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Sample GSM1100059 Query DataSets for GSM1100059
Status Public on Mar 21, 2013
Title NUH.BT086
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): 40
patient age: 35
histology: invasive ductal carcinoma
adjuvant treated? (0=no, 1=yes): 1
characteristics: endocrine? (0=no, 1=yes): 1
chemo? (0=no, 1=yes): 1
treatment type: Tam+ACx4 cycles
dfs time: 4.67
dfs event (defined as any type of recurrence or death from breast cancer): 0
dmfs time: 4.67
dmfs event (defined as distant metastasis or death from breast cancer): 0
DSS time: 4.67
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 SIN_BT086
included in study population (n=1,954) of Nagalla, et. al., Genome Biology, 2013
reanalysis of:
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
Reanalysis of GSM119962

Data table header descriptions
VALUE Normalized log2 intensity

Data table
1007_s_at 11.3621
1053_at 8.6568
117_at 7.4144
121_at 9.1249
1255_g_at 4.9473
1294_at 9.6975
1316_at 6.4646
1320_at 5.8217
1405_i_at 10.5735
1431_at 6.2411
1438_at 4.687
1487_at 8.9206
1494_f_at 7.1597
1598_g_at 10.1671
160020_at 9.0626
1729_at 8.2827
177_at 5.9911
1773_at 7.0197
179_at 8.0731
1861_at 7.9366

Total number of rows: 22268

Table truncated, full table size 391 Kbytes.

Supplementary file Size Download File type/resource
GSM1100059_GSM119962.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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