|
| Status |
Public on Jul 14, 2017 |
| Title |
Right upper quadrant metastasis, Shrinking |
| Sample type |
RNA |
| |
|
| Source name |
Shrinking right upper quadrant metastasis resected 6 years after primary tumor and after 12 different chemotherapy drugs
|
| Organism |
Homo sapiens |
| Characteristics |
gender: female
tissue: Right Upper Quadrant
condition: Malignant
tumor type: High grade serous ovarian cancer
tumor stage: Metastasis
sample type: FFPE
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from FFPE samples using the RecoverAll Total Nucleic Acid Isolation from Thermo Fisher Scientific (Catalog Number: AM1975).
|
| Label |
biotin
|
| Label protocol |
Labeling was performed using the following protocol: "GeneChip WT Pico Reagent Kit Manual Target Preparation for GeneChip Whole-Trascript Expression Arrays".
|
| |
|
| Hybridization protocol |
Hybridization was performed using the following protocol: "GeneChip WT Pico Reagent Kit Manual Target Preparation for GeneChip Whole-Transcript Expression Arrays".
|
| Scan protocol |
The Affymetrix GCS3000 scanner was used along with Affymetrix GeneChip Command Console software for imaging processing.
|
| Description |
RUQ-1-4
Gene expression data from right upper quadrant metastasis
|
| Data processing |
Affymetrix Expression Console software version 1.4.1.46 was used for primary analysis, and SST-RMA was used as the processing algorithm. To define whether a gene was expressed or not we used the Affymetrix Transcriptome Analysis Console version 3.1.0.5 and implemented an alternative-splicing analysis, which gives an Expressed column with True or False values. For genes for which this approach gives an ambiguous result (e.g. since some genes have more than one probe aligning to it, if one probe gives True and the other False), then we used the median expression level (accross probes) of the SRY gene for each sample as threshold for that tumor sample. For indivudal gene expression level analysis, we first filtered the probes that hybridize with protein coding genes. Then we assigned the median gene expression value for each gene. Then we normalize the gene expression values using the normalize.loess function of the R package affy, and we selected the distributions that were not statistically significant between them. The gene expression levels obtained were then compared between samples. Here we provide the CHP files with the SST-RMA normalization alone, but we can provide the SST-RMA+loess normalize gene expression values upon request. The HeLa cell lines were used only by Affymetrix as their internal controls and were not incorporated in any analysis in the study.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = Clariom_D_Human
program-name = Expression Console
program-version = 1.4.1.46
|
| |
|
| Submission date |
Dec 22, 2016 |
| Last update date |
Jan 25, 2018 |
| Contact name |
Martin Lee Miller |
| E-mail(s) |
martin.miller@cruk.cam.ac.uk
|
| Phone |
+44 (0) 1223 769 657
|
| Organization name |
University of Cambridge
|
| Department |
Cancer Research UK Cambridge Institute
|
| Lab |
Cancer Systems Biology
|
| Street address |
Robinson Way
|
| City |
Cambridge |
| State/province |
Cambridgeshire |
| ZIP/Postal code |
CB2 0RE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL23126 |
| Series (1) |
| GSE92780 |
Heterogeneous tumor-immune microenvironments among differentially growing metastases in an ovarian cancer patient |
|
