, 2016 |
| Title |
lim mac e10.5_2 |
| Sample type |
SRA |
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| Source name |
limbs Mac, E10.5
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| Organism |
Mus musculus |
| Characteristics |
cell type: Mac
tissue: limbs
tissue group: Caudal / skin
time: E10.5
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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 limbs at day E10.5
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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 |
SAMN05151692 |
| SRA |
SRX1782863 |
| 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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