|
| Status |
Public on Apr 21, 2016 |
| Title |
Patient028-time2 |
| Sample type |
protein |
| |
|
| Source name |
serum
|
| Organism |
Homo sapiens |
| Characteristics |
database.no.: LARC-RRP-028
sampling point: 2
sampling date: 2006-08-25
t stage: 3
n stage: 2
inclusion date: 2006-07-26
date of local relapse: NA
date of metastatic disease: NA
censoring date: 2013-08-08
trg score: 2
ypt stage: 1
ypn stage: 0
ctcae grade diarrhea at crt completion: 0
slide block: 1
hybridization order: 49
hybridization date: 2012-05-14
barcode: 14340539
pmt: 30
slide print batch: 4
|
| Extracted molecule |
protein |
| Extraction protocol |
Serum samples.
|
| Label |
biotin
|
| Label protocol |
Serum extracted from peripheral blood were assayed on the RayBio Biotin Label-Based Human Antibody Array1 L Series 507 (Cat#AAH-BLG-1-4, RayBiotech Inc, Atlanta, GA, US) according to the manufactures protocol. In brief, 20 µl of the serum samples were diluted 1:5 in PBS and dialyzed over night (ON) at 4C. The following day the samples were labeled with biotin, dialyzed (ON at 4C) and stored at -80C until further processing.
|
| |
|
| Hybridization protocol |
Hybridization of samples were done on glass chips, consisting of two sub-arrays that were pre-treated according to the manufactures instructions. The biotin labeled samples were diluted 1:20 and added onto the glass chips followed by ON incubation at 4C. The following day the glass slides were washed and incubated with a Cy3-conjugated streptavidin for two hours before they were washed again, dried and developed. See manufacturer´s manual for more, http://www.raybiotech.com/files/manual/Antibody-Array/AAH-BLG-1.pdf.
|
| Scan protocol |
The hybridized arrays were scanned for fluorescence using the Agilent scanner G2505C. The scans were obtained with photomultiplier tube (PMT) settings at 60% of maximal intensity. Tiff images were made from these scans
|
| Description |
Sample name: LARC-RRP-028-2
Raw data file: 14340539_30%pmt_LARC_STUDIE_S01.gpr (see slide "Block" 1)
|
| Data processing |
The tiff images were segmented using GenePix 6.0, i.e. converted from image spots to numerical values of grey scale levels per spot. There is one GenePix result file (gpr-file) per slide (or chip), and each slide consists of two arrays (samples), thus there are measurements from two samples in each gpr-file. The Slide block column in the sample annotation denotes whether this sample is hybridized to the first block (rows 1-1050 in gpr) or to the second block(rows 1051-2100 in gpr). The gpr-files were read into the R statistical environment using the limma-package. The F532 Median column was chosen as signal without background subtraction. About 10% of the measurements were judged as unreliable and removed. Data was normalized between arrays with global median normalization and print-batch normalized with the ComBat method without using covariates. See pre-process-script attached as supplementary file for details.
Replicate spots were averaged. Each sample´s values were adjusted to make a common median across samples, i.e global median normalization. Batch adjustment was performed with ComBat, with slide print batch as batch and no covariate. See pre-process-script attached as supplementary file (preprocess_geo.r) for details.
|
| |
|
| Submission date |
Feb 04, 2015 |
| Last update date |
Apr 21, 2016 |
| Contact name |
Anne Hansen Ree |
| E-mail(s) |
a.h.ree@medisin.uio.no
|
| Organization name |
Akershus University Hospital
|
| Department |
Division of Medicine - Oncology
|
| Street address |
Sykehusveien 25
|
| City |
Lørenskog |
| ZIP/Postal code |
1478 |
| Country |
Norway |
| |
|
| Platform ID |
GPL19737 |
| Series (1) |
| GSE65622 |
Locally Advanced Rectal Cancer - Radiation Response Prediction Study - Serum Proteins |
|
