|
| Status |
Public on Feb 24, 2021 |
| Title |
UND_VEH_A |
| Sample type |
SRA |
| |
|
| Source name |
UND_VEH
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: Mutant RNF40RosaCreERT2 mouse
cell type: Primary Calvarial Osteoblasts
treatment: for 7 d with vehicle(ethanol)
library prep kit: NEXTflex Rapid Directional mRNA-Seq Kit, Bioo Scientific
|
| Treatment protocol |
For induction of RNF40 knockout, the cells were treated with 250nM of 4-hydroxytamoxifen or equivalent volume of vehicle (ethanol). For differentiation, cells were treated with 5 mM β-glycerophosphate and 0.2 mM ascorbate. For vitamin D studies, cells were treated for 7 days with 10nM calcitriol or equal volume of vehicle (DMSO).
|
| Growth protocol |
Mouse calvarial osteoblasts were maintained in aMEM complete media with 10% FBS and 1% P/S
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total cell RNA was isolated with standard TRIzol extraction protocol
4 µg of total cell RNA was used for library preparation with NEXTflex Rapid Directional mRNA-Seq from Bioo Scientific and 500ng of total cell RNA was used for library preparation with TruSeq RNA Smaple Prep Kit-v2 following manufacturers' protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The FASTQ files were mapped to the mouse mm9 genome using TopHat Gapped-read mapper for RNA-seq data with very-sensitive BOWTIE2 settings. The differential analysis was performed by using Cuffdiff with default settings.
Genome_build: mm9
Supplementary_files_format_and_content: The provided mRNA-Seq analysis files present the differentially regulated genes between the indicated conditions in excel file format.
|
| |
|
| Submission date |
Aug 09, 2019 |
| Last update date |
Feb 24, 2021 |
| Contact name |
Steven A. Johnsen |
| Organization name |
Robert Bosch Center for Tumor Diseases
|
| Lab |
Molecular Cancer Epigenetics
|
| Street address |
Auerbachstraße 112
|
| City |
Stuttgart |
| State/province |
BW |
| ZIP/Postal code |
70376 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE135628 |
RNF40 exerts stage-dependent functions in differentiating osteoblasts and is essential for bone cell crosstalk [RNA-seq] |
| GSE135629 |
RNF40 exerts stage-dependent functions in differentiating osteoblasts and is essential for bone cell crosstalk |
|
| Relations |
| BioSample |
SAMN12542669 |
| SRA |
SRX6686948 |
