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Sample GSM1595837 Query DataSets for GSM1595837
Status Public on Jan 30, 2015
Title MCF7colonies_cisplatin_1
Sample type RNA
Source name Breast cancer cell, drug-tolerant colony, 13-days-after dissemination
Organism Homo sapiens
Characteristics cell line: MCF7
gender: female
age (years): 69
Treatment protocol MCF7 cells were diluted to single cell suspensions, and seeded in the presence or absence of 0.8 uM cisplatin at low density (8 cells/cm^2). Colonies were collected 13 days after dissemination.
Extracted molecule total RNA
Extraction protocol RNA was prepared using the RNeasy kit (QIAGEN) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression 8x60K Microarray Kit (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression in bulk human cancer cell colonies emerged in the presence of cisplatin
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20110819) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Jan 29, 2015
Last update date May 14, 2015
Contact name Kohei Kume
Organization name Iwate Medical University
Street address 19-1 Uchimaru
City Morioka
ZIP/Postal code 0808505
Country Japan
Platform ID GPL13607
Series (1)
GSE65419 Transcriptional profiling of drug-tolerant cancer cell subpopulations

Data table header descriptions
VALUE Normalized signal intensity

Data table
4 -0.01231491
5 0.795745761
6 -0.329752563
7 5.700754677
8 6.483045167
9 -0.345860346
10 -0.315807866
11 -0.346518478
12 0.935159247
13 1.527151966
14 1.692582378
15 25.55184663
16 -0.346476637
17 -0.231062006
18 -0.346471833
19 -0.346471589
20 1.041656767
21 2.134744591
24 -0.075348666
25 1.147308582

Total number of rows: 58717

Table truncated, full table size 1051 Kbytes.

Supplementary file Size Download File type/resource
GSM1595837_US82800151_252800416623_S01_GE1_107_Sep09_2_2.txt.gz 12.4 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

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