|
| Status |
Public on Feb 25, 2020 |
| Title |
MEF_VECTOR__OSTEOMAX_DAY21_3_S12_R1_001 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse embryonic fibroblasts cell line
|
| Organism |
Mus musculus |
| Characteristics |
organ site: Mouse embryos
|
| Treatment protocol |
Mouse embryonic fibroblasts (MEFs) from β-actin-TVA/p53−/− mice were transduced with RCAS-GFP or RCAS-HOXB13. Expression of GFP and HOXB13 was confirmed by immunofluorescence.
|
| Growth protocol |
MEF-GFP and MEF-HOXB13 cells where plated in triplicates in 6-well plates coated with 0.1% gelatin (Millipore) in DMEM media (Corning) supplemented with 5% FBS. After an overnight incubation cells where confluent. At this timepoint one plate was harvested for RNA extraction (DAY 1) while in the other plate, media was replaced with OsteoMAX-XF differentiation medium (Millipore). Cells where cultured in the differentiation media for 21 days (media was replaced every 2-3 days). Cells where harvested at day 21 (OSTEOMAX DAY 21) for RNA extraction. Transcriptome was analyzed by bulk RNA sequencing of triplicate samples.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA was isolated by RNeasy Mini Kit from Qiagen. The integrity of total RNA was examined by the Agilent 4200 TapeStation System.
Libraries for RNA-Seq were constructed with Biomek® NuGEN mRNA-Seq Kit to generate strand-specific RNA-seq libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Sequencing was performed on Illumina Hiseq3000 for a single read 50bp run
Sequenced reads were aligned to Human Genome version GRCh38 using STAR aligner version 2.7.2a
The raw read counts were estimated using HTSeq-0.6.1
Reads per gene was quantified using STAR version 2.7.2a with Ensembl GRCh38.98 GTF file
EdgeR’s [4] TMM (trimmed mean of M-values) algorithm was used to normalize the gene expression data
Genome_build: GRCh38.98
Supplementary_files_format_and_content: xlsx files for Raw.Read.Count and Normalized.Read.Count(using DESeq2 for normalization)
|
| |
|
| Submission date |
Feb 24, 2020 |
| Last update date |
Feb 25, 2020 |
| Contact name |
Sandra Orsulic |
| E-mail(s) |
msrecouvreux@gmail.com, sorsulic@mednet.ucla.edu
|
| Organization name |
UCLA
|
| Department |
OBGYN
|
| Street address |
10833 Le conte ave
|
| City |
los angeles |
| State/province |
california |
| ZIP/Postal code |
90095-3075 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE145813 |
Effect of HOXB13 overexpression on osteogenic differentiation in mouse embryonic fibroblasts (MEFs) |
|
| Relations |
| BioSample |
SAMN14170058 |
| SRA |
SRX7789756 |
