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Sample GSM6149952 Query DataSets for GSM6149952
Status Public on Aug 31, 2024
Title peripheral blood, breast cancer-r1 (SN0006)
Sample type RNA
 
Source name peripheral blood
Organism Homo sapiens
Characteristics tissue: peripheral blood
gender: NaN
age: NaN
cancer dx: breast cancer
Treatment protocol Blood plasma was removed after centrifugation and a hypotonic buffer was added at a 3:1 volume ratio to lyse the red blood cells. The mixture was centrifuged to yield a pellet for subsequent total RNA isolation.
Growth protocol NA
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA from the pelleted cells was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, 701021 Rev. 4, Affymetrix).
 
Hybridization protocol Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.
Description Human peripheral blood collected in EDTA blood collection tubes, total RNA isolated from remaining cells collected after red blood cell lysis.
Gene expression data from peripheral blood cells collected after red blood cell lysis.
Data processing The data were analyzed with GeneChip Operating Software (GCOS) v1.1.1 using Affymetrix default analysis settings and global scaling (MAS 5.0) as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
 
Submission date May 14, 2022
Last update date Aug 31, 2024
Contact name Adam Dempsey
E-mail(s) [email protected]
Phone 804-655-6595
Organization name StageZero Life Sciences
Street address ​8751 Park Central Drive, Suite 200
City Richmond
State/province VA
ZIP/Postal code 23227
Country USA
 
Platform ID GPL570
Series (1)
GSE203024 Gene Expression Data from Human Peripheral Blood

Data table header descriptions
ID_REF
VALUE MAS5 signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 398.59 P 0.00110197
AFFX-BioB-M_at 584.455 P 0.000258358
AFFX-BioB-3_at 383.44 P 0.000340305
AFFX-BioC-5_at 947.234 P 0.000126798
AFFX-BioC-3_at 1129.97 P 4.42873e-05
AFFX-BioDn-5_at 2270.93 P 4.42873e-05
AFFX-BioDn-3_at 6104.35 P 0.000169227
AFFX-CreX-5_at 13948.1 P 5.16732e-05
AFFX-CreX-3_at 16783.9 P 4.42873e-05
AFFX-DapX-5_at 6.5422 A 0.51489
AFFX-DapX-M_at 38.7957 A 0.327079
AFFX-DapX-3_at 7.72302 A 0.921998
AFFX-LysX-5_at 3.91994 A 0.945787
AFFX-LysX-M_at 49.7679 A 0.5
AFFX-LysX-3_at 26.5771 A 0.275146
AFFX-PheX-5_at 4.9269 A 0.852061
AFFX-PheX-M_at 6.00861 A 0.937071
AFFX-PheX-3_at 71.1452 A 0.455413
AFFX-ThrX-5_at 9.34365 A 0.860518
AFFX-ThrX-M_at 19.7478 A 0.51489

Total number of rows: 54675

Table truncated, full table size 1631 Kbytes.




Supplementary file Size Download File type/resource
GSM6149952_SN0006_20060126_U133Plus2.CEL.gz 5.2 Mb (ftp)(http) CEL
GSM6149952_SN0006_20060126_U133Plus2.mas5.CHP.gz 487.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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