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Sample GSM1661402 Query DataSets for GSM1661402
Status Public on Sep 20, 2020
Title MCF7_S_3
Sample type RNA
Source name Cultured MCF-7 spheroid cells
Organism Homo sapiens
Characteristics cell line: MCF-7
cell source: Estrogen-dependent human breast adenocarcinoma
culture condition: Spheroid
Growth protocol The monolayer and spheroid MCF-7 cells were cultured in tissue culture-treated flasks and as suspension spheroid respectively. Both are maintained in 5% CO2 humidified incubator.
Extracted molecule total RNA
Extraction protocol Total RNA with retention of small RNAs from the cells were extracted using miRNeasy kit according to the manufacturer's instructions
Label Biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (FlashTaq Biotin HSR RNA Labeling kit, Affymetrix, 2013).
Hybridization protocol Following ligation, 21.5ul of biotin-labeled sample were hybridized for 16 hours at 48C on GeneChip miRNA 4.0 arrays.GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000 7G
Description Gene expression data of MCF-7 spheroid
Data processing The raw CEL files were processed using the Affymetrix Expression Console Software (build 1.3.1) with microRNA arrays-RNA + DABG-Human only normalization to produce CHP files for each of the 6 samples. The six CHP files were then imported into the Affymetrix Transcriptome Analysis Console (TAC) 3.0 (build using the Gene Level Differential Analysis option. Three conditions were created using TAC. One-way between-subject ANOVA (unpaired) were used as the algorithm options, and the default filter criteria was fold change >2 and <-2. The ANOVA p-value was set at <0.05.
Submission date Apr 20, 2015
Last update date Sep 20, 2020
Contact name norlaily mohd ali
Organization name Universiti Tunku Abdul Rahman
Department Faculty of Medicine and Health Sciences
Street address Universiti Tunku Abdul Rahman, Jln Sg Long
City Cheras
State/province Selangor
ZIP/Postal code 43000
Country Malaysia
Platform ID GPL19117
Series (1)
GSE68031 miRNA transcriptome profiling of spheroid-enriched cells with cancer stem cell properties in human breast MCF-7 cell line.

Data table header descriptions
VALUE log2-rma dabg

Data table
ID_REF VALUE Detection
MIMAT0000062_st 12.893567 0
MIMAT0004481_st 0.768902 0.691151
MIMAT0010195_st 0.871739 0.565378
MIMAT0000063_st 13.860157 0
MIMAT0004482_st 1.057035 0.202049
MIMAT0000064_st 12.896503 0
MIMAT0026472_st 0.723261 0.791547
MIMAT0000065_st 12.207229 0
MIMAT0004484_st 2.12841 0.000653
MIMAT0000066_st 10.741416 0
MIMAT0004485_st 0.671548 0.404342
MIMAT0000067_st 8.88645 0
MIMAT0004486_st 1.057035 0.161242
MIMAT0004487_st 0.497073 0.936433
MIMAT0000068_st 7.951409 0
MIMAT0004488_st 1.043635 0.065323
MIMAT0000069_st 11.717702 0
MIMAT0004489_st 0.777022 0.504491
MIMAT0000070_st 11.334518 0
MIMAT0000071_st 3.412445 0

Total number of rows: 6658

Table truncated, full table size 215 Kbytes.

Supplementary file Size Download File type/resource
GSM1661402_C5_miRNA-4_0_2.CEL.gz 767.3 Kb (ftp)(http) CEL
GSM1661402_C5_miRNA-4_0_2.rma-dabg.chp.gz 66.5 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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