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Sample GSM1906778 Query DataSets for GSM1906778
Status Public on Nov 30, 2015
Title Control siRNA-treated HCC1937 cells
Sample type RNA
 
Source name HCC1937 cells, control siRNA
Organism Homo sapiens
Characteristics cell line: HCC1937
cell type: breast cancer cell line
sirna: control
Treatment protocol Following overnight attachment to a 6-well plate, 3.0 x 10^5 cells per well were transfected for 48 hours using Lipofectamine® RNAiMAX Reagent (Invitrogen by Life Technologies) according to the manufacturer's protocol. Sixteen hours after the medium change, siRNA-transfected cells were used for further experiments.
Growth protocol The culture condition for CD24-siRNA-treated HCC1937 cells was as following: RPMI1640 medium supplemented with 10% FCS, L-Gln and penicillin-streptomycin, 5% CO2/air.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated and purified from CD24-treated HCC1937 cells using High Pure RNA Isolation Kit (Roche, #11 828 665 001).
Label Cy3
Label protocol cRNA was amplified and labelled using a Low Input Quick Amp Labelling Kit (Agilent Technologies).
 
Hybridization protocol cRNA was hybridized to a 60K 60-mer oligomicroarray (Agilent-039494 SurePrint G3 Human Gene Expression Microarray 8x60K v2; Agilent Technologies) according to the manufacturer's instructions.
Scan protocol The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).
Data processing The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.
 
Submission date Oct 13, 2015
Last update date Apr 23, 2018
Contact name Hideya Onishi
E-mail(s) ohnishi@surg1.med.kyushu-u.ac.jp
Organization name Graduate School of Medical Sciences, Kyushu University
Department Department of Cancer Therapy and Research
Street address 3-1-1 Maidashi, Higashi-ku
City Fukuoka
ZIP/Postal code 812-8582
Country Japan
 
Platform ID GPL17077
Series (2)
GSE73960 CD24 suppresses malignant phenotype by downregulation of SHH transcription through STAT1 inhibition in breast cancer cells [HCC1937]
GSE73961 CD24 suppresses malignant phenotype by downregulation of SHH transcription through STAT1 inhibition in breast cancer cells
Relations
Reanalyzed by GSE113533

Data table header descriptions
ID_REF
VALUE Quantile normalized signal, non-log scaled
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
A_19_P00315452 331.06535 P
A_19_P00315459 39.826875 P
A_19_P00315482 6.3837675 A
A_19_P00315492 5.167476 A
A_19_P00315493 55.737155 P
A_19_P00315502 5078.519504 P
A_19_P00315506 454.5044 P
A_19_P00315518 11.981895 A
A_19_P00315519 2.753248 A
A_19_P00315524 10.634887 A
A_19_P00315528 18.479025 P
A_19_P00315529 21.27898 P
A_19_P00315538 54.13277 P
A_19_P00315541 23.119215 P
A_19_P00315543 9.0043205 A
A_19_P00315550 129.71045 P
A_19_P00315551 68.39098333 P
A_19_P00315554 2.773795 A
A_19_P00315581 8080.081 P
A_19_P00315583 49.664165 P

Total number of rows: 50599

Table truncated, full table size 1240 Kbytes.




Supplementary file Size Download File type/resource
GSM1906778_US11030397_253949431401_S02_GE1_107_Sep09_1_1.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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