GSE118782 ( miRNA )

breast cancer ( breast )

Small noncoding RNA levels in plasma from breast cancer patients and healthy controls

Cancer : 30 / Control : 10

Robust multi-array average (RMA) normalisation of data was undertaken with background correction in the R statistical programming environment.

Plasma small noncoding RNA levels were measured in breast cancer patients and healthy control women, to determine whether any of these were associated with either patient prognosis, or as diagnostic markers for breast cancer.

RNAs were extracted from plasma from 30 breast cancer patients and from 10 healthy, control women. The levels of small noncoding RNAs were quantitated using Affymetrix microarrays

n/a

RNA was extracted from 250ml of plasma using Trizol LS and the Purelink RNA Mini kit (both Thermofisher) according to the manufacturer's guidelines. RNA was eluted in 30ml of water.

total RNA

biotin

8ml RNA was labelled using the FlashTag™ Biotin HSR RNA Labeling Kit (Genisphere) according to manufacturer's instructions.

Samples, including eukaryotic controls (bioB, bioC, bioD, cre), were hybridised at 48°C and 60 rpm to Affymetrix GeneChip v1.0 miRNA arrays for 16 hours, washed and stained on an Affymetrix Fluidics Station, according to manufacturer's instructions.

An Affymetrix GeneChip Scanner was used to scan and extract raw intensity values, following manufacturer's instructions.