|
| Status |
Public on Oct 24, 2022 |
| Title |
LysM-Cre;Rosa26-Runx1tg3_Day3_MCSF_RANKL |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow derived macrophage
|
| Organism |
Mus musculus |
| Characteristics |
cell line: Bone marrow derived macrophage
cell type: Osteoclasts
genotype: Runx1 over expression
time: Day 3
treatment: MCSF_RANKL
|
| Treatment protocol |
Osteoclast differentiation was done in 48-well plate at aseeding density of BMMs (15 000 cells/well) and trated with osteoclast media. Media was every 2 days.
Osteoclast media consist of α-MEM supplemented with 10% FBS, 1× penicillin-streptomycin, 30 ng/mL M-CSF and 50 ng/mL RANKL (R&D Systems)
|
| Growth protocol |
Bone marrow was isolated from long bones by flushing in α-MEM (10% fetal bovine serum [FBS], 1× penicillin-streptomycin) and erythrocytes were lysed using RBC lysis buffer. Cells were plated on a petri dish to expand bone marrow macrophages which were used for osteoclast differentiation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy kit (Qiagen). 250 ng of total RNA was used for the generation of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Osteoclast differentiation
|
| Data processing |
NovaSeq 6000 Paired-end sequencing was used, PE150, Q30≥85%.
Clean reads were mapped to mouse reference genome (GRCm39) using STAR alignment.
Read count extraction and normalization were performed using DESeq2 method.
Pairwise gene expression levels were calculated using fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) value
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample
|
| |
|
| Submission date |
Oct 21, 2022 |
| Last update date |
Oct 24, 2022 |
| Contact name |
Mohd Nazir Khan |
| E-mail(s) |
[email protected]
|
| Phone |
3303894492
|
| Organization name |
Emory University
|
| Department |
Orthopaedics
|
| Street address |
21 Ortho Lane
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30329 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE216312 |
Sexually Dimorphic Increases in Bone Mass Following Tissue-specific Overexpression of Runx1 in Osteoclast Precursors |
|
| Relations |
| BioSample |
SAMN31405612 |
| SRA |
SRX17989570 |
