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Sample GSM50987 Query DataSets for GSM50987
Status Public on Jun 01, 2006
Title U133Plus-P008 (TT2 pre-treatment)
Sample type RNA
 
Source name pre-treatment bone marrow
Organism Homo sapiens
Characteristics [SURIND=0 (Indicator of disease-related death; integer, 0=alive or death by other cause, 1=disease related death, na=death cause undetermined)]

[SURTIM=66.67 (Follow-up time in months from Pre-Treatment baseline; integer)]

[PCTCELLS=0%/0%/100%/0%/0% (Percentage of cells with 0 copy/1 copy/2 copies/3 copies/4+ copies; percentage)]

[AMPIND=2 copies (Indicator of FISH 1q21 Amplification; string, na=not available)]

[CONTAMIND=1 (Indicator of myeloid cell and normal plasma cell contamination; integer, 0=NO, 1=YES, na=Not Available)]

[Subgrp7=MY]

Extracted molecule total RNA
Extraction protocol Total RNA was isolated with RNeasy Mini Kit (Qiagen, Valencia, CA).
Label biotin
Label protocol As recommended by manufacturer
 
Hybridization protocol As recommended by manufacturer
Scan protocol As recommended by manufacturer
Description Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA)
More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining
The clinic survival follow-up is through November 5, 2004
Disease-related survival: Deaths were coded as disease-related according to a physician chart review. Three deaths had not been coded as of the time of the analysis and these corresponding to the three missing status indicators in the data set. Non-disease related deaths are competing risks, so distribution estimates should use cumulative incidence of disease-related death as the outcome, rather than survival
Censored data analysis: Analyses using the status indicator as a grouping variable directly are not recommended. Tests for censored data can be applied, gene-by-gene, as in the published analysis, or disease-related deaths can be matched to a random sample of longer survivors
Keywords = CKS1B in Multiple Myeloma
Data processing All data used in these analyses were derived with the Affymetrix Microarray Suite GCOS1.1 software.

CEL files are available upon request via a Materials Transfer Agreement. Please contact Dr. John Shaughnessy for details.

 
Submission date May 13, 2005
Last update date Apr 01, 2010
Contact name Shaughnessy Jr. John
E-mail(s) shaughnessyjohn@uams.edu
Phone (501)296-1503 1410
Organization name Myeloma Institute for Research and Therapy
Department
Lab Donna D. and Donald M. Lambert Laboratory of Myeloma Genetics
Street address 4301 West Markham St., Slot 776
City Little Rock
State/province AR
ZIP/Postal code 72205
Country USA
 
Platform ID GPL570
Series (2)
GSE2658 Gene Expression Profiles of Multiple Myeloma
GSE4204 Gene Expression Profiles of Multiple Myeloma Before Treatment

Data table header descriptions
ID_REF probset name
VALUE A quantitative measure of the relative abundance of a transcript
ABS_CALL A qualitative measurement indicating if a given transcript is detected (Present), not detected (Absent), or marginally detected (Marginal)

Data table
ID_REF VALUE ABS_CALL
1552256_a_at 966.90002 P
1552257_a_at 2149.8999 P
1552258_at 279.29999 A
1552261_at 36.700001 A
1552263_at 276.5 A
1552264_a_at 254.60001 A
1552266_at 53.299999 A
1552269_at 9.3000002 A
1552271_at 31.1 A
1552272_a_at 238.39999 P
1552274_at 388.89999 A
1552275_s_at 132.2 A
1552276_a_at 58.299999 A
1552277_a_at 1230.5 P
1552278_a_at 153.7 A
1552279_a_at 470.60001 P
1552280_at 182.89999 A
1552281_at 154.7 A
1552283_s_at 257.39999 P
1552286_at 454.0 P

Total number of rows: 54675

Table truncated, full table size 1115 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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