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mRNA-seq study performed on MCF-7 breast cancer cells treated with a combination of vitamins A and D

GSE221019 Homo sapiens Expression profiling by high throughput sequencing 6 samples Submitted 2025/07/30 Platform GPL24676
Summary
MCF-7 breast cancer cells were grown and maintained and treated with a combination of Vitamin D2 and D3 and all trans-retinoic acid (ATRA) at 1.5 µg/ml for four hours. The cells were harvested, RNA was isolated and analyzed for integrity using Agilent 4200 TapeStation and RNA Screen Tape. RNA-seq libraries were prepared using a Universal Plus mRNASeq kit, and library fragment size distribution was confirmed by electrophoresis using a 2200 TapeStation system with D1000 ScreenTape. Sequencing was carried out on NovaSeq 6000, SP flowcell, 2x50 nt reads. General quality-control metrics were obtained using FastQC and raw reads were aligned to human reference genome hg38 using STAR and BWA MEM. ENSEMBL genes were quantified using FeatureCounts, and differential expression statistics were computed using edgeR. Specific gene expression was measured and verified using qPCR.
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Direct links to NCBI, no account and no request form: the whole study as GSE221019_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 6 samples. Raw sequencing reads are also available from ENA.

Also filed as BioProject PRJNA912599 and SRA study SRP413206. Searching any of these in the dataset finder brings you back here.

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