|
| Status |
Public on Aug 06, 2015 |
| Title |
Naïve rat UCMSC_48hr_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
naïve rat UCMSC, 48hrs
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: umbilical cord matrix mesenchymal stem cells (UCMSC)
co-culture: none
|
| Treatment protocol |
Mat B III cells (1.5x10^6 cells) were added in Transwell inserts for 48 hours.
|
| Growth protocol |
Rat UCMSC (1x10^5 cells) were seeded in defined medium in the bottom of a 10 cm Transwell culture dish and allowed to settle for 24 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from naïve and Mat B III co-cultured UCMSC cells using TRIzol® reagent (Invitrogen) using the standard manufacturer's protocol. Samples were assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Nano Chips (Aligent Technologies).
|
| Label |
biotin
|
| Label protocol |
Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791). In short, 0.5ug of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double-stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.
|
| |
|
| Hybridization protocol |
Standard Illumina protocol. In short, a total of 0.75ug of biotin-labeled cRNA was hybridized at 58 degrees C for 16 hours to Illumina's Rat Ref-12 v1 BeadChips (Illumina, San Diego, CA). Each BeadChip has ~22,000 well-annotated RefSeq transcripts with approximately 30-fold redundancy. The arrays were washed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-Cy3.
|
| Scan protocol |
Arrays were scanned at a resolution of 0.8um using the BeadStation 500 X from Illumina.
|
| Description |
MAT-1
Streptavidin-Cy3 bound to biotin-labeled cRNA.
|
| Data processing |
Data was extracted using the Illumina BeadStudio software 3.4.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below. Z-score = (raw value - avg)/std. Complete data including detection scores is supplied.
|
| |
|
| Submission date |
Jan 09, 2015 |
| Last update date |
Jun 22, 2020 |
| Contact name |
Supriyo De |
| Organization name |
NIA-IRP, NIH
|
| Department |
Laboratory of Genetics and Genomics
|
| Lab |
Computational Biology & Genomics Core
|
| Street address |
251 Bayview Blvd
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL17223 |
| Series (2) |
| GSE64838 |
Human umbilical cord matrix mesenchymal stem cells suppress the growth of breast cancer by expression of tumor suppressor genes [rat] |
| GSE64839 |
Human umbilical cord matrix mesenchymal stem cells suppress the growth of breast cancer by expression of tumor suppressor genes |
|
