|
| Status |
Public on May 12, 2020 |
| Title |
Primary CRC tissues from CRC patient 2 |
| Sample type |
RNA |
| |
|
| Source name |
primary colorectal cancer tissues
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: Male
age: 61y
tissue: colorectal cancer
tumor location: Colon
regional lymph nodes metastasis: Yes
Stage: III
recurrence after operation: Yes
status after 5 years: Dead
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from tissues using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer(Thermo Fisher Scientific, Waltham, MA) and RNA integrity was assessed by standard denaturing agarose gel electrophoresis and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Cyanine-3 (Cy3) labeled cRNA was prepared from 1ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop NanoDrop-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
One μg of each Cy3-labeled, linearly amplified cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.
|
| Scan protocol |
The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).
|
| Description |
histological diagnosis confirmed
|
| Data processing |
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 6 out of 12 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs between two samples were identified through Fold Change filtering. Differentially expressed LncRNAs and mRNAs between two groups were identified through Volcano Plot filtering.
|
| |
|
| Submission date |
Jul 29, 2016 |
| Last update date |
May 12, 2020 |
| Contact name |
Xin Zhang |
| E-mail(s) |
zhangxin_21@126.com
|
| Organization name |
Qilu Hospital, Shandong University
|
| Street address |
107 Wenhua Xi Road
|
| City |
Jinan |
| State/province |
Shandong |
| ZIP/Postal code |
250012 |
| Country |
China |
| |
|
| Platform ID |
GPL16956 |
| Series (1) |
| GSE84983 |
Long noncoding RNA (lncRNA) expression profiles in colorectal cancer tissues and paired adjacent normal tissues |
|
