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Sample GSM822408 Query DataSets for GSM822408
Status Public on Oct 21, 2013
Title Control_day8_rep1
Sample type RNA
 
Source name Control cells_day8_replicate 1
Organism Homo sapiens
Characteristics cell type: HMEC
day: 8
Growth protocol Cells were cultured in a 1:1 mix of DME and Ham’s F12 media supplemented with 2% equine serum, 10 ug/ml insulin, 5 ng/ml EGF, 100 ng/ml cholera toxin, 0.5 ug/ml hydrocortisone, and 2% reconstituted basement membrane (Matrigel; BD Bioscuences).
Extracted molecule total RNA
Extraction protocol RNA was prepared using the AllPrep DNA/RNA Mini kit (QIAGEN) following the manufacturer's recommendations.
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.4 ug RNA using the One-Color Quick Amp Labeling 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 1.65 ug of Cy3-labelled cRNA (specific activity >11.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 ul 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 65C 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).
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression in 3D culture of control cells at day 8
Data processing The scanned images were analyzed with Feature Extraction Software 11.5.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014850_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 Oct 25, 2011
Last update date Oct 21, 2013
Contact name Kazuhiro DAINO
E-mail(s) daino.kazuhiro@qst.go.jp
Organization name National Institutes for Quantum and Radiological Science and Technology
Street address 4-9-1 Anagawa, Inage-ku
City Chiba
ZIP/Postal code 263-8555
Country Japan
 
Platform ID GPL6480
Series (1)
GSE33218 Identification of dysregulated genes in 3D culture of BRIP1 knockdown cells

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
GE_BrightCorner -0.38678265
DarkCorner 0.21243
A_24_P66027 0
A_32_P77178 -0.43270397
A_23_P212522 -0.3729868
A_24_P934473 -1.6095195
A_24_P9671 -0.22970009
A_32_P29551 0.091543674
A_24_P801451 0.009908199
A_32_P30710 -0.082253456
A_32_P89523 -0.13176918
A_24_P704878 0.27823734
A_32_P86028 0.21462154
A_24_P470079 -0.24538994
A_23_P65830 -0.041586876
A_23_P109143 0.03672123
A_24_P595567 0.43614626
A_24_P391591 0
A_24_P799245 0.12661648
A_24_P932757 0.12955475

Total number of rows: 41093

Table truncated, full table size 900 Kbytes.




Supplementary file Size Download File type/resource
GSM822408.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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