Expression of Genes Associated with Epithelial to Mesenchymal Transition in MCF-7 Breast Cancer Cells Treated with Monocarbonyl Analogs of Curcumin C66 and B2BrBC—RT-qPCR Array Dataset

Abstract

Curcumin is a polyphenolic bio-compound derived from the rhizomes of the turmeric plant (Curcuma longa) that has proven anti-carcinogenic properties but poor bioavailability. By modifying its chemical structure, the monocarbonyl analogs of curcumin (MACs) possess improved stability, resorption, and circulation. This dataset presents RT-qPCR array analysis of 84 genes associated with Epithelial to Mesenchymal Transition (EMT), a key early event in cancer progression and metastasis, in human MCF-7 breast cancer cells. Cells were stimulated toward EMT reprogramming by treatment with a combination of EMT-inducing factors and co-treated with two experimental MACs, C66 or B2BrBC. Gene expression was measured using the human EMT QIAGEN RT² Profiler kit, and results were obtained from three independent experiments. Gene expression changes are presented as both fold regulation and fold change values, with statistical significance determined by Student’s t-test (p < 0.05). This comprehensive dataset enables investigation into how MACs modulate the EMT transcriptome in breast cancer cells, with potential applications for understanding EMT mechanisms. The raw and processed data are publicly available and can be used for comparative analyses, validation studies, and bioinformatic analyses of EMT-related signaling pathways.

Dataset: DOI: 10.17632/zn8rpyh9v4.2

Dataset License: CC-BY 4.0

1. Summary

1.1. Background and Rationale

Curcumin, a phytochemical from turmeric (Curcuma longa), exhibits promising anti-carcinogenic properties but has limited clinical use due to poor bioavailability, low stability, and rapid metabolism [1,2]. To overcome these pharmacokinetic limitations, synthetic monocarbonyl analogs of curcumin (MACs) have been developed by removing the β-diketone moiety, yielding compounds with improved chemical stability, absorption, and tissue distribution while preserving therapeutic potential [3,4].

Epithelial to Mesenchymal Transition (EMT) is a cellular process in which epithelial cells acquire mesenchymal characteristics, promoting migration, invasion, and metastasis through coordinated changes in gene expression, including downregulation of genes encoding for epithelial proteins such as E-cadherin and claudin, and upregulation of those characteristic of mesenchymal cells such as N-cadherin, fibronectin, and vimentin [5,6,7].

This dataset reports a comprehensive RT-qPCR array analysis of 84 EMT-associated genes in human MCF-7 breast cancer cells treated with two MACs, C66 ((2E,6E)-2,6-bis[(2-trifluoromethyl)benzylidene]cyclohexanone) and B2BrBC ((2E,6E)-2,6-bis(2-bromobenzylidene)cyclohexanone), which show enhanced stability, favorable drug-like properties, and selective proapoptotic activity in cancer cells [4].

The dataset accompanies our main article, published in Cancer Cell International [8], and supports the emerging therapeutic potential of these MACs for cancer treatment.

1.2. Scope, Aims, and Objectives

This data descriptor presents raw and processed RT-qPCR array data from MCF-7 cells treated with 100 µM C66 or B2BrBC for 72 h post-EMT induction, focusing exclusively on RNA-level changes in 84 EMT-related genes.

The aim of this data descriptor is to complement the original study by providing full transparency of the raw Ct values, fold changes (ΔΔCt method), and statistical analyses.

This dataset enables secondary analyses, including pathway, co-expression network, and clustering analyses, as well as machine-learning applications, to identify regulatory modules associated with MACs-mediated suppression of EMT. It also provides a mechanistic foundation for subsequent functional studies that investigate how MACs modulate EMT and identify specific genes as therapeutic targets.

