|
| Status |
Public on Aug 25, 2024 |
| Title |
Biol.repl.2 (wt/d21) |
| Sample type |
SRA |
| |
|
| Source name |
neonatal calvarial bone
|
| Organism |
Mus musculus |
| Characteristics |
tissue: neonatal calvarial bone
cell type: osteoblast
genotype: wt
treatment: osteogenic induction media (d21)
|
| Treatment protocol |
OIM pre-osteoblasts samples F2Tand E2T cells were also additionally treated by coculturing with human fetal liver MSCs over 21 days.
|
| Growth protocol |
Primary osteoblasts like cells (pre-osteoblasts) were isolated from the calvarial bone of neonatal WT and OIM mice. Cells were cultured in alpha modified Eagle’s medium (alpha-MEM) (Invitrogen) supplemented with 10% fetal bovine serum (Gibco), 2 mM L-glutamine, 50 IU/ml penicillin and 50 mg/ml streptomycin (Gibco), at 37 °C in a 5% CO2 incubator. Cells were expanded for about a week until there was a homogeneous population of ALP (alkaline phosphatase) positive cells at subconfluency. In vitro osteogenic differentiation. Cells were differentiated down the osteoblast lineage for up to 3 weeks (d21) in alpha-MEM supplemented with 2 mM β-glycerophosphate, 0.2 mM ascorbic acid and 10−8 M dexamethasone.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA TRIZOL extraction
Pre-made library -- no library preparation performed
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
E1-2
|
| Data processing |
Genewiz bioinformatics analysis workflow. (Standard Package)
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted.
Assembly: Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Supplementary files format and content: tab delimited text includes raw counts for each sample
|
| |
|
| Submission date |
Aug 01, 2024 |
| Last update date |
Aug 25, 2024 |
| Contact name |
Michelangelo Corcelli |
| E-mail(s) |
m.corcelli@ucl.ac.uk
|
| Phone |
07756750648
|
| Organization name |
UCL
|
| Street address |
Zayed Centre for Research, 20 Guilford Street, London,
|
| City |
London |
| State/province |
London |
| ZIP/Postal code |
WC1N 1DZ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE273779 |
Effect of Col1a2 mutation in the gene expression of immature and mature osteoblasts in a mouse model of osteognesis imperfecta (OI) |
|
| Relations |
| BioSample |
SAMN42993249 |
| SRA |
SRX25574497 |
