|
| Status |
Public on Jun 21, 2017 |
| Title |
HCC008N [lncRNA expression] |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
paired adjacent non-tumor liver tissue
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: HCC patient
subject id: HCC008
gender: Male
age: 39
tnm staging: T2N0M0
tissue: liver
tissue subytpe: paired adjacent non-tumor tissue
|
| Treatment protocol |
not applicable
|
| Growth protocol |
Tumor tissues and non-tumor liver tissues from 38 HCC patients
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNAs were extract with Qiagen Rneasy mini kit according to the manufacturer’s protocols.
|
| Label |
cy3, experiment
|
| Label protocol |
Double-strand cDNA (ds-cDNA) was synthesized from 5 μg of 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., 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/Cy5 labeling of cDNA, the NimbleGen Dual-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/Cy5-9mer 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.
|
| |
|
| Channel 2 |
| Source name |
adjacent non-tumor liver tissues
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: pooled reference
|
| Treatment protocol |
not applicable
|
| Growth protocol |
Tumor tissues and non-tumor liver tissues from 38 HCC patients
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNAs were extract with Qiagen Rneasy mini kit according to the manufacturer’s protocols.
|
| Label |
cy5, reference
|
| Label protocol |
Double-strand cDNA (ds-cDNA) was synthesized from 5 μg of 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., 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/Cy5 labeling of cDNA, the NimbleGen Dual-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/Cy5-9mer 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 |
HMicroarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3/Cy5 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA).
|
| Scan protocol |
Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000 B 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 intensity extraction.
|
| Description |
SAMPLE 46
|
| Data processing |
Raw signal intensities were normalized in RMA method by NimbleScan v2.5
|
| |
|
| Submission date |
Jul 05, 2016 |
| Last update date |
Jun 21, 2017 |
| Contact name |
Jin Song |
| E-mail(s) |
hanhui@stu.ahmu.edu.cn
|
| Phone |
18601331131
|
| Organization name |
Beijing Institute of Radiation Medicine
|
| Street address |
No.38 shengmingyuan Road
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL22109 |
| Series (2) |
| GSE84004 |
Integrative omics analysis in HCC samples [lncRNA expression] |
| GSE84006 |
Integrative omics analysis in HCC samples |
|
