|
| Status |
Public on Mar 14, 2020 |
| Title |
NAC31A |
| Sample type |
RNA |
| |
|
| Source name |
Peritoneal box
|
| Organism |
Homo sapiens |
| Characteristics |
treatment status: pre-treatment
gender: Female
tissue: Peritoneal box
condition: Malignant
tumor type: High grade serous ovarian cancer
tumor stage: IIIC
sample type: FFPE
|
| Treatment protocol |
Samples with A suffix did not receive any treatment. Samples with the B suffix, were collected after patients were treated with neoadjuvant chemotherapy (cisplatin + taxane) as the standard of cancer in HGSOC requires.
|
| 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 |
Gene expression data
|
| 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 a threshold for that tumor sample. For indivdual 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, and we normalized the gene expression values using the "normalize.loess" function of the R package "affy". We selected the distributions that were not significantly different between them. The gene expression levels obtained were then compared between samples. Here we provide the CHP files and gene level values after the SST-RMA normalization only, but we can provide the SST-RMA+loess normalized 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.
|
| |
|
| Submission date |
Mar 13, 2020 |
| Last update date |
Mar 14, 2020 |
| 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 (2) |
| GSE146963 |
Unraveling Tumor-Immune Heterogeneity in Advanced Ovarian Cancer Uncovers Immunogenic Effect of Chemotherapy [Pre&Post-Tx] |
| GSE146965 |
Unraveling Tumor-Immune Heterogeneity in Advanced Ovarian Cancer Uncovers Immunogenic Effect of Chemotherapy |
|
