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Sample GSM2876101 Query DataSets for GSM2876101
Status Public on Dec 27, 2018
Title WT_UN_2_S2
Sample type SRA
 
Source name bone marrow derived macrophages
Organism Mus musculus
Characteristics strain: C57BL/6
genotype/variation: Wild-type
Treatment protocol No treatment
Growth protocol Bone marrow cells were isolated from femurs of C57BL/6 WT and AEG-1KO mice and were differentiated into macrophages using RMPI-1640 medium supplemented with 10% heat-inactivated FBS and 20% L929 conditioned media for 7days at which point cells were harvested.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed using QIAGEN columns according to the manufacturer's instruction.
RNA-Seq library was prepared using Illumina TruSeq RNA sample preparation kit and sequenced on Illumina HiSeq3000 platform.
RNA-Seq libraries were pooled together to aim about 25-40M read passed filtered reads per sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Description WT_UN_2_S2_L001_R1_001
Data processing All sequencing reads were quality controlled using FastQC v0.11.2. Illumina adapters were trimmed using Cutadapt v1.9.dev2, replicates were merged and aligned with their reference genome (UCSC mouse genome build mm10) using subread-align v1.4.6-p4. The BAM files from alignment were processed using featureCounts v1.4.6-p4 to obtain the counts per gene in all samples. Mus_musculus.GRCm38.83.gtf gene definition file was used. The differential expression analysis was performed using edgeR v3.18.1. Genes having counts per million less than 2 in all samples were excluded. Differentially expressed genes were defined using p-value < 0.01 and FDR-corrected p-value < 0.1 cutoffs. All bioinformatics analyses were conducted in R/Bioconductor computing environment v3.4.0.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text, counts
 
Submission date Dec 05, 2017
Last update date May 15, 2019
Contact name Mikhail Dozmorov
E-mail(s) mdozmorov@vcu.edu
Organization name Virginia Commonwealth University
Department Biostatistics
Street address 830 E Main St
City Richmond
State/province VA
ZIP/Postal code 23298
Country USA
 
Platform ID GPL21493
Series (1)
GSE107691 Expression data from Wild-type (WT) and Astrocyte elevated gene-1 (AEG-1) knockout (KO) bone marrow derived macrophages (BMDM)
Relations
BioSample SAMN08131891
SRA SRX3444817

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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