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Sample GSM2170396 Query DataSets for GSM2170396
Status Public on Aug 08, 2016
Title liv mac e12.5_2
Sample type SRA
 
Source name liver Mac, E12.5
Organism Mus musculus
Characteristics cell type: Mac
tissue: liver
tissue group: Liver
time: E12.5
Extracted molecule polyA RNA
Extraction protocol SMART-Seq2
SMART-Seq2
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description mouse Macs from liver at day E12.5
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
 
Submission date May 20, 2016
Last update date May 15, 2019
Contact name Christoph Bock
E-mail(s) cbock@cemm.oeaw.ac.at
Organization name CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Street address Lazarettgasse 14
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platform ID GPL17021
Series (2)
GSE81686 Differentiation and specification of resident tissue macrophages [SMART-Seq2]
GSE81774 Differentiation and specification of resident tissue macrophages
Relations
BioSample SAMN05151701
SRA SRX1782872

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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