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Sample GSM379875 Query DataSets for GSM379875
Status Public on Dec 31, 2009
Title CN_AML Patient 1: Biallelic CEBPA mutation
Sample type RNA
 
Source name bone marrow mononuclear cells: AML, normal karyotype
Organism Homo sapiens
Characteristics tissue: bone-marrow mononuclear cells from CN-AML patient
genotype: Biallelic CEBPA mutation
Treatment protocol Pretreatment bone marrow or peripheral blood mononuclear cells from patients with newly diagnosed acute myeloid leukemia (AML) with a normal karyotype
Extracted molecule total RNA
Extraction protocol Mononuclear cells from bone marrow (BM) or peripheral blood (PB) were enriched by Ficoll gradient centrifugation. Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany). cDNA preparation and in vitro transcription were performed according to standard Affymetrix protocols.
Label biotin
Label protocol Biotin labeling of antisense cRNA was performed according to standard Affymetrix protocols
 
Hybridization protocol Sample hybridisation was performed for 16 hours according to standard Affymetrix protocols
Scan protocol Samples were scanned using an Affymetrix GeneChip scanner
Description CN_AML Patient 1
Data processing Normalization was performed using the variance stabilizing normalization algorithm. Custom chip definition files based on the GeneAnnot database were used for probe-set summarization, and probe set expression values were calculated by the median polish method. Quality control consisted of visual inspection of the array image for artifacts, assessment of RNA degradation plots, and inspection of rank-vs.-residual plots after normalization and probe set summarization.
 
Submission date Mar 12, 2009
Last update date Mar 12, 2009
Contact name Klaus H Metzeler
E-mail(s) klaus.metzeler@med.uni-muenchen.de
Organization name University of Munich
Department Department of Internal Medicine III
Lab Laboratory for Leukemia Diagnostics
Street address Marchioninistr. 15
City Munich
ZIP/Postal code 81377
Country Germany
 
Platform ID GPL8289
Series (1)
GSE15210 Gene expression profiles of mono- and biallelic CEBPA mutations in cytogenetically normal AML

Data table header descriptions
ID_REF
VALUE Expression values after variance stabilizing normalization and probe set summarization are provided.

Data table
ID_REF VALUE
GC00U921857_at 7.845602489
GC00U990452_at 6.582200172
GC00U990668_at 6.855464177
GC00U990680_at 7.855839516
GC00U990706_at 7.921872534
GC00U990780_at 8.327410443
GC00U990809_at 7.841457273
GC00U990811_at 7.39364344
GC00U990813_at 8.318171593
GC01M001136_at 8.702972627
GC01M001143_at 9.004240239
GC01M001236_at 9.86414787
GC01M001329_at 7.523833544
GC01M001646_at 7.470675914
GC01M001715_at 8.805896765
GC01M001748_at 11.02903116
GC01M001843_at 8.511834555
GC01M001916_at 8.943763836
GC01M002145_at 8.754071468
GC01M002285_at 8.549635556

Total number of rows: 11174

Table truncated, full table size 293 Kbytes.




Supplementary file Size Download File type/resource
GSM379875.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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