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Sample GSM1431409 Query DataSets for GSM1431409
Status Public on Jul 07, 2016
Title DCIS-FW08_429_rep1
Sample type RNA
 
Source name Ductal carcinoma in situ (DCIS)
Organism Homo sapiens
Characteristics tissue type: Ductal carcinoma in situ (DCIS)
er (ihc): 1
pr (ihc): 1
her2 (ihc): 0
grade (combined): 3
grade (elston): NA
grade (eortc): 3
lymph node: 0
age (years): 42
size (mm): 35
pam50: LumB
death event: 0
iPSilateral event: 0
dmfs event: 0
recurrence event: 0
recurrence location: NA
recurrence type: NA
follow-up time: 40
source: Uppsala
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 ductal carcinoma in situ.
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 -10.898371
NC1_00000197 -10.898371
NC1_00000215 -10.898371
NC2_00079215 -10.898371
NC2_00092197 -10.898371
NC2_00106057 -10.898371
NC2_00122731 -10.898371
NegativeControl -10.898371
bkv-miR-B1-3p -10.898371
bkv-miR-B1-5p -10.898371
dmr_285 2.8963866
dmr_3 6.1794896
dmr_308 -10.898371
dmr_316 -10.898371
dmr_31a 1.7037368
dmr_6 4.765718
ebv-miR-BART1-3p -10.898371
ebv-miR-BART1-5p -10.898371
ebv-miR-BART10 -10.898371
ebv-miR-BART10* -10.898371

Total number of rows: 1368

Table truncated, full table size 32 Kbytes.




Supplementary file Size Download File type/resource
GSM1431409_300312_253118112259_S01_miRNA_107_Sep09_patch_2_2.txt.gz 8.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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