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Sample GSM2406884 Query DataSets for GSM2406884
Status Public on Feb 28, 2017
Title MDA-MB-436 Parental 1 N=4
Sample type RNA
Source name MDA-MB-436 Cell line_Parental
Organism Homo sapiens
Characteristics cell line: MDA-MB-436
cell type: Breast Cancer Cell Line
treated with: none (parental)
Growth protocol Parental and resistant cells were seeded at a density of 1x106 per well in 6 well-plates and incubated without drug for 24 hours
Extracted molecule total RNA
Extraction protocol Cells were harvested and total RNA from parental and resistant cell lines were extracted simultaneously using the AllPrep DNA/RNA Mini kit (Qiagen, Canada). The quality of RNA was determined with the NanoDrop™ spectrophotometer (ND-1000) (Wilmington, DE, USA). All RNA samples with A260/A280 ratio higher than 1.8 and DNA with A260/A280 ratio higher than 2 were selected for further analysis. The RNA integrity number (RIN) was measured with a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA with RIN higher than 8 qualified forgene expression profiling.
Label Cy3
Label protocol Cy3 labeled cRNA was prepared from 100ng RNA using the One-Color Low Input Quick Amp labeling kit (Agilent Technologies). The amplified labeled cRNA was purified using the RNeasy Mini Kit (Qiagen, Canada) assessed for dye incorporation and cRNA yield using the NanoDrop™ Spectrophotometer (ND-1000.)
Hybridization protocol Labeled cRNA was hybridized onto SurePrint G3 Human GE 8X60K microarrays (Agilent Technologies) at 65 °C for 17h in a rotating Agilent hybridization oven.
Scan protocol Following hybridization, arrays were washed and scanned using the Agilent Scanner G2505B.
Data processing Microarray data were extracted and visualized using the Feature Extraction Software v8.1. (Agilent), default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) was used to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Nov 27, 2016
Last update date Feb 28, 2017
Contact name Elaheh Ahmadzadeh
Phone 5149981730
Organization name McGill University
Street address 3220 Ridgewood, apt 319
City Montreal
State/province Please select
ZIP/Postal code H3V1B9
Country Canada
Platform ID GPL13607
Series (1)
GSE90564 Paclitaxel resistance in triple negative breast cancer involves novel functional genomic aberrations in the ABCB1 gene.

Data table header descriptions
VALUE processed Cy3 signal intensity (Agilent gProcessedSignal)

Data table
1 7.936308e+004
2 4.101327e+000
3 4.131522e+000
4 4.350671e+002
5 2.458920e+003
6 5.218944e+001
7 3.855579e+004
8 2.204912e+004
9 3.044006e+001
10 2.059890e+001
11 4.293389e+000
12 7.515171e+002
13 4.291038e+003
14 5.591439e+003
15 2.819532e+004
16 4.342697e+000
17 1.290064e+002
18 2.156609e+001
19 4.355829e+000
20 2.351184e+003

Total number of rows: 62976

Table truncated, full table size 1219 Kbytes.

Supplementary file Size Download File type/resource
GSM2406884_MDA-MB-436_P1_N_4.txt.gz 3.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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