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Sample GSM4418125 Query DataSets for GSM4418125
Status Public on Mar 27, 2020
Title WHEL ID 1400
Sample type RNA
 
Source name primary breast cancer
Organism Homo sapiens
Characteristics tissue: primary breast cancer
Treatment protocol Refer to https://library.ucsd.edu/dc/object/bb2493244b
Extracted molecule total RNA
Extraction protocol Unstained slides from archival specimens with ≥ 40% tumor cellularity were incubated at 65 °C for 30 minutes and deparaffinized using Citrisolv (Fisher Scientific, Pittsburgh, PA) followed by ethanol wash. Tumor tissues were macrodissected into RNAse-free microfuge tubes, and nucleic acids isolated using the Qiagen AllPrep FFPE kit (#80234). Manufacturer’s instructions were followed with the exception that the proteinase K digestion step was extended to an overnight incubation for the DNA isolation.
Label n/a
Label protocol See manufacturer's website http://www.nanostring.com for procedures
 
Hybridization protocol Transcript expression was quantified with 250 ng of total RNA using the NanoString nCounter analysis system with a custom miRGE CodeSet. Assay reactions were assembled per manufacturer’s specifications (NanoString Technologies, INC Seattle, WA).
Scan protocol See manufacturer's website http://www.nanostring.com for procedures. Digital Analyzer was set to scan at 1155 FOV (fields of view).
Description NanoString reporter probe
X2895383296_6
Data processing R-NanoStringNorm package was used to normalize data. Code count normalization used 6 positive controls and background subtraction used 8 negative controls. All expression values were first log2 transformed. For mRNAs, five (ACTB, PSMC4, MRPL19, RPLPO, SF3A1) genes were used as housekeepers; the data matrix elements are relative gene expression values (log2 transformed) compared to log2 value of the geometric mean of the five house-keepers within each sample. For miRNAs, log2 expression values are presented. For miRNAs, quantile normalization was performed. Normalized datasets for both mRNA and miRNA are available on the series record. Sample data tables include data only for mRNAs.
 
Submission date Mar 17, 2020
Last update date Mar 27, 2020
Contact name Loki Natarajan
E-mail(s) loki@math.ucsd.edu
Organization name University of California, San Diego
Street address 3855 Health Sciences DR
City La Jolla
ZIP/Postal code 92093-0901
Country USA
 
Platform ID GPL28286
Series (1)
GSE147126 mRNAs and miRNAs for Women's Healthy Eating and Living (WHEL) Study

Data table header descriptions
ID_REF
VALUE normalized nCounter signal intensity

Data table
ID_REF VALUE
KRT17 -4.4692
CD68 -1.7722
SPINT2 0.2938
ESRP1 0.9448
KRT8 1.9548
NUF2 -3.1272
MYBL2 -2.0692
FGFR4 -2.6042
ALDOA 2.1348
MELK -3.1562
FOXC1 -5.1522
ACTR3B -3.3262
RRAGD -5.2122
GUS -2.6762
MRPS17 -2.8662
GRB7 -2.4002
UCHL1 -6.1092
TPI1 0.8548
MLPH 0.5848
PNP -2.2842

Total number of rows: 123

Table truncated, full table size 1 Kbytes.




Supplementary file Size Download File type/resource
GSM4418125_20150825_70004M_2895383296_06.RCC.gz 2.2 Kb (ftp)(http) RCC
Processed data included within Sample table
Processed data are available on Series record

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