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Sample GSM2197923 Query DataSets for GSM2197923
Status Public on Jun 28, 2017
Title control2
Sample type RNA
 
Source name age-matched healthy controls
Organism Homo sapiens
Characteristics gender: female
sample type: blood
Treatment protocol The unprocessed whole blood sample was immediately stored at -80°C until further analysis.
Growth protocol Blood samples were collected from 12 females, including 6 breast cancer patients and 6 healthy age-matched female volunteers who served as controls for this study, at Qilu Hospital of Shandong University (Shandong, China). All patients had histologically confirmed breast cancer. The control blood samples were collected from healthy women with no current or previous malignancy, or inflammatory condition. All blood samples were collected before any therapeutic procedures, such as surgery, chemotherapy and radiotherapy, were performed.
Extracted molecule total RNA
Extraction protocol Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
Label Cy3
Label protocol Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.
 
Hybridization protocol Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner.
Scan protocol Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon).Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.
Description healthy controls
Data processing Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization.All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes were identified through Fold Change filtering.
 
Submission date Jun 13, 2016
Last update date Jun 28, 2017
Contact name Ya-Wen Wang
E-mail(s) wangyawen@sdu.edu.cn
Organization name Shandong University
Street address Wen Hua Xi Road 107
City Jinan
ZIP/Postal code 250012
Country China
 
Platform ID GPL22003
Series (1)
GSE83270 Identification of microRNA biomarkers in the blood of breast cancer patients based on microRNA profiling

Data table header descriptions
ID_REF
VALUE Quantile and RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
46202 10.20935961
146014 0.017241379
146185 0.820197044
17415 0.017241379
42485 0.024630542
42545 0.027093596
17283 0.009852217
17306 0.068965517
27537 3.236453202
42882 0.009852217
17519 0.039408867
17623 0.041871921
17655 0.073891626
42897 0.032019704
17541 0.206896552
17358 0.753694581
42773 0.21182266
46818
42466 0.231527094
17657 0.022167488

Total number of rows: 2158

Table truncated, full table size 36 Kbytes.




Supplementary file Size Download File type/resource
GSM2197923_control2.gpr.gz 930.8 Kb (ftp)(http) GPR
Processed data included within Sample table
Processed data are available on Series record

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