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Sample GSM1431376 Query DataSets for GSM1431376
Status Public on Jul 07, 2016
Title IBC-BRC_14
Sample type RNA
 
Source name Invasive breast cancer (IBC)
Organism Homo sapiens
Characteristics tissue type: Invasive breast cancer (IBC)
er (ihc): 0
pr (ihc): 0
her2 (ihc): NA
grade (combined): 2
grade (elston): NA
grade (eortc): NA
lymph node: 1
age (years): 53
size (mm): 13
pam50: Her2
death event: NA
iPSilateral event: NA
dmfs event: NA
recurrence event: NA
recurrence location: NA
recurrence type: NA
follow-up time: NA
source: Trondheim
Extracted molecule total RNA
Extraction protocol Tumor tissues were homogenized using TRIzol Reagent (Invitrogen, Life Technologies, USA), and purified with RNeasy mini columns (Qiagen, Netherlands). The quality of RNA was assessed using NanoDrop ND-1000 Spectrophotometer, version 3.7.1 (NanoDrop Technologies, Thermo Fisher Scientific Inc, USA).
Label Cy3
Label protocol 200ng RNA was used as input for labeling according to manufacturer's protocol.
 
Hybridization protocol RNA was hybridized to Human miRNA Microarray Release 16.0, 8x60K (G4872A-031181) according to manufacturer's instructions.
Scan protocol Feature extraction was performed using Agilent Scanner G2565A and Feature Extraction software version 10.7.3.1.
Description miRNA profile of human whole invasive breast cancer.
Data processing Data was normalized using the GeneSpring version 12 software environment provided by Agilent. Probe spots were either marked as detected with errors lower than 3 times the signal, or if flagged were given a value of 0.1. Probe spots for the same miRNA were summed, individual arrays were log2 transformed, and subsequently 90th percentile normalized.
 
Submission date Jul 09, 2014
Last update date Jul 07, 2016
Contact name Robert Lesurf
Organization name Washington University in St. Louis
Department McDonnell Genome Institute
Lab Griffith Lab
Street address 4444 Forest Park Ave
City St. Louis
State/province MO
ZIP/Postal code 63112
Country USA
 
Platform ID GPL15019
Series (2)
GSE59247 Molecular features of subtype-specific progression from ductal carcinoma in situ to invasive breast cancer [miRNA data]
GSE59248 Molecular features of subtype-specific progression from ductal carcinoma in situ to invasive breast cancer

Data table header descriptions
ID_REF
VALUE log2 transformed 90th percentile normalized.

Data table
ID_REF VALUE
Blank -10.787798
NC1_00000197 -10.787798
NC1_00000215 -10.787798
NC2_00079215 -10.787798
NC2_00092197 -10.787798
NC2_00106057 -10.787798
NC2_00122731 -10.787798
NegativeControl -10.787798
bkv-miR-B1-3p -10.787798
bkv-miR-B1-5p -10.787798
dmr_285 2.7103896
dmr_3 6.447127
dmr_308 -10.787798
dmr_316 -10.787798
dmr_31a 1.7714229
dmr_6 5.4021773
ebv-miR-BART1-3p -10.787798
ebv-miR-BART1-5p -10.787798
ebv-miR-BART10 -10.787798
ebv-miR-BART10* -10.787798

Total number of rows: 1368

Table truncated, full table size 32 Kbytes.




Supplementary file Size Download File type/resource
GSM1431376_230312_253118112250_S01_miRNA_107_Sep09_patch_2_1.txt.gz 8.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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