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Sample GSM1068111 Query DataSets for GSM1068111
Status Public on Nov 01, 2013
Title MPI-913_GC_B_cells
Sample type RNA
 
Source name GC_B_cells
Organism Homo sapiens
Characteristics type: GC_B_cells
tumor_cell_line: NA
tumor: NA
Extracted molecule total RNA
Extraction protocol GC B cells were isolated from suspended tonsillar cells of healthy individuals. For the isolation, FACS sorting employing antibodies against CD20 and CD38 was used. RNA was isolated using RNeasy Mini Kit (QIAGEN) and the concentration was determined photometrically (NanoDrop). The quality of the RNA was assessed based on the presence of the tht 18S and 28S tRNA by analysis of an aliquot in the Agilent BioAnalyzer (Agilent)
Label biotin
Label protocol For Affymetrix GeneChip hybridization, 5 microgram of total RNA was employed to generate a double-stranded cDNA with the help of the INVITROGEN Superscript kit. After removal of small molecular components (Affymetrix Clean-up Module), Biotin-labelled cRNA was synthesized by application of the ENZO Labeling kit (T7 RNA polymerase). The concentration of the produced cRNA was determined photometrically (NanoDrop) and the size range of the labelled products was evaluated by BioAnalyzer (Agilent) measurement before and after fragmentation
 
Hybridization protocol Affymetrix hybridization was carried on U133A GeneChips according to the manufacturer's recommendations. In brief, 15 microgram of Biotin-labelled and fragmented cRNA were mixed with 20x GeneChip Eukaryotic Hybridization Control (Affymetrix) and supplemented with B2 control oligonucletide, salmon sperm DNA, acetylated bovine serum albumin and hybridization buffer and water making up a total volume of 300 microliter
Scan protocol After hybridization of night (16 hours, 45° C) the hybridization mixture was removed from the GeneChip and washing and staining of the GeneChips was performed in a fluidics station (Affymetrix). The detection of the Biotin-labeled cRNA was mediated by a streptavidin-phycoerythrin complex. The measurement of the fluorescence intensity was carried out in an Agilent scanner (GA2500)
Data processing Probe level normalization was done using the calibration and variance stabilization method by Huber et al. (Bioinformatics 2002, PMID: 12169536). Probe-set summarization was performed using the median polish method on the normalised data (Irizarry et al. Nucleic Acids Research 2003, PMID: 12582260)
 
Submission date Jan 23, 2013
Last update date Sep 01, 2016
Contact name Maciej Rosolowski
E-mail(s) maciej.rosolowski@imise.uni-leipzig.de
Organization name Institute for Medical Informatics, Statistics and Epidemiology (IMISE)
Street address Härtelstr. 16-18
City Leipzig
ZIP/Postal code 04107
Country Germany
 
Platform ID GPL96
Series (1)
GSE43677 Massive Transcriptional Perturbation in Subgroups of Diffuse Large B-cell Lymphomas
Relations
Reanalyzed by GSE86363

Data table header descriptions
ID_REF
VALUE Normalized and summarized probeset expression value on additive arsinh (log-like) scale

Data table
ID_REF VALUE
1007_s_at 8.719696407
1053_at 8.64881843
117_at 7.94483078
121_at 9.727579603
1255_g_at 6.537294393
1294_at 8.837174797
1316_at 7.698711731
1320_at 7.075221086
1405_i_at 6.795090248
1431_at 6.332583974
1438_at 8.035903801
1487_at 8.367821679
1494_f_at 8.052278825
1598_g_at 9.456246661
160020_at 9.082183483
1729_at 8.517323339
1773_at 7.517742242
177_at 7.217764892
179_at 9.95795483
1861_at 7.452564009

Total number of rows: 22283

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM1068111_MPI-913.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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