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Sample GSM759021 Query DataSets for GSM759021
Status Public on Nov 25, 2011
Title T-cell ALL PICALM-MLLT10 fusion MLL_00208
Sample type RNA
 
Source name mononuclear cells after Ficoll purification
Organism Homo sapiens
Characteristics disease state: T-cell acute lymphoblastic leukemia
gene fusion: PICALM-MLLT10 fusion
genotype: EZH2-unmutated
lineage: PICALM-MLLT10 fusion
cell type: mononuclear cells
Extracted molecule total RNA
Extraction protocol The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.
Label Biotin
Label protocol For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).
 
Hybridization protocol Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
Scan protocol Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
Data processing The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)
 
Submission date Jul 12, 2011
Last update date Nov 26, 2011
Contact name Hans-Ulrich Klein
E-mail(s) h.klein@uni-muenster.de
Organization name Columbia University Medical Center
Department Neurology
Lab Center for Translational and Computational Neuroimmunology
Street address 622 W 168th St
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platform ID GPL570
Series (1)
GSE30599 EZH2 mutations can be detected in 23% of PICALM-MLLT10 (CALM-AF10) positive acute leukemias

Data table header descriptions
ID_REF
VALUE The Robust Multichip Average (RMA) expression measure

Data table
ID_REF VALUE
1007_s_at 7.802158932
1053_at 7.556053479
117_at 6.221922483
121_at 7.374148652
1255_g_at 2.750271147
1294_at 7.930042883
1316_at 6.35898457
1320_at 3.49751281
1405_i_at 10.88244989
1431_at 4.547734535
1438_at 4.818535286
1487_at 7.264613368
1494_f_at 5.355635804
1552256_a_at 6.809000001
1552257_a_at 6.999107861
1552258_at 5.568951767
1552261_at 3.801913851
1552263_at 7.169084442
1552264_a_at 7.82145098
1552266_at 2.831638362

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM759021_MLL_00208.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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