|
| Status |
Public on Sep 11, 2020 |
| Title |
Irf8_cWT_BMMs_1 |
| Sample type |
SRA |
| |
|
| Source name |
cultured BMM
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone Marrow Derived Monocytes
genotype: Irf8_cWT
strain: C57BL/6
cell type: BMMs
time point: day 0
|
| Treatment protocol |
BMMs from Irf8 cWT, Irf8 cKO, Irf8 gWT, and Irf8 gKO mice were cultured in the presence of 20 ng/ml MCSF and 40 ng/mL RANKL for 6 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
Unsorted cells: Map to mm9 using Tophat 2.1.0
Unsorted cells: calculate RPKM using Partek GS 6.6
Unsorted cells: ANOVA comparisons on Log2 RPKM (with 0.1 offse) using Partek GS 6.6
Unsorted Cells: PCA plots of RPKM values using Partek GS 6.6
Normalized BigWig files using deepTools bamCoverage
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files
Supplementary_files_format_and_content: Excel ANOVA table
Supplementary_files_format_and_content: Excel RPKM table
|
| |
|
| Submission date |
May 28, 2020 |
| Last update date |
Sep 11, 2020 |
| Contact name |
Stephen R Brooks |
| E-mail(s) |
stephen.brooks@nih.gov
|
| Organization name |
NIAMS/NIH
|
| Department |
Biodata Mining and Discovery Section
|
| Street address |
50 SOUTH DR, RM 1140
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20814 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE151388 |
Monocyte Subsets with High Osteoclastogenic Potential and Their Epigenetic Regulation Orchestrated by IRF8 [RNA-Seq] |
| GSE151483 |
Monocyte Subsets with High Osteoclastogenic Potential and Their Epigenetic Regulation Orchestrated by IRF8 |
|
| Relations |
| BioSample |
SAMN15048611 |
| SRA |
SRX8418578 |