2. Data Description

This dataset comprises three primary tables (

Table 1. EMT-associated genes affected by treatment with EMT-inducing media supplement. This table presents gene expression data from EMT-treated cells. All values represent fold-changes relative to control cells (vehicle-treated, no EMT-inducing supplement; EMT vs. Control), identifying baseline changes in the EMT transcriptome during EMT induction. Statistically significant values are shown in bold. ns, non-significant data (p > 0.05); *, p < 0.05; **, p < 0.01; ***, p < 0.001; ****, p < 0.0001.

Gene Symbol	Fold Regulation	Fold Change	p-Value	Significance
AHNAK	1.06	1.06	0.8576	ns
AKT1	−1.80	0.55	0.0852	ns
BMP1	2.28	2.28	0.1856	ns
BMP2	22.12	22.12	0.3539	ns
BMP7	1.72	1.72	0.1557	ns
CALD1	9.57	9.57	0.3575	ns
CAMK2N1	−1.15	0.87	0.5695	ns
CAV2	−1.43	0.70	0.4896	ns
CDH1	−5.28	0.19	0.0057	**
CDH2	4.69	4.69	0.3745	ns
COL1A2	16.32	16.32	0.3615	ns
COL3A1	1.34	1.34	0.4603	ns
COL5A2	1.06	1.06	0.5048	ns
CTNNB1	−1.90	0.53	0.0198	*
DSC2	1.81	1.81	0.3756	ns
DSP	−1.93	0.52	0.0812	ns
EGFR	4.93	4.93	0.3141	ns
ERBB3	1.23	1.23	0.4232	ns
ESR1	−1.73	0.58	0.2850	ns
F11R	−1.59	0.63	0.4123	ns
FGFBP1	2.59	2.59	0.3787	ns
FN1	2.13	2.13	0.2089	ns
FOXC2	1.14	1.14	0.4957	ns
FZD7	1.27	1.27	0.4761	ns
GNG11	12.31	12.31	0.3595	ns
GSC	−1.56	0.64	0.1755	ns
GSK3B	2.07	2.07	0.0001	****
IGFBP4	−2.18	0.46	0.1641	ns
IL1RN	5.20	5.20	0.3642	ns
ILK	−1.08	0.92	0.7568	ns
ITGA5	1.34	1.34	0.4802	ns
ITGAV	−1.06	0.94	0.9873	ns
ITGB1	−1.31	0.76	0.3158	ns
JAG1	3.04	3.04	0.0846	ns
KRT14	1.53	1.53	0.4307	ns
KRT19	−1.52	0.66	0.0325	*
KRT7	−1.56	0.64	0.2319	ns
MAP1B	4.83	4.83	0.2354	ns
MMP2	35.46	35.46	0.3626	ns
MMP3	14.71	14.71	0.3572	ns
MMP9	2.23	2.23	0.3753	ns
MSN	7.07	7.07	0.3617	ns
MST1R	2.40	2.40	0.3853	ns
NODAL	3.79	3.79	0.3732	ns
NOTCH1	4.79	4.79	0.0162	*
NUDT13	−1.30	0.77	0.3397	ns
OCLN	−1.88	0.53	0.0056	**
PDGFRB	3.48	3.48	0.3771	ns
PLEK2	2.65	2.65	0.3199	ns
PPPDE2	1.10	1.10	0.6134	ns
PTK2	−1.35	0.74	0.3887	ns
PTP4A1	−1.28	0.78	0.3534	ns
RAC1	−1.03	0.97	0.7411	ns
RGS2	12.89	12.89	0.2174	ns
SERPINE1	83.12	83.12	0.1003	ns
SIP1	1.56	1.56	0.3275	ns
SMAD2	−1.46	0.68	0.0063	**
SNAI1	8.95	8.95	0.0872	ns
SNAI2	20.82	20.82	0.1840	ns
SNAI3	3.65	3.65	0.3356	ns
SOX10	6.07	6.07	0.3583	ns
SPARC	22.17	22.17	0.3586	ns
SPP1	27.06	27.06	0.3586	ns
STAT3	−2.04	0.49	0.0554	ns
STEAP1	3.26	3.26	0.3588	ns
TCF3	1.98	1.98	0.2513	ns
TCF4	1.17	1.17	0.5018	ns
TFPI2	−1.12	0.89	0.7700	ns
TGFB1	1.38	1.38	0.1791	ns
TGFB2	10.91	10.91	0.2963	ns
TGFB3	2.01	2.01	0.3591	ns
TIMP1	−1.35	0.74	0.0073	**
TMEFF1	4.78	4.78	0.0147	*
TMEM132A	−1.45	0.69	0.3363	ns
TSPAN13	−1.78	0.56	0.0005	***
TWIST1	25.16	25.16	0.3391	ns
VCAN	3.01	3.01	0.3816	ns
VIM	3.32	3.32	0.3030	ns
VPS13A	−1.44	0.69	0.3412	ns
WNT11	4.48	4.48	0.2793	ns
WNT5A	1.70	1.70	0.2516	ns
WNT5B	4.40	4.40	0.2849	ns
ZEB1	4.97	4.97	0.3683	ns
ZEB2	3.01	3.01	0.3767	ns

