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Sample GSM1100143 Query DataSets for GSM1100143
Status Public on Mar 21, 2013
Title 95_5655
Sample type RNA
Source name Breast tumor
Organism Homo sapiens
Characteristics ln status: LN-
er status: ER-
pgr status: PgR-
her2 status: He-
histological grade: G2
size (mm): 13
patient age: 36
histology: NA
adjuvant treated? (0=no, 1=yes): 1
characteristics: endocrine? (0=no, 1=yes): 1
chemo? (0=no, 1=yes): 1
treatment type: Tamoxifen+Zoledronic acid
dfs time: NA
dfs event (defined as any type of recurrence or death from breast cancer): NA
dmfs time: 2.42
dmfs event (defined as distant metastasis or death from breast cancer): 1
DSS time: 7.07945205479452
dss event (defined as death from breast cancer): 0
Extracted molecule total RNA
Extraction protocol Tumor specimens from the IJB and JRH we processed and profiled at the IJB (Christos Sotiriou). Specimens from the NUH were processed and profiled at the Genome Institute of Singapore. Total RNA was extracted from fozen tumor specimens by the Trizol method, cleaned on Qiagen RNeasy columns and analyzed for integrity on the Agilent Bioanalyzer.
Label biotin
Label protocol Five micrograms of total RNA was used to generate cRNA (target) according to the standard Affymetrix (3' IVT) protocol.
Hybridization protocol The standard Affymetrix GeneChip hyridization protocol was followed.
Scan protocol The standard Affymetrix GeneChip scanning protocol was followed.
Description IJB_5440
included in study population (n=1,954) of Nagalla, et. al., Genome Biology, 2013
Data processing The raw data were normalized by using MAS5 and batch-corrected by using Combat
Submission date Mar 18, 2013
Last update date Jun 06, 2022
Contact name Jeff Chou
Phone 3367572617
Organization name Atrium Health Wake Forest Baptist
Street address Medical Center Blvd
City Winston-Salem
State/province NC
ZIP/Postal code 27157
Country USA
Platform ID GPL96
Series (1)
GSE45255 Expression Profiles of Breast Tumors from Singapore and Europe

Data table header descriptions
VALUE Normalized log2 intensity

Data table
1007_s_at 11.2868
1053_at 8.4095
117_at 7.5518
121_at 9.9926
1255_g_at 6.008
1294_at 9.3396
1316_at 7.9328
1320_at 6.2928
1405_i_at 7.6709
1431_at 6.2142
1438_at 7.5265
1487_at 8.7925
1494_f_at 8.1806
1598_g_at 11.3192
160020_at 10.3393
1729_at 8.8166
177_at 7.542
1773_at 8.0193
179_at 9.2036
1861_at 8.2346

Total number of rows: 22268

Table truncated, full table size 390 Kbytes.

Supplementary file Size Download File type/resource
GSM1100143_OXF5440.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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