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Sample GSM1252033 Query DataSets for GSM1252033
Status Public on Oct 29, 2013
Title bone marrow_case_rep2
Sample type RNA
Source name case 2
Organism Homo sapiens
Characteristics tissue: bone marrow
gender: female
age: 87y
disease state: myelodysplastic syndrome
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 cases
Data processing The scanned images were analyzed with Feature Extraction Software (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
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

Data table header descriptions
VALUE Normalized signal intensity

Data table
A_23_P326296 7.88
A_24_P287941 7.19
A_24_P325046 6.57
A_23_P200404 11.87
A_19_P00800513 7.78
A_23_P15619 2.62
A_33_P3402354 4.88
A_33_P3338798 2.68
A_32_P98683 10.24
A_23_P137543 10.17
A_19_P00803040 6.04
A_23_P117852 13.59
A_33_P3285585 2.60
A_24_P328231 5.12
A_33_P3415668 2.59
A_23_P73609 2.41
A_24_P186124 9.16
A_23_P369983 9.90
A_23_P325676 4.56
A_24_P37441 9.70

Total number of rows: 42405

Table truncated, full table size 776 Kbytes.

Supplementary file Size Download File type/resource
GSM1252033_5157.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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