,

Table 2. EMT-associated genes affected by treatment with C66 alongside EMT-inducing media supplement. The table presents gene expression data from cells treated with both the EMT-inducing supplement and C66. All values represent fold changes relative to EMT-induced cells alone (EMT + C66 vs. EMT). Statistically significant values (p < 0.05) are shown in bold. ns, non-significant data (p > 0.05); *, p < 0.05.

Gene Symbol	Fold Regulation	Fold Change	p-Value	Significance
AHNAK	−1.47	0.68	0.6327	ns
AKT1	−1.28	0.78	0.4814	ns
BMP1	1.26	1.26	0.7370	ns
BMP2	1.54	1.54	0.6570	ns
BMP7	−1.06	0.95	0.9637	ns
CALD1	2.37	2.37	0.8817	ns
CAMK2N1	−1.12	0.90	0.8106	ns
CAV2	−1.11	0.90	0.7174	ns
CDH1	−1.11	0.90	0.6614	ns
CDH2	3.12	3.12	0.8044	ns
COL1A2	2.21	2.21	0.9410	ns
COL3A1	1.80	1.80	0.8155	ns
COL5A2	2.13	2.13	0.8730	ns
CTNNB1	1.26	1.26	0.4807	ns
DSC2	2.05	2.05	0.5331	ns
DSP	1.15	1.15	0.8258	ns
EGFR	−1.04	0.96	0.8817	ns
ERBB3	−1.16	0.86	0.8595	ns
ESR1	−1.11	0.90	0.8632	ns
F11R	−1.62	0.62	0.2545	ns
FGFBP1	1.80	1.80	0.9261	ns
FN1	−1.53	0.65	0.5221	ns
FOXC2	1.44	1.44	0.8787	ns
FZD7	1.07	1.07	0.9870	ns
GNG11	2.18	2.18	0.9295	ns
GSC	1.25	1.25	0.5380	ns
GSK3B	−1.21	0.83	0.5408	ns
IGFBP4	−1.55	0.65	0.2983	ns
IL1RN	3.33	3.33	0.8836	ns
ILK	−1.16	0.86	0.4519	ns
ITGA5	1.04	1.04	0.9171	ns
ITGAV	1.27	1.27	0.5315	ns
ITGB1	−1.04	0.96	0.8324	ns
JAG1	−1.28	0.78	0.6642	ns
KRT14	1.42	1.42	0.9099	ns
KRT19	−1.13	0.89	0.8666	ns
KRT7	1.05	1.05	0.9588	ns
MAP1B	1.80	1.80	0.6635	ns
MMP2	2.35	2.35	0.9653	ns
MMP3	2.52	2.52	0.9135	ns
MMP9	1.83	1.83	0.8243	ns
MSN	2.00	2.00	0.9943	ns
MST1R	1.35	1.35	0.8274	ns
NODAL	2.41	2.41	0.8567	ns
NOTCH1	−1.67	0.60	0.2964	ns
NUDT13	−1.08	0.93	0.6407	ns
OCLN	1.11	1.11	0.5386	ns
PDGFRB	1.81	1.81	0.8965	ns
PLEK2	1.50	1.50	0.8772	ns
PPPDE2	1.26	1.26	0.6253	ns
PTK2	1.24	1.24	0.5494	ns
PTP4A1	1.18	1.18	0.4682	ns
RAC1	−1.08	0.92	0.5616	ns
RGS2	1.18	1.18	0.9894	ns
SERPINE1	3.04	3.04	0.1949	ns
SIP1	1.13	1.13	0.8783	ns
SMAD2	1.34	1.34	0.0320	*
SNAI1	−1.57	0.63	0.6722	ns
SNAI2	−1.33	0.75	0.7115	ns
SNAI3	−1.11	0.90	0.9671	ns
SOX10	1.35	1.35	0.7800	ns
SPARC	1.55	1.55	0.8652	ns
SPP1	3.05	3.05	0.8769	ns
STAT3	1.34	1.34	0.4180	ns
STEAP1	3.11	3.11	0.6782	ns
TCF3	−1.06	0.95	0.7917	ns
TCF4	1.24	1.24	0.9708	ns
TFPI2	1.82	1.82	0.5579	ns
TGFB1	−1.33	0.75	0.1690	ns
TGFB2	1.64	1.64	0.9271	ns
TGFB3	1.04	1.04	0.9694	ns
TIMP1	1.21	1.21	0.0780	ns
TMEFF1	−1.25	0.80	0.6229	ns
TMEM132A	−1.13	0.89	0.7289	ns
TSPAN13	−1.12	0.90	0.5709	ns
TWIST1	−1.01	0.99	0.8922	ns
VCAN	3.60	3.60	0.7976	ns
VIM	−1.16	0.86	0.9312	ns
VPS13A	1.18	1.18	0.8261	ns
WNT11	−1.11	0.90	0.8706	ns
WNT5A	−1.23	0.81	0.8925	ns
WNT5B	1.05	1.05	0.9676	ns
ZEB1	2.65	2.65	0.9846	ns
ZEB2	2.09	2.09	0.9057	ns

