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Sample GSM142412 Query DataSets for GSM142412
Status Public on Oct 28, 2006
Title BCell_lymphoma_transitional_sample3
Sample type RNA
 
Source name transitional E-mu-BRD2 mediated lymphoma
Organism Mus musculus
Characteristics genotype: E-mu-BRD2
cell-type: lymphoma_transitional
splenomegaly: mild
Ig clonality: oligoclonal
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with the guanidinium thiocyanate method, extracted with acid phenol and precipitated from 2-propanol.
Label biotin
Label protocol Using a poly-dT primer incorporating a T7 promoter, double-stranded cDNA was synthesized from 10 micrograms total RNA using a cDNA synthesis kit (SuperScript double-stranded cDNA synthesis kit; Invitrogen, Carlsbad, CA). Double-stranded cDNA was purified by phenol/chloroform extraction using a Phase-Lock Gel (PLG Heavy Brinkmann Instruments, Westbury, NY) followed by ethanol precipitation. Biotin-labeled cRNA was generated from the double-stranded cDNA template though in-vitro transcription with T7 polymerase, and a nucleotide mix containing biotinylated CTP and UTP (Enzo RNA Transcript Labeling Kit; Enzo Diagnostics, Farmingdale, NY). The biotinylated cRNA was purified using RNeasy affinity columns (Qiagen, Valencia, MD).
 
Hybridization protocol For each GeneChip, 20 micrograms of the labeled product was fragmented in 40 mM Tris-acetate, pH 8.1, 100mM KOAc, 30mM MgOAc, for 35 minutes at 94 degrees-Celsius, to an average size of 35 to 200 bases. 15 micrograms of this fragmented, biotinylated cRNA, along with hybridization controls supplied by the manufacturer (Affymetrix), were hybridized to the arrays for 16 hours at 45 degrees-Celsius and 60 rpm. Arrays were washed and stained according to the standard Antibody Amplification for Eukaryotic Targets protocol (Affymetrix).
Scan protocol The stained GeneChip arrays were scanned at 488 nm using an Affymetrix Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA).
Description flow-cytometry: ND; clinical-signs: failure to nest
Data processing MAS5.0, target intensity = 500
 
Submission date Oct 25, 2006
Last update date Mar 18, 2009
Contact name Marc E. Lenburg
E-mail(s) mlenburg@bu.edu
Phone 617-414-1375
Fax 617-414-1646
URL http://gg.bu.edu
Organization name Boston University School of Medicine
Department Genetics and Genomics
Street address 715 Albany Street, E613B
City Boston
State/province MA
ZIP/Postal code 02130
Country USA
 
Platform ID GPL8321
Series (1)
GSE6136 Expression data from murine BRD2-mediated lymphomas

Data table header descriptions
ID_REF
VALUE MAS5-calculated Signal Intensity
ABS_CALL a call that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)

Data table
ID_REF VALUE ABS_CALL
AFFX-BioB-5_at 932.8 P
AFFX-BioB-M_at 1714 P
AFFX-BioB-3_at 1175.9 P
AFFX-BioC-5_at 2066.3 P
AFFX-BioC-3_at 2114.1 P
AFFX-BioDn-5_at 2595 P
AFFX-BioDn-3_at 8898.1 P
AFFX-CreX-5_at 24142.3 P
AFFX-CreX-3_at 29518.3 P
AFFX-DapX-5_at 1662.9 P
AFFX-DapX-M_at 3928.9 P
AFFX-DapX-3_at 5109.1 P
AFFX-LysX-5_at 264.8 P
AFFX-LysX-M_at 329.4 P
AFFX-LysX-3_at 685.7 P
AFFX-PheX-5_at 369.7 P
AFFX-PheX-M_at 519.7 P
AFFX-PheX-3_at 541.8 P
AFFX-ThrX-5_at 574 P
AFFX-ThrX-M_at 807 P

Total number of rows: 22690

Table truncated, full table size 421 Kbytes.




Supplementary file Size Download File type/resource
GSM142412.CEL.gz 1.8 Mb (ftp)(http) CEL

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