|
| Status |
Public on Sep 11, 2020 |
| Title |
s31_BMMs_cKO_int |
| Sample type |
SRA |
| |
|
| Source name |
cultured BMMs
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone Marrow Derived Monocytes
genotype: Irf8_cKO
cell type: BMMs
|
| Treatment protocol |
FACS sorted BMMs from Irf8 cWT and Irf8 cKO mice were cultured in the presence of 20 ng/ml MCSF and 40 ng/mL RANKL for 4 days to generate terminally differentiated osteoclasts.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAeasy extraction of total RNA was performed according to the manufacturer's (Qiagen) instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Convert from BCL and demultiplex using Casava 1.8.4 or bcl2fastq 2.17.1
Sorted cells: Map to mm10 using HISAT2
Sorted cells: calculate normalized counts using DESeq2
Sorted cells: ANOVA comparisons done using DESeq2
Sorted Cells: PCA plots were generated using R statistical analysis software
Normalized BigWig files using deepTools bamCoverage
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and 34 samples as 2 samples (outliers) were excluded from the analysis.
|
| |
|
| Submission date |
May 29, 2020 |
| Last update date |
Sep 11, 2020 |
| Contact name |
Vivek Thumbigere Math |
| E-mail(s) |
vthumbigere@umaryland.edu
|
| Phone |
6127108608
|
| Organization name |
Universityof Maryland
|
| Department |
Periodontics
|
| Street address |
650 W Baltimore Street
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21201 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE151480 |
Monocyte Subsets with High Osteoclastogenic Potential and Their Epigenetic Regulation Orchestrated by IRF8 [RNA-Seq sorted cells] |
| GSE151483 |
Monocyte Subsets with High Osteoclastogenic Potential and Their Epigenetic Regulation Orchestrated by IRF8 |
|
| Relations |
| BioSample |
SAMN15060685 |
| SRA |
SRX8428312 |