and

Table 3. EMT-associated genes affected by treatment with B2BrBC alongside EMT-inducing media supplement. The table presents gene expression data from cells treated with both the EMT-inducing supplement and B2BrBC. All values represent fold-changes relative to EMT-induced cells alone (EMT + B2BrBC vs. EMT). Statistically significant values are shown in bold. ns, non-significant data (p > 0.05); *, p < 0.05; **, p < 0.01; ***, p < 0.001.

Gene Symbol	Fold Regulation	Fold Change	p-Value	Significance
AHNAK	1.42	1.42	0.3682	ns
AKT1	−1.01	0.99	0.7589	ns
BMP1	1.37	1.37	0.4372	ns
BMP2	9.09	9.09	0.3455	ns
BMP7	1.09	1.09	0.5505	ns
CALD1	6.82	6.82	0.3162	ns
CAMK2N1	−1.11	0.90	0.5801	ns
CAV2	1.10	1.10	0.9019	ns
CDH1	−2.10	0.48	0.2298	ns
CDH2	12.75	12.75	0.2792	ns
COL1A2	7.91	7.91	0.3349	ns
COL3A1	7.14	7.14	0.1721	ns
COL5A2	5.05	5.05	0.2761	ns
CTNNB1	1.16	1.16	0.5810	ns
DSC2	3.77	3.77	0.1895	ns
DSP	−1.11	0.90	0.8669	ns
EGFR	3.96	3.96	0.2732	ns
ERBB3	−1.06	0.94	0.9219	ns
ESR1	1.03	1.03	0.7765	ns
F11R	−2.03	0.49	0.1831	ns
FGFBP1	5.10	5.10	0.2991	ns
FN1	−1.03	0.97	0.6603	ns
FOXC2	3.19	3.19	0.3804	ns
FZD7	1.59	1.59	0.3917	ns
GNG11	13.61	13.61	0.2704	ns
GSC	1.21	1.21	0.4862	ns
GSK3B	1.09	1.09	0.4016	ns
IGFBP4	−9.38	0.11	0.0702	ns
IL1RN	8.21	8.21	0.3060	ns
ILK	−1.19	0.84	0.5006	ns
ITGA5	3.25	3.25	0.0240	*
ITGAV	2.82	2.82	0.0044	**
ITGB1	−1.36	0.74	0.2466	ns
JAG1	2.11	2.11	0.2297	ns
KRT14	4.39	4.39	0.3209	ns
KRT19	−3.05	0.33	0.0106	*
KRT7	1.41	1.41	0.3650	ns
MAP1B	12.61	12.61	0.0064	**
MMP2	12.55	12.55	0.3182	ns
MMP3	11.10	11.10	0.2638	ns
