|
| Status |
Public on Jul 22, 2020 |
| Title |
Aged eWAT SVF Non-phagocytic rep1 |
| Sample type |
SRA |
| |
|
| Source name |
SVF of pooled eWAT, pooled from 6 old mice
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
age: 80 weeks old
tissue: epididymal white adipose tissue (eWAT)
cell-enriched fraction: Non-phagocytic stromal vascular fractions (SVF) sub-population
|
| Treatment protocol |
Single cell suspension of stromal vascular fraction was obtained from pooled epididymal white adipose tissue using the Adipose Tissue Dissociation Kit (Miltenyi Biotec). Cell pellets were suspended in DMEM containing 10% heat-inactivated FBS and adjusted to 4 million cells per milliliter. One milliliter of washed superparamagnetic nanoparticles (~150-nm) suspension was incubated with five milliliters of cell suspension for 2 hours at 37 degrees Celsius with intermittent agitation. Cells that phagocytized the magnetic particles were then enriched via positive magnetic-activated selection for 5 minutes using EasySep magnets. Cells were washed and selection was repeated three times with non-selected cells pooled at each step to create phagocyte-enriched and phagocyte-depleted stromal vascular fractions, respectively.
|
| Growth protocol |
Mice were aged naturally, housed under standard conditions and fed a rodent chow diet
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell pellets of isolated and phagocyte-enriched/depleted SVF were flash frozen and RNA was extracted in QIAzol reagent and isolated via miRNeasy Mini Kit (Qiagen)
Sequencing libraries were prepared using the TruSeq Stranded Total RNA kit (Illumina) from 700 ng total RNA, following manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RQ_007851_004
RS-02623858_CTTGTA_L001
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Sequence reads were trimmed using Trimmomatic v0.36, read quality was estimated using Fastqc. The reads were aligned with TopHat v2.1.0 to mm10 genome in -very-sensitive mode.
Transcript counts were obtained using HTseq-count.
Normalized expression values were measured using DEseq.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with DEseq-normalized raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jul 21, 2020 |
| Last update date |
Jul 22, 2020 |
| Contact name |
Brandon Hall |
| E-mail(s) |
bhall@genomeprotection.com
|
| Organization name |
Everon Biosciences, Inc.
|
| Street address |
640 Ellicott Street, Ste. 444
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14203 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE154832 |
Age-related transcriptional profiling of phagocytic cells isolated from murine epididymal white adipose tissue |
|
| Relations |
| BioSample |
SAMN15590893 |
| SRA |
SRX8784743 |
