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Sample GSM4294066 Query DataSets for GSM4294066
Status Public on Feb 04, 2020
Title Sciatic nerve macrophage, replicate 2
Sample type SRA
 
Source name Sciatic nerve
Organism Mus musculus
Characteristics strain: C57BL/6J
Growth protocol All Methods listed in Ydens et al. Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system . Nature Neuroscience. 2019.
Extracted molecule total RNA
Extraction protocol All Methods listed in Ydens et al. Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system . Nature Neuroscience. 2019.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1000
 
Description Sciatic nerve macrophage, replicate 2
Data processing Image analysis and base calling resulted in .bcl files, which were converted into .fastq files with the CASAVA1.8.2 software.
No Quality Trimming was done.
Star was used for mapping with Star version 2.5.2b and the following command line: STAR --runThreadN 10 --genomeDir XXX --genomeLoad LoadAndKeep --limitBAMsortRAM 20000000000 --readFilesIn SampleFastQs --readFilesCommand zcat --outFileNamePrefix YYY --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical --seedSearchStartLmax 30 --outSAMtype BAM SortedByCoordinate
featureCounts v1.5.1 was used for count file generation with the following command line: featureCounts –a GTFFile –G FASTAFile –o OutFile -p -F GTF -g gene_name -t exon -T 10 –largestOverlap
Genome_build: Gencode M11 was used for mapping and counting (mm10)
Supplementary_files_format_and_content: tab-delimited text files including raw counts for each sample
 
Submission date Feb 03, 2020
Last update date Feb 04, 2020
Contact name Liesbet Martens
E-mail(s) liesbet.martens@irc.vib-ugent.be
Organization name VIB-University of Ghent
Department VIB Inflammation Research Center
Street address Technologiepark 927
City Zwijnaarde
ZIP/Postal code 9052
Country Belgium
 
Platform ID GPL15103
Series (2)
GSE144705 Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system (bulk)
GSE144708 Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system
Relations
BioSample SAMN13977040
SRA SRX7668394

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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