MMP9	5.54	5.54	0.1943	ns
MSN	6.97	6.97	0.3459	ns
MST1R	7.10	7.10	0.2724	ns
NODAL	11.07	11.07	0.2393	ns
NOTCH1	1.76	1.76	0.0671	ns
NUDT13	−1.28	0.78	0.3323	ns
OCLN	1.48	1.48	0.0909	ns
PDGFRB	6.37	6.37	0.3969	ns
PLEK2	5.62	5.62	0.0992	ns
PPPDE2	5.45	5.45	0.0004	***
PTK2	2.15	2.15	0.0396	*
PTP4A1	1.70	1.70	0.0715	ns
RAC1	1.13	1.13	0.1019	ns
RGS2	5.27	5.27	0.1012	ns
SERPINE1	1.27	1.27	0.5273	ns
SIP1	1.57	1.57	0.3798	ns
SMAD2	1.48	1.48	0.0786	ns
SNAI1	1.72	1.72	0.3531	ns
SNAI2	1.54	1.54	0.5394	ns
SNAI3	4.14	4.14	0.2584	ns
SOX10	3.37	3.37	0.6731	ns
SPARC	10.16	10.16	0.3316	ns
SPP1	22.91	22.91	0.1439	ns
STAT3	1.75	1.75	0.0977	ns
STEAP1	2.80	2.80	0.5374	ns
TCF3	−1.15	0.87	0.6873	ns
TCF4	3.43	3.43	0.3132	ns
TFPI2	9.02	9.02	0.0067	**
TGFB1	−1.07	0.93	0.8974	ns
TGFB2	3.50	3.50	0.2845	ns
TGFB3	2.94	2.94	0.2623	ns
TIMP1	2.10	2.10	0.0119	*
TMEFF1	2.01	2.01	0.0694	ns
TMEM132A	1.21	1.21	0.6962	ns
TSPAN13	−1.10	0.91	0.3211	ns
TWIST1	5.07	5.07	0.4240	ns
VCAN	6.17	6.17	0.2604	ns
VIM	3.21	3.21	0.2349	ns
VPS13A	2.35	2.35	0.0244	*
WNT11	3.80	3.80	0.2421	ns
WNT5A	−1.19	0.84	0.8780	ns
WNT5B	2.66	2.66	0.3527	ns
ZEB1	11.59	11.59	0.2470	ns
ZEB2	7.31	7.31	0.3052	ns

) of gene expression data derived from QIAGEN RT² Profiler PCR array analysis, along with three figures (Figure 1, Figure 2 and Figure 3) showing the resulting heatmaps.

3. Methods

3.1. Materials

All materials and equipment used in this study are listed in

Table 4. Materials and equipment used in this study, including name, catalog number, and source (company or institution).

