|
| Status |
Public on Jan 03, 2023 |
| Title |
Osteoclasts, Slc37a2 WT, biol rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
bone
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone
cell line: NA
cell type: Bone marrow macrophage-derived osteoclasts
genotype: WT
treatment: M-CSF/RANKL-stimulation (5-days)
|
| Treatment protocol |
Osteoclast differentation was induced by stimulating bone marrow macrophages for 5 days in the presence of RANKL (10ng/ml, R&D Systems) and M-CSF (2ng/ml).
|
| Growth protocol |
Bone marrow macrophages were maitained in aMEM-supplemented with 10% fetal bovine serum (FBS), antibiotics and M-CSF (2ng/ml)in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol reagent (Cat#. 15596026, Invitrogen), followed by purification using the PureLink RNA mini kit (Cat#. 12183020, Invitrogen) with in-column DNase I treatment (Cat# 12185010, Invitrogen) according to manufacturer's instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CAGRF20083572-WT_F_v_KO_F-top1000_genes.csv
CAGRF20083572-WT_F_v_KO_F-all_genes.csv
|
| Data processing |
Image analysis was performed in real time by the NovaSeq Control Software (NCS) v1.7.0 and Real Time Analysis (RTA) v3.4.4, running on the instrument computer. RTA performs real-time base calling on the NovaSeq instrument computer. Then the Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data. The data generated here meet the AGRF quality standards.
edgeR (version 3.30.3) to perform differential expression analysis.
(https://bioconductor.org/packages/release/bioc/html/edgeR.html) using R
4.0.0.
Assembly: mm10
Supplementary files format and content: The processed data files contain:
Supplementary files format and content: GeneID from the reference genome annotation
Supplementary files format and content: logFC: log2-fold change of expression between WT and KO groups
Supplementary files format and content: logCPM: average log count per million for the gene across all samples
Supplementary files format and content: LR: likelihood ratio test for the gene across all samples
Supplementary files format and content: PValue: p-values for test of expression
Supplementary files format and content: FDR: False discovery rate
Supplementary files format and content: SamplesCounts: Raw gene counts for each sample
|
| |
|
| Submission date |
Dec 02, 2022 |
| Last update date |
Jan 03, 2023 |
| Contact name |
Nathan J Pavlos |
| E-mail(s) |
nathan.pavlos@uwa.edu.au
|
| Organization name |
The University of Western Australia
|
| Department |
School of Biomedical Sciences
|
| Lab |
The Bone Biology and Disease Laboratory
|
| Street address |
35 Stirling Highway
|
| City |
Crawley |
| State/province |
WA |
| ZIP/Postal code |
6009 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE219216 |
Effect of genetic deletion of Slc37a2 on gene expression of mouse bone marrow macrophage-derived osteoclasts |
|
| Relations |
| BioSample |
SAMN31989290 |
| SRA |
SRX18464949 |
