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Sample GSM1100111 Query DataSets for GSM1100111
Status Public on Mar 21, 2013
Title NUH.BT059
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: G3
size (mm): 15
patient age: 61
histology: invasive ductal carcinoma
adjuvant treated? (0=no, 1=yes): 1
characteristics: endocrine? (0=no, 1=yes): 0
chemo? (0=no, 1=yes): 1
treatment type: CAFx6 cycles
dfs time: 5.83
dfs event (defined as any type of recurrence or death from breast cancer): 0
dmfs time: 5.83
dmfs event (defined as distant metastasis or death from breast cancer): 0
DSS time: 5.83
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_BT059
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
E-mail(s) jchou@wakehealth.edu
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
ID_REF
VALUE Normalized log2 intensity

Data table
ID_REF VALUE
1007_s_at 11.1579
1053_at 7.6471
117_at 6.8159
121_at 9.0601
1255_g_at 2.1755
1294_at 10.0863
1316_at 6.5828
1320_at 5.747
1405_i_at 10.9273
1431_at 5.7585
1438_at 9.0719
1487_at 8.4825
1494_f_at 6.9323
1598_g_at 11.2229
160020_at 9.103
1729_at 9.5544
177_at 6.9691
1773_at 7.034
179_at 8.6038
1861_at 8.1167

Total number of rows: 22268

Table truncated, full table size 390 Kbytes.




Supplementary file Size Download File type/resource
GSM1100111_NUH_BT59_A.CEL.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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