Material/Equipment	Company/Source	Catalog #
MCF-7 cells	ATCC (Manassas, VA, USA)	HTB-22
DMEM/F12 (50:50)	ATCC (Manassas, VA, USA)	10-090-CM
Antibiotic/Antimycotic Mixture	Corning Life Sciences (Corning, NY, USA)	30-004-Cl
Tissue Culture 6-Well Plates	Corning Life Sciences (Corning, NY, USA)	07-200-83
StemXVivo EMT Inducing Media Supplement *	Bio-Techne, (Minneapolis, MN, USA)	CCCM017
C66 ((2E,6E)-2,6-bis[(2-trifluoromethyl)benzylidene]cyclohexanone)	Institute of Chemistry, Ss. Cyril and Methodius University in Skopje, North Macedonia	N/A (self-synthesized)
B2BrBC ((2E,6E)-2,6-bis(2-bromobenzylidene)cyclohexanone)	Institute of Chemistry, Ss. Cyril and Methodius University in Skopje, North Macedonia	N/A (self-synthesized)
TRIzol Reagent	Invitrogen, Thermo Fisher Scientific (Waltham, MA, USA)	15596026
qScript cDNA SuperMix	Quantabio (Beverly, MA, USA)	95048
PerfeCTa SYBR Green FastMix	Quantabio (Beverly, MA, USA)	95072
RT2 Profiler PCR Array Human Epithelial to Mesenchymal Transition (EMT)	QIAGEN (Hilden, Germany)	330231, PAHS-090ZA
NanoDrop One Spectrophotometer	Thermo Fisher Scientific (Wilmington, DE, USA)	ND-ONE-W
SimpliAmp Thermal Cycler	Applied Biosystems, Thermo Fisher Scientific (Wilmington, DE, USA)	A24811
QuantStudio 3 Real-Time PCR System	Applied Biosystems, Thermo Fisher Scientific (Wilmington, DE, USA)	A28567
QuantStudio Design & Analysis Software (v1.5.1)	Applied Biosystems, Thermo Fisher Scientific (Wilmington, DE, USA)	N/A

* Containing anti-human E-cadherin, anti-human sFRP-1, anti-human DKK-1, recombinant human Wnt-5a, and recombinant human TGFβ.

.

3.2. Experimental Design

MCF-7 cells were seeded at 0.3 × 10⁶ cells per well into 6-well culture plates in DMEM/F12 (50:50) medium supplemented with antibiotic/antimycotic solution and StemXVivo EMT Inducing Media Supplement (1:100) and cultured at 37 °C in 5% CO₂ with 95% atmospheric air. After 48 h to allow cell attachment and equilibration, the culture medium was replaced with fresh medium containing one of the following: (1) EMT-inducer (EMT-inducing medium supplement with vehicle—DMSO); (2) EMT + C66 (EMT-inducing medium supplement with C66 in DMSO with a final concentration of 100 µM); or (3) EMT + B2BrBC (EMT-inducing medium supplement with B2BrBC in DMSO with a final concentration of 100 µM). Untreated MCF-7 cells (vehicle control) were cultured in medium without the EMT-inducing supplement. All treatment conditions were maintained for 72 h without refreshing the treatment solutions before sample harvesting. Each experimental condition was performed in duplicate, and the experiment was repeated three times for statistical analysis.

3.3. RNA Extraction

At the end of the 72 h treatment period, cells were washed 2× with phosphate-buffered saline (PBS, pH 7.4) and total RNA was extracted using the TRIzol/chloroform method: cells were lysed in TRIzol reagent (1 mL per well of a 6-well plate), followed by the addition of chloroform (0.2 mL per mL of TRIzol), vigorous mixing, and centrifugation. The aqueous phase containing RNA was carefully transferred to a fresh tube, and RNA was precipitated with isopropanol, washed with 75% ethanol, and resuspended in nuclease-free water.

