|
| Status |
Public on Feb 16, 2019 |
| Title |
4T1-HD-1 |
| Sample type |
RNA |
| |
|
| Source name |
4T1 mammary carcinoma cells in HD collagen gel
|
| Organism |
Mus musculus |
| Characteristics |
cell line: 4T1 mammary carcinoma cell line
gel density: 3.5 mg/mL
|
| Treatment protocol |
Density of collagen in the gel was changed between 2 mg/mL (LD) and 3.5 mg/mL HD. For information on collagen gel protocol see Burkel et al. JOVE 2016
|
| Growth protocol |
Gels were cultured 5 days in a 5% CO2 37 C incubator in RPMI 1640 media +10% FBS. Media was changed on the evening of day 3.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
Fragment ss cDNA end-terminus labeled with biotin following procedure outlined Affymetrix GeneChip WT Plus Reagent Kit Manual
|
| |
|
| Hybridization protocol |
All samples hybridized to Mouse Transcriptome 1.0 ST arrays at 45°C for 16 hrs O/N following all procedures outlined in Affymetrix GeneChip WT Plus Reagent Kit User Guide (Rev.2)
|
| Scan protocol |
GeneChips post processed on the AFX Fluidics 450 Station according to all AFX protocols and procedures defined for the Mouse Transcriptome 1.0 ST Array (FS450_0001) GC scanned on the GC3000 G7 Scanner (Serial #50208130)
|
| Description |
Gene expression data from 4T1 cells cultured in a HD collagen matrix
|
| Data processing |
Data extracted and processed using Affymetrix Command Console version 4.0.0.1567G. The data were analyzed with RMA:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
|
| |
|
| Submission date |
Feb 17, 2016 |
| Last update date |
Feb 16, 2019 |
| Contact name |
Patricia Keely |
| E-mail(s) |
[email protected]
|
| Phone |
6082655094
|
| Organization name |
University of Wisconsin-Madison
|
| Street address |
1111 Highland Ave
|
| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL20775 |
| Series (1) |
| GSE78022 |
Expression data from 4T1 cells in low density (LD = 2 mg/mL) or high density (HD = 3.5 mg/mL) collagen gels |
|
