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Sample GSM4483912 Query DataSets for GSM4483912
Status Public on May 31, 2020
Title MDA-MB-231-214-3p Rep1
Sample type RNA
 
Source name MDA-MB-231-214-3p
Organism Homo sapiens
Characteristics cell line: MDA-MB-231
cell type: Breast cancer cell line
miRNA: has-miR-214-3p precursor
Treatment protocol MDA-MB-231 cells (0.168 x 10e6 cells/ml) were transfected with the selected miRNA precursors (pre-miR–negative control, hsa-miR-205-5p and hsa-miR-214-3p) purchased from Ambion. Cell transfection was conducted employing a reverse transfection protocol.
Growth protocol MDA-MB-231 cells were grown in DMEM supplemented with 10% fetal bovine serum, 1% NEAA, 1% L-glutamine, 100 mg/l penicillin, and 100 mg/l streptomycin.
Extracted molecule total RNA
Extraction protocol Total RNA were isolated from control and treated cells using Total RNA Purification Kit (Norgen-Biotek Corp., Canada) according to the manufacturer’s instructions. The concentrations of total RNA were measured using NanoDrop 2000 (Thermo-Scientific).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.
 
Hybridization protocol 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 ul of 2× Hi-RPM Hybridization Buffer (Agilent) was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome GE 4x44K v2 Microarray chip 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.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.
Description Gene expression in MDA-MB-231 breast cancer cell line transfected with has-miR-214-3p precursor replica 1.
Data processing The scanned images were analyzed with Feature Extraction Software 11.0 (Agilent) using default parameters. Data were analyzed using Agilent GeneSpring X software.
 
Submission date Apr 17, 2020
Last update date Jun 01, 2020
Contact name Nehad M Alajez
E-mail(s) nalajez@gmail.com
Organization name King Saud University College of Medicine
Department Anatomy
Lab Stem Cell Unit
Street address 1st floor College of Medicne
City Riyadh
ZIP/Postal code 11461
Country Saudi Arabia
 
Platform ID GPL17077
Series (2)
GSE148847 Gene expression profiling of MDA-MB-231 cells transfected with hsa-miR-205-5p and hsa-miR-214-3p compared to scrambled miRNA precursors
GSE148848 microRNA expression profiling of paired primary and lymph node metastatic breast cancer patients, and gene expression profiling of MDA-MB-231 cells transfected with hsa-miR-205-5p and hsa-miR-214-3p compared to scrambled miRNA precursors

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
A_33_P3634364 2.757301069
A_32_P167076 3.154351129
A_19_P00326532 2.851692323
A_23_P158925 8.195414052
A_32_P118847 5.297011387
A_23_P165521 4.592190891
A_23_P123193 8.501029636
A_33_P3376007 6.44581197
A_24_P219785 11.08002234
A_33_P3243649 6.34869574
A_24_P126060 8.511108271
A_23_P84202 5.552977931
A_32_P151366 7.576955897
A_24_P186124 7.73949826
A_24_P44596 8.267117396
A_33_P3264780 5.34662198
A_33_P3695548 7.747653221
A_21_P0010658 4.098879588
A_19_P00802390 3.43850962
A_23_P335495 4.733088566

Total number of rows: 50739

Table truncated, full table size 1259 Kbytes.




Supplementary file Size Download File type/resource
GSM4483912_MDA-MB-231-214-3p_Rep1.txt.gz 3.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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