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Sample GSM4318395 Query DataSets for GSM4318395
Status Public on Feb 19, 2020
Title C3_R3_Mature macrophage_mouse3
Sample type SRA
 
Source name bone marrow derived
Organism Mus musculus
Characteristics strain: C57BL/6
Sex: male
age: 8 to 10 weeks
Growth protocol After 1 day in 0.6ng/ml CSF1 in alpha+ MEM /15% FCS, non-adherent cells were incubated for two days in a fresh dish containing 12ng/ml CSF1 in alpha+ MEM /10% FCS and then for 7 days in 120ng/ml CSF1 in alpha+ MEM /10% FCS.
Extracted molecule total RNA
Extraction protocol mRNA was harvested using RNeasy kit( QIAGEN) with DNase treatment on column. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Ion Torrent protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Ion Torrent Proton
 
Description C3_R3
C1_C2_C3_allprobes_reads.txt
C1_C2_C3_allprobes_log2_RPM.txt
Data processing Torrent Suite Software 5.10 used for basecalling and sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence- returning a fastq file (raw data)
Reads were then mapped to the GRCm38.p6 genome using the open source Hisat2-2.0.5 aligner.
The Hisat2 generated BAM files were uploaded into SeqMonk (version 1.42) with minimum mapping quality set to 60
The edgeR platform, within SequeMonk, was uesed to generate lists of differential gene expression from the raw reads as is required in analysis of negative binomial distributions
Tab-delimited text files of all genes and differentially expressed genes (at p<0.05, p<0.01 and p<0.001) showing raw reads or log2 RPM were output (processed files)
Ampliseq
Torrent Suite Software 5.10 used for basecalling and sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Returning a fastq file (raw data) of reads associated with each of the 16000 barcoded primer pairs.
Reads were then mapped to the GRCm38.p6 genome using the open source Hisat2-2.0.5 aligner.
The Hisat2 generated BAM files were uploaded into SeqMonk (version 1.42) with minimum mapping quality set to 60
The edgeR platform, within SequeMonk, was uesed to generate lists of differential gene expression from the raw reads as is required in analysis of negative binomial distributions
Tab-delimited text files of all genes and differentially expressed genes (at p<0.05, p<0.01 and p<0.001) showing raw reads or log2 RPM were output (processed files)
Genome_build: Genome Reference Consortium mouse genome (GRCm39.p6)
Supplementary_files_format_and_content: tab-delimited text files include reads or log2 RPM for each sample showing all genes or differential expression between conditions.
 
Submission date Feb 18, 2020
Last update date Feb 19, 2020
Contact name James Harvey Steer
E-mail(s) jaysteer@gmail.com
Organization name University of Western Australia
Street address Hospital Avenue, QEII Medical Centre, M Block
City Perth
State/province Western Australia
ZIP/Postal code 6009
Country Australia
 
Platform ID GPL18635
Series (1)
GSE145437 Adhesion, motility and matrix-degrading gene expression changes in CSF-1-induced mouse macrophage differentiation
Relations
BioSample SAMN14124408
SRA SRX7738695

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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