|
| Status |
Public on Apr 01, 2021 |
| Title |
Bulk RNA Seq of FACS Sorted Pup Perivascular Progenitor Cells [Prog2] |
| Sample type |
SRA |
| |
|
| Source name |
Mouse Pup Aorta and Perivascular Adipose Tissue
|
| Organism |
Mus musculus |
| Characteristics |
age: 3 days old (P3)
gender: Mixed male and female
strain: CD-1
tissue: Aorta and Perivascular Adipose Tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Aortas along with associated perivascular adipose tissue were isolated from P3 mice, minced and placed into digestion medium (DMEM, Collagenase D: 6.1mg/ml (Roche), Dispase II: 2.4 mg/ml (Roche) and placed at 37C with constant agitation at 200 rpm. FACS was performed as decribed in the manuscript to isolate intermediate cells, progenitor cells, preadipocytes, and smooth muscle cells. Cells were sorted into FBS catch buffer. After sorting, cells were spun down and the cells were resuspended in 250uL of FACS buffer. Cells were then lysed with the addition of 750uL of Trizol LS (Invitrogen) and RNA was purified by phenol chloroform extraction.
Genewiz Ultra Low Input Library Protocol "RNA was quantified using Qubit and TapeStation. RNA sequencing libraries were made using the SMART-Seq v4 Ultra Low Input Kit. This library prep uses Poly(A) selection to target mRNA, with enrichment for full length transcripts."
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Prog2
|
| Data processing |
Samples were sequenced on an Illumina HiSeq with a 2x150 Paired End (PE) configuration to generate FASTQ files
FASTQ files were aligned to mm10 using STAR (2.5.2a) with quantMode = GeneCounts
The unstranded genecounts for each sample were analyzed for differential gene expression using the R (3.6.3) package DESeq2 (1.26.0).
DESeq2 model was built with the design (~CellType) where “CellType” refers to the different sorted populations, with all CellTypes included in the model, and Raw gene count data, DESeq2 normalized gene count data, and RLD (regularized log transformed data) were extracted from the resulting DeSeq2 object
Genome_build: mm10
Supplementary_files_format_and_content: Raw gene counts, DESeq2 Normalized Gene Counts, DESeq2 RLD (Regularized log transformed) Gene Counts
|
| |
|
| Submission date |
Jan 10, 2021 |
| Last update date |
Apr 01, 2021 |
| Contact name |
Patrick Seale |
| E-mail(s) |
sealep@pennmedicine.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Street address |
Smilow Center for Translational Research, 12th Floor 3400 Civic Center Blvd.
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE164526 |
Defining the lineage of thermogenic perivascular adipose tissue [Pup Aorta] |
| GSE164528 |
Defining the lineage of thermogenic perivascular adipose tissue |
|
| Relations |
| BioSample |
SAMN17277322 |
| SRA |
SRX9817605 |
