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Sample GSM1431394 Query DataSets for GSM1431394
Status Public on Jul 07, 2016
Title IBC-BRC_239
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): 1
grade (combined): 3
grade (elston): NA
grade (eortc): NA
lymph node: 1
age (years): 46
size (mm): 15
pam50: LumB
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 -9.684586
NC1_00000197 -9.684586
NC1_00000215 -9.684586
NC2_00079215 -9.684586
NC2_00092197 -9.684586
NC2_00106057 -9.684586
NC2_00122731 -9.684586
NegativeControl -9.684586
bkv-miR-B1-3p -9.684586
bkv-miR-B1-5p -9.684586
dmr_285 4.0206237
dmr_3 7.095774
dmr_308 -9.684586
dmr_316 -9.684586
dmr_31a 3.033441
dmr_6 5.8327565
ebv-miR-BART1-3p -9.684586
ebv-miR-BART1-5p -9.684586
ebv-miR-BART10 -9.684586
ebv-miR-BART10* -9.684586

Total number of rows: 1368

Table truncated, full table size 31 Kbytes.




Supplementary file Size Download File type/resource
GSM1431394_230312_253118112257_S01_miRNA_107_Sep09_patch_2_3.txt.gz 8.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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