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Sample GSM7904864 Query DataSets for GSM7904864
Status Public on Dec 01, 2023
Title Fibroblast cell, 3D, rep1
Sample type RNA
 
Source name Fibroblast cell, 3D, replicate 1
Organism Homo sapiens
Characteristics cell type: fibroblast cell
Treatment protocol DMEM+10%FBS+1%P/S
Extracted molecule total RNA
Extraction protocol A total of 100 µL of cell disruption fluid was added to QIAzol Lysis Reagent to reach 700 µL, and the cells were further disrupted by centrifugation on a QIAshredder column (79656, Qiagen N.V.). Thereafter, 20% (vol) of the filtrate was added to chloroform, mixed thoroughly and centrifuged. After the supernatant was separated, a 1.5-fold volume of 100% ethanol was added to precipitate total RNA and RNA purification was performed using a miRNeasy Micro Kit (217084, Qiagen N.V.). Finally, 20 µL of nuclease-free water was added to elute the total RNA.
Label Cy3
Label protocol Using 100 ng of total RNA as template, the one-color method protocol recommended by Agilent (file name; One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling), ver6.9, December 2015). cDNA synthesis was followed by purification of the amplified and labeled cRNA product obtained from cDNA synthesis, and then absorbance was measured with NanoDrop One to calculate concentrations and other parameters. At that time, samples with an amplification factor of at least 15-fold and an incorporation efficiency of at least 6 pmol/μg of purified labeled cRNA product were considered acceptable.
 
Hybridization protocol 600 ng of cRNA was aliquoted and incubated with the microarray in the DNA Microarray Hybridization Oven for 17 hours (65°C, 10 rpm).
Scan protocol Microarray scanning was performed using a DNA Microarray Scanner.The scanned image data was quantified and the QC report obtained at the same time was reviewed. The spike-in control added as an external standard was considered acceptable if the slope was 0.85 or greater, the R2 was 0.95 to 1.0, and the median %CV was 20% or less.
Data processing As an interarray normalization method for the one-color method, the Agilent recommended global normalization was performed under the following conditions.Threshold raw signals: 1.0.Normalization algorithm: Percentile Shift.Percentile target: 75
 
Submission date Nov 16, 2023
Last update date Dec 01, 2023
Contact name Rii Morimura
E-mail(s) rii.morimura@toppan.co.jp
Organization name TOPPAN Holdings Inc.
Street address 4-2-3 Takanodaiminami
City Sugito-machi
State/province Saitama
ZIP/Postal code 345-8508
Country Japan
 
Platform ID GPL21185
Series (1)
GSE248026 In vitro throughput screening of anticancer drugs by patient-derived cell lines cultured on vascularized three-dimensional stromal tissues

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
(+)E1A_r60_1 1716.605
(+)E1A_r60_3 0.014
(+)E1A_r60_a104 0.024
(+)E1A_r60_a107 0.223
(+)E1A_r60_a135 1.882
(+)E1A_r60_a20 4.411
(+)E1A_r60_a22 12.154
(+)E1A_r60_a97 63.162
(+)E1A_r60_n11 277.051
(+)E1A_r60_n9 567.663
3xSLv1 0.012
A_19_P00315452 1.078
A_19_P00315492 0.032
A_19_P00315493 1.397
A_19_P00315502 0.085
A_19_P00315506 0.057
A_19_P00315518 0.012
A_19_P00315519 0.012
A_19_P00315529 0.064
A_19_P00315541 0.011

Total number of rows: 58341

Table truncated, full table size 1133 Kbytes.




Supplementary file Size Download File type/resource
GSM7904864_US09503747_257236328379_S01_GE1_107_Sep09_1_2.txt.gz 3.1 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table

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