|
| Status |
Public on Dec 27, 2018 |
| Title |
WT_UN_1_S1 |
| 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_1_S1_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 |
SAMN08131892 |
| SRA |
SRX3444816 |