3.4. RNA Quantification and Quality Control

RNA concentration and purity were determined using a NanoDrop One Spectrophotometer, measuring absorbance at 260 nm and 280 nm. The quality of RNA was assessed via the A260/A280 ratio (target range 1.8–2.0). All RNA samples were normalized to a final concentration of 1 μg total RNA in a total volume of 16 μL using nuclease-free water.

3.5. cDNA Synthesis

Complementary DNA (cDNA) was synthesized from 1 µg of total RNA using qScript cDNA SuperMix according to the manufacturer’s specifications. Briefly, 16 μL RNA was mixed with 4 µL qScript cDNA SuperMix and incubated in a SimpliAmp Thermal Cycler under the following conditions: 25 °C for 5 min, 42 °C for 30 min, and 85 °C for 5 min. The resulting cDNA was diluted 10-fold and stored at −20 °C until further use.

3.6. Quantitative RT² Profiler PCR Array

RT-qPCR was performed using the Human Epithelial to Mesenchymal Transition RT² Profiler PCR Array.

qPCR reactions were prepared according to the manufacturer’s protocol using the template cDNA, PerfeCTa SYBR Green FastMix, and nuclease-free water to a final volume of 25 µL per well. Reactions were loaded into the PCR array plate and analysis was performed on a QuantStudio 3 Real-Time PCR System with the following thermal cycling conditions: initial denaturation (10 min at 95 °C), PCR amplification (40 cycles; denaturation: 15 s at 95 °C, annealing/extension: 1 min at 60 °C), and dissociation curve analysis (denaturation: 15 s at 95 °C, annealing: 1 min at 60 °C, final denaturation: 15 s at 95 °C). Cycle threshold (Ct) values were detected using the QuantStudio Design & Analysis Software (v1.5.1) with default settings, including automatic baseline and threshold determination.

3.7. Data Analysis

Raw Ct values from the PCR array [9] were imported into the QIAGEN web-based analysis portal (GeneGlobe Data Analysis Center) [10] for statistical analysis and data normalization. Gene expression levels were normalized using the geometric mean of five housekeeping genes (ACTB, B2M, GAPDH, HPRT1, and RPLP0) to account for variations in RNA quantity and quality between samples. Relative gene expression differences between treatment groups were calculated using the comparative cycle threshold (ΔΔCt) method. For each gene, a fold change threshold of 2 was applied. To facilitate intuitive interpretation, fold regulation was also calculated. Statistical significance was assessed using a two-sample Student’s t-test, with p < 0.05 considered significant. Probability p-values from Student’s t-test were as follows: non-significant (ns; p > 0.05), * (0.01 < p < 0.05), ** (0.001 < p < 0.01), *** (0.001 < p < 0.0001), and **** (p < 0.0001). All three biological replicates were included in the analysis; no samples were excluded.

4. Limitations

This dataset has several major limitations. First, the data were generated in the MCF-7 breast cancer cell line; thus, the results may not be generalizable to other breast cancer subtypes, other cancer types, or normal epithelial cells. MCF-7 cells are of the luminal A subtype, and EMT characteristics may differ across basal-like or other molecular breast cancer subtypes. While this dataset focuses only on RNA-level changes in MCF-7 cells, complementary protein-level validations and functional assays across MCF-7, MDA-MB-231, and BT-474 cell lines are detailed in the original study [2]. Second, gene expression was measured at a single time point (72 h post-treatment), which does not capture the temporal dynamics of changes in gene expression, and the compounds’ long-term effects remain unknown. Earlier or later points might reveal additional effects. Third, although three biological replicates (separate experiments) per condition were used, the sample size limits the ability to detect subtle expression changes and may not capture them. Fourth, all experiments were performed in vitro using a two-dimensional cell culture, which does not adequately represent in vivo conditions. Additionally, EMT was induced using the StemXVivo EMT Inducing Media Supplement, which differs from other EMT induction methods (e.g., TGF-β, hypoxia, or combination approaches). Finally, although the RT² Profiler PCR array focuses on EMT-associated genes, other important genes involved in EMT regulation or cellular response may not be represented on this array.