|
| Status |
Public on Mar 27, 2020 |
| Title |
WHEL ID 3348 |
| Sample type |
RNA |
| |
|
| Source name |
primary breast cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: primary breast cancer
|
| Treatment protocol |
Refer to https://library.ucsd.edu/dc/object/bb2493244b
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Unstained slides from archival specimens with ≥ 40% tumor cellularity were incubated at 65 °C for 30 minutes and deparaffinized using Citrisolv (Fisher Scientific, Pittsburgh, PA) followed by ethanol wash. Tumor tissues were macrodissected into RNAse-free microfuge tubes, and nucleic acids isolated using the Qiagen AllPrep FFPE kit (#80234). Manufacturer’s instructions were followed with the exception that the proteinase K digestion step was extended to an overnight incubation for the DNA isolation.
|
| Label |
n/a
|
| Label protocol |
See manufacturer's website http://www.nanostring.com for procedures
|
| |
|
| Hybridization protocol |
Transcript expression was quantified with 250 ng of total RNA using the NanoString nCounter analysis system with a custom miRGE CodeSet. Assay reactions were assembled per manufacturer’s specifications (NanoString Technologies, INC Seattle, WA).
|
| Scan protocol |
See manufacturer's website http://www.nanostring.com for procedures. Digital Analyzer was set to scan at 1155 FOV (fields of view).
|
| Description |
NanoString reporter probe
X2895383103_4
|
| Data processing |
R-NanoStringNorm package was used to normalize data. Code count normalization used 6 positive controls and background subtraction used 8 negative controls. All expression values were first log2 transformed. For mRNAs, five (ACTB, PSMC4, MRPL19, RPLPO, SF3A1) genes were used as housekeepers; the data matrix elements are relative gene expression values (log2 transformed) compared to log2 value of the geometric mean of the five house-keepers within each sample. For miRNAs, log2 expression values are presented. For miRNAs, quantile normalization was performed. Normalized datasets for both mRNA and miRNA are available on the series record. Sample data tables include data only for mRNAs.
|
| |
|
| Submission date |
Mar 17, 2020 |
| Last update date |
Mar 27, 2020 |
| Contact name |
Loki Natarajan |
| E-mail(s) |
loki@math.ucsd.edu
|
| Organization name |
University of California, San Diego
|
| Street address |
3855 Health Sciences DR
|
| City |
La Jolla |
| ZIP/Postal code |
92093-0901 |
| Country |
USA |
| |
|
| Platform ID |
GPL28286 |
| Series (1) |
| GSE147126 |
mRNAs and miRNAs for Women's Healthy Eating and Living (WHEL) Study |
|
