|
| Status |
Public on Jul 01, 2016 |
| Title |
Patient 7_tumor |
| Sample type |
RNA |
| |
|
| Source name |
Patient 7_tumor
|
| Organism |
Homo sapiens |
| Characteristics |
lcm_location: tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Depending on the amount of available tissue, laser capture microdissection (LCM) was performed on 30 to 50 sections (5μm) of frozen breast cancer needle core biopsies using the Arcturus PixCell IIe microscope. RNA from LCM-captured tumor and adjacent stromal cells was isolated using the RNAqueous-Micro kit (Ambion). RNA was validated for quality and subsequent cDNA synthesis and amplification performed (on 10 ng of total RNA)
|
| Label |
biotin
|
| Label protocol |
Affymetrix protocol
|
| |
|
| Hybridization protocol |
The reactions were run through first strand and second strand synthesis, followed by two rounds of single primer isothermal amplification (NuGEN) amplification. The amplified cDNA product was hybridized to the Affymetrix HuGene 1.0ST array.
|
| Scan protocol |
Affymetrix Gene Chip Scanner
|
| Data processing |
Raw Affymetrix Human Gene CEL files were normalized using the Robust MultiChip Averaging (RMA) algorithm implemented in the Bioconductor package Affy. The probes were annotated using Bioconductor package hugene10sttranscriptcluster.db and the normalized, log2-transformed gene level expression data used for further analysis.
|
| |
|
| Submission date |
May 24, 2016 |
| Last update date |
Jul 01, 2016 |
| Contact name |
Brian David Lehmann |
| E-mail(s) |
brian.d.lehmann@vanderbilt.edu
|
| Organization name |
Vanderbilt University
|
| Department |
Biochemistry
|
| Street address |
2220 Pierce Ave
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL6244 |
| Series (1) |
| GSE81838 |
Gene expression anlaysis of laser-capture microdissected tumor and stroma from triple negative breast cancer |
|
