|
| Status |
Public on Oct 29, 2013 |
| Title |
bone marrow_control_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
control 1
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow
gender: female
age: 49y
disease state: normal
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's
|
| Label |
cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
gene expression in controls
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.
|
| |
|
| Submission date |
Oct 28, 2013 |
| Last update date |
Oct 29, 2013 |
| Contact name |
xiaoqin wang |
| E-mail(s) |
wangxiaoqin@hotmail.com
|
| Organization name |
Huashan hospital
|
| Street address |
12 wulumuqi road central
|
| City |
Shanghai |
| ZIP/Postal code |
200040 |
| Country |
China |
| |
|
| Platform ID |
GPL14550 |
| Series (2) |
| GSE51757 |
Genome-wide profiling of DNA methylation and expression identifies CIMP in myelodysplastic syndrome [Agilent] |
| GSE51759 |
Genome-wide profiling of DNA methylation and expression identifies CIMP in myelodysplastic syndrome |
|
