|
| Status |
Public on May 23, 2024 |
| Title |
Saos2, 40 nM Roc, biol replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Saos2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Saos2
cell type: osteosarcoma
genotype: WT
treatment: 40 nM Roc
treatment: 24 hours
|
| Treatment protocol |
Cells were treated with 0.04% DMSO as a vehicle control or 1x growth-inhibitory IC50 concentration of Roc or DDR for 24 hours. Cells were harvested by scraping down on ice, cell pellets rinsed with cold PBS, and snap-frozen on dry ice
|
| Growth protocol |
Human osteosarcoma cell lines MG-63 and Saos2 were grown in standard 10-centimeter dishes in high-glucose DMEM with glutamine and 10% heat-inactivated FBS at 37° C in a 5% CO2 humifiied incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Maxwell RSC simplyRNA Cells kit (Cat. #AS1390; Promega).
Illumina TruSeq stranded mRNA kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Non-polyA-tailed RNA species, including mitochondrial transcripts, rRNAs, and tRNAs, were filtered out using Bowtie 2 (v.2.5.1).
STAR v2.7.3a was used to align reads to the GRCh37/hg19 reference human genome (released February 2009). Raw read counts were estimated via HTSeq v0.11.225 and normalized with the DESeq2 package26. Cufflinks v2.2.1 was used to estimate the gene expression levels27, and the values were reported as FPKM (fragments per kilobase per million) units per gene. DESeq2 was employed to estimate the differential expression of gene counts relative to the DMSO-treated controls.
Raw read counts were estimated via HTSeq v0.11.2 and normalized with the DESeq2 package. Cufflinks v2.2.1 was used to estimate the gene expression levels27, and the values were reported as FPKM (fragments per kilobase per million) units per gene. DESeq2 was employed to estimate the differential expression of gene counts relative to the DMSO-treated controls.
Cufflinks v2.2.1 was used to estimate the gene expression levels, and the values were reported as FPKM (fragments per kilobase per million) units per gene. DESeq2 was employed to estimate the differential expression of gene counts relative to the DMSO-treated controls.
DESeq2 was used to estimate the differential expression of gene counts relative to the DMSO-treated controls.
Assembly: GRCh37/hg19 reference human genome (released February 2009)
Supplementary files format and content: Excel (xlsx) file containing the raw and normalized counts (in FPKM) for all replicates
Supplementary files format and content: Excel (xlsx) file containing the log2-fold change (log2FC) of DDR- and Roc-treated cells compared to DMSO-treated control cells, statstics including P-values and adjusted P-values, and raw and normalized FPKM counts for replicates
|
| |
|
| Submission date |
May 18, 2024 |
| Last update date |
May 23, 2024 |
| Contact name |
Long-Sheng Chang |
| E-mail(s) |
Long-Sheng.Chang@nationwidechildrens.org
|
| Phone |
6143552658
|
| Organization name |
Research Institute at Nationwide Children's Hospital
|
| Department |
Center for Childhood Cancer
|
| Lab |
Chang Lab
|
| Street address |
575 Children's Crossroad, WC-5574, Ctr for Childhood Cancer & Dept of Pediatrics, Nationwide Children's Hosp & The Ohio State U
|
| City |
Columbus |
| State/province |
Ohio |
| ZIP/Postal code |
43215 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE267810 |
Anti-tumor effects of the eIF4A Inhibitor didesmethylrocaglamide and its derivatives in human and canine osteosarcomas |
|
| Relations |
| BioSample |
SAMN41447735 |
| SRA |
SRX24600914 |
