|
| Status |
Public on Dec 22, 2021 |
| Title |
Treated by Adenovirus encoding Cre recombinase (Ad-Cre), biological rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Mesenchymal stem cells from p75 floxed mice (p75fl/fl) calvarial tissue
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Cre-treated
cell type: Mesenchymal stem cells from p75 floxed mice (p75fl/fl) calvarial tissue
treatment: Adenovirus encoding Cre recombinase (Ad-Cre)
|
| Treatment protocol |
For p75 deletion, cells were stimulated with an adenovirus encoding either Cre Recombinase (Ad-Cre, 1045-HT, Vector Biosystems, Malvern, PA) or GFP (Ad-GFP, 1060-HT, Vector Biosystems). Cells were resuspended in Trizol (Life technologies corporation, Gaitherburg, MD, USA) for RNA isolation.
|
| Growth protocol |
Calvarial bones were dissected from p75 floxed embryos at postnatal day 1-5. Frontal and parietal bones were subjected to six sequential enzymatic digestions with a mixture containing 1 mg/mL collagenase type I (Worthington Biochemical Corporation, Lakewood, NJ) and 1 mg/mL collagenase type II (Worthington Biochemical Corporation). Cell fractions (from sequential digestions 3-6) were collected and filtered at 40 μm and centrifuged. Cells were resuspended in αMEM (Gibco) containing 15% FBS (Gibco) and 1% penicillin/streptomycin (Gibco).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extract from cells by Trizol (Life technologies corporation, Gaitherburg, MD, USA).
TruSeq Stranded Total RNA LT Sample Prep Kit (Human Mouse Rat)/TruSeq Stranded Total RNA Sample Prep Guide, Part # 15031048 Rev. E
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
JXu-KO1_S4
|
| Data processing |
Base calling with RTA version 2.4.11
Data filtering to strip adapters with bcl2fastq 2.17.1.14
The reads were aligned to NCBI GRCm38 using tophat v.2.1.1
FPKMs were generated using Cufflinks v. 2.2.1
FPKM vaues log2 converted (FPKM = 0 ignored) and quantile normalized with Partek Genomics Suite v7.0
Genome_build: Mus musculus sequence GRCm38
Supplementary_files_format_and_content: Single tab-delimeted text file of quantile normalized log2 FPKM values for all samples.
|
| |
|
| Submission date |
Jul 11, 2021 |
| Last update date |
Dec 22, 2021 |
| Contact name |
Aaron W James, MD, PhD |
| Organization name |
Johns Hopkins University School of Medicine
|
| Department |
Pathology
|
| Lab |
Ross 524
|
| Street address |
600 North Wolfe Street
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21287 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE179889 |
Expression data of mouse calvarial stem cells from p75 floxed mice (p75fl/fl) stimulated with Adenovirus encoding Cre recombinase (Ad-Cre) or control (Ad-GFP) [RNA-seq] |
| GSE179891 |
Myeloid-to-mesenchymal NGF-p75 signaling coordinates cell migration during repair. |
|
| Relations |
| BioSample |
SAMN20166702 |
| SRA |
SRX11407652 |
