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Sample GSM622239 Query DataSets for GSM622239
Status Public on Nov 13, 2010
Title CNSlymphoma_rep6
Sample type RNA
 
Source name CNS lymphoma
Organism Homo sapiens
Characteristics tissue: Brain
Treatment protocol Fresh-frozen samples were obtained from 14 patients including 7 primary central nervous system diffuse large B cell lymphoma and 7 normal lymph nodes.
Extracted molecule total RNA
Extraction protocol RNA was extracted from 14 fresh-frozen tumor samples using standard proteinase K/RNAse treatment and phenol-chloroform extraction method. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol 0.5 ug of total RNA was amplified and labeled using Agilent Quick Amp Labeling Kit. After labeling, cRNA was purified with Qiagen’s RNeasy Mini-spin columns (QIAGEN, Germantown, MD) and quantified using NanoDrop ND-1000 UV-VIS Spectrophotometer for cyanine 3 dye concentration, RNA absorbance ratio (260 nm/280 nm), and cRNA concentration.
 
Hybridization protocol Cyanine 3-labled linearly amplified cRNA was mixed with 10X blocking agent, nuclease-free water, and 25X fragmentation buffer provided in the Agilent Gene Expression Hybridization Kit (Agilent Technologies), and incubated for 30 min at 60oC to fragment RNA. After adding 2X GEx hybridization buffer Hi-RPM, the amplified fragmented RNA was hybridized on a 4 x 44K Whole Human Genome Oligo Microarray Chip (Agilent Technologies) containing 44,000 cDNA clones using a SureHyb DNA Microarray Hybridization Chamber in a DNA Microarray Hybridization Oven (Agilent Technologies) at 10 rpm, 65oC for 17 hours.
Scan protocol Slides were scanned with an Agilent DNA microarray scanner (Agilent Microarray Scanner–G2565BA, Agilent Technologies).
Description Gene expression
Data processing Feature Extraction Software v9 (Agilent Technologies) was used to extract and analyze the signals. To validate the amplification process, amplified and unamplified RNAs were labeled, hybridized and compared.
 
Submission date Nov 12, 2010
Last update date Nov 12, 2010
Contact name Chang Ohk Sung
Organization name Asan Medical Center
Department Pathology
Street address Song-Pa gu,Pung-nap dong
City Seoul
ZIP/Postal code 05505
Country South Korea
 
Platform ID GPL6480
Series (2)
GSE25297 Genome-wide gene expression comparison (primary central nervous system lymphoma (PCNSL) vs normal lymph node)
GSE25299 Genomic profiling combined with gene expression profiling in primary central nervous system lymphoma

Data table header descriptions
ID_REF
VALUE Normalized signal intensity after VSN normalization method.

Data table
ID_REF VALUE
A_24_P66027 6.273322856
A_32_P77178 1.626968407
A_23_P212522 5.967163549
A_24_P934473 3.008708884
A_24_P9671 8.689526062
A_32_P29551 2.71639381
A_24_P801451 5.369234753
A_32_P30710 9.77000471
A_32_P89523 2.78477991
A_24_P704878 1.663942858
A_32_P86028 10.70933856
A_24_P470079 2.879986782
A_23_P65830 8.427710882
A_24_P595567 4.055337688
A_24_P391591 7.085071983
A_24_P799245 1.840717023
A_24_P932757 1.939749568
A_24_P835500 6.374910736
A_23_P54340 2.759627331
A_23_P67555 2.308335764

Total number of rows: 36922

Table truncated, full table size 885 Kbytes.




Supplementary file Size Download File type/resource
GSM622239.txt.gz 1.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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