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Sample GSM3163389 Query DataSets for GSM3163389
Status Public on Jun 11, 2019
Title Macro-6
Sample type SRA
 
Source name Dermis
Organism Mus musculus
Characteristics strain: Cx3cr1+/gfp
tissue: ear skin
age: 7 weeks
cell type: Cx3cr1gfp/+ Dermis Macrophages
Treatment protocol untreated
Growth protocol SPF animal facility, no earclipping
Extracted molecule total RNA
Extraction protocol Mouse ears were digested with Dispase (0.25 U/ml), Collagenase II (1 mg/ml), and DNase I in HBSS with 10% FCS for 2 h at 1400 rpm and 37°C. Cells were filtered, stained and sorted as CD45+, CD11b+, CD64+, Lin- in a 384-well plate.
As described in CEL-Seq2 protocol (Hashimshony et al. 2016)
Adapted from TruSeq Small RNA Library Preparation Protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description library of 96 Cx3cr1gfp/+ Dermis Macrophages
Data processing For image aquisition, intensity extraction and basecalling HiSeq Control Software 2.0.2, RTA 2.4.11 / Recipe Fragment 2.0.0.2(Hiseq2500) or Control Software HD 3.4.0.38 / RTA2.7.7 / Recipe Fragment HD 3.5.0.4(Hiseq3000)​ was used. Conversion of bcl2fastq files was performed using bcl2fastq 2.17.1.14
Paired end reads were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all gene models based on the mouse ENCODE VM9 release downloaded from the UCSC genome browser comprising 57,207 isoforms derived from 57,207 gene loci with 57,114 isoforms mapping to fully annotated chromosomes (1 to 19, X, Y, M). All isoforms of the same gene were merged to a single gene locus. Furthermore, gene loci overlapping by >75% were merged to larger gene groups. In addition we annotated the EGFP sequence from the pEGFP-N1 vector (https://www.ncbi.nlm.nih.gov/nuccore/U55762) used to generate the CX3CR1-GFP reporter mice. This procedure resulted in 34,112 gene groups.
The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first six bases correspond to the cell specific barcode followed by six bases representing the unique molecular identifier (UMI). The remainder of the left read contains a poly(T) stretch. The left read was not used for quantification. For each cell barcode, the number of UMIs per transcript was counted and aggregated across all transcripts derived from the same gene locus.
Based on binomial statistics, the number of observed UMIs was converted into transcript counts (Gruen et al., 2014).
Genome_build: ENCODE VM9 + gfp sequence from pEGFP-N1 vector (https://www.ncbi.nlm.nih.gov/nuccore/U55762)
Supplementary_files_format_and_content: TSV files, columns represent CXR3CR1 high/mid/low macrophages, rows represent the geneid and the values in the file are the quantified number of transcripts.
 
Submission date May 29, 2018
Last update date Jun 11, 2019
Contact name Patrice Zeis
E-mail(s) zeis@ie-freiburg.mpg.de
Organization name Max Planck Institute of Immunobiology and Epigenetics
Lab Dominic Grün
Street address Stübeweg 51
City Freiburg
ZIP/Postal code 79108
Country Germany
 
Platform ID GPL21493
Series (2)
GSE114526 Genome-wide expression study of macrophage subsets in mouse skin
GSE115030 A subset of skin macrophages modulates surveillance and regeneration of local nerves
Relations
BioSample SAMN09275767
SRA SRX4136236

Supplementary file Size Download File type/resource
GSM3163389_Macro-6.coutt.tsv.gz 368.1 Kb (ftp)(http) TSV
GSM3163389_readme_Macro-6.coutt.tsv.gz 1.2 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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