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Sample GSM4056961 Query DataSets for GSM4056961
Status Public on Dec 16, 2020
Title HuCCT1_shNontarget_1
Sample type RNA
Source name HuCCT1 cells, transfected shNontarget vector
Organism Homo sapiens
Characteristics shRNA: control
cell line: HuCCT1
Extracted molecule total RNA
Extraction protocol RNA from HuCCT1 cells was purified using RNeasy Mini Kits (Qiagen, Canada)
Label Cy3
Label protocol 100 ng of total RNA was labeled using Low Input Quick Amp Labeling Kit
Hybridization protocol 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) 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 (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).
Description control cells
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (GE1_107_Sep09) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Sep 03, 2019
Last update date Dec 16, 2020
Contact name Keiichi Tamai
Organization name Miyagi Cancer Center
Street address 1-47, Nodayama, Shiote, Medeshima
City Natori, Miyagi
ZIP/Postal code 981-1293
Country Japan
Platform ID GPL13607
Series (1)
GSE136741 BEX2 suppresses mitochondrial activity and is required for dormant cancer stem cell maintenance in intrahepatic cholangiocarcinoma

Data table header descriptions
VALUE Normalized signal intensity

Data table
1 7.59E+04
2 4.20E+00
3 2.05E+01
4 1.71E+02
5 3.11E+02
6 6.68E+01
7 3.57E+03
8 8.47E+02
9 4.38E+00
10 6.02E+01
11 4.41E+00
12 2.00E+03
13 7.16E+02
14 8.84E+02
15 5.60E+03
16 4.47E+00
17 1.78E+02
18 4.49E+00
19 5.02E+01
20 8.39E+02

Total number of rows: 62976

Table truncated, full table size 911 Kbytes.

Supplementary file Size Download File type/resource
GSM4056961_20121217HuCCTnontarget.txt.gz 12.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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