|
| Status |
Public on Jan 26, 2022 |
| Title |
BM cells with supernatant from 4T1 cells, replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
BM cells cultured for 4h with RPMI supplemented with 30% of supernatant from 4T1 mammary carcinoma cells
|
| Organism |
Mus musculus |
| Characteristics |
strain background: Balb/c
cell type: BM cells
treatment: stimulated by tumor conditioned media
|
| Treatment protocol |
cultured cells were lysed with TRIZOL and stored at -80◦C till RNA extraction was performed.
|
| Growth protocol |
BM cells were harvested from the femur and tibia of Balb/c mice, ACK red cell lysis, and then were cultured for 4 hours in the presence of RPMI (10%FCS), RPMI supplemented with 30% of filtered supernatant from confluent 4T1 cultured with complete media, or RPMI supplemented with 30% of filtered supernatant from confluent 4T1 cultured with complete media and BX471 and Maraviroc.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified using the miRNA easy kit from Qiagen and following the manufacture instruction.
|
| Label |
biotin
|
| Label protocol |
Affymetrix GeneChip WT Terminal Labeling Kit - sense-strand cDNA is fragmented with a combination of uracil DNA glycosylase and apurinic/apyrimidinic endonuclease 1 and its yield is further labeled by terminal deoxynucleotidyl transferase (TdT) with the Affymetrix® proprietary DNA Labeling Reagent that is covalently linked to biotin.
|
| |
|
| Hybridization protocol |
GeneChip® Hybridization, Wash, and Stain Kit - Following labeling, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 ST arrays. GeneChips were washed and stained (streptavidin,R-phycoerythrin conjugate and biotinylated anti-streptavidin) in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
Standard Affymetrix scanning procedures on a GeneChip® Scanner 3000 7G . Affymetrix GeneChip® Command Console® Software (AGCC)- used to view CEL file images.
|
| Description |
Gene expression data of Balb/c BM cells cultured for 4h with RPMI supplemented with 30% of supernatant from 4T1 mammary carcinoma cells
|
| Data processing |
RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization
|
| |
|
| Submission date |
Apr 14, 2020 |
| Last update date |
Jan 26, 2022 |
| Contact name |
Silvio Bicciato |
| E-mail(s) |
silvio.bicciato@unipd.it
|
| Phone |
+39-049-827-6108
|
| Organization name |
University of Padova
|
| Department |
Molecular Medicine
|
| Street address |
via U. Bassi 59/b
|
| City |
Padova |
| ZIP/Postal code |
35131 |
| Country |
Italy |
| |
|
| Platform ID |
GPL23092 |
| Series (1) |
| GSE148615 |
Molecular and cellular characterization of MDSC differentiated from the bone marrow of Balb/c mice with tumor conditioned media or tumor conditioned media and antagonists for CCR1 and CCR5 |
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