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DAC for the BCTL

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david.venet@bordet.be

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This DAC controls 7 datasets

Dataset ID	Description	Technology	Samples
EGAD50000000678	Zephir trial gene expression	Illumina NovaSeq 6000	24
EGAD50000000686	Spatial transcriptomics analysis of triple negative breast cancers Both bulk sequencing and ST were performed Counts, images etc are available at https://zenodo.org/doi/10.5281/zenodo.8135721	Illumina NovaSeq 6000 NextSeq 500	94
EGAD50000000746	Transcriptomics for the ALTTO study by high-throughput sequencing. 386 HER2+ breast cancers treated by trastuzumab were sequenced. Two fastq files are given for each sample.	Illumina NovaSeq 6000	386
EGAD50000002038	This dataset comprises bulk and single-nuclei multiomic profiles from patients with ER+/HER2- early breast cancer enrolled in the NeoRHEA phase 2 trial. The bulk RNA-seq component includes 78 pre-treatment and 49 post-treatment tumor samples from 97 patients. The single-nuclei component includes matched pre- and post-treatment samples from 37 patients, totaling 63 samples analyzed by simultaneous snRNA-seq and snATAC-seq. Combined, the data contains bulk transcriptional profiles and single-nuclei gene expression/chromatin accessibility matrices for over 226,000 high-quality nuclei, encompassing tumor, immune, and stromal cells. Technologies used include Illumina NovaSeq 6000 for sequencing and the 10x Genomics Chromium platform (Multiome kit for single-nuclei, standard RNA library prep for bulk).	Illumina NovaSeq 6000	130
EGAD50000002446	The dataset comprises whole-exome sequencing (WES) data generated from 160 samples, corresponding to matched tumor–normal pairs from breast cancer patients. For each subject, one tumor biopsy sample and one matched white blood cell (WBC) sample (germline control) are included. Sequencing data are provided as aligned BAM files with corresponding BAI index files. The data were generated using Illumina paired-end sequencing technology following hybrid-capture exome enrichment. The matched tumor–normal design enables accurate identification of somatic variants by filtering germline alterations, supporting downstream analyses such as mutation profiling, biomarker discovery, and personalized circulating tumor DNA (ctDNA) assay development.		160
EGAD50000002552	ER+/HER2- early breast cancer were treated with neoadjuvant immune-modulating SBRT and anti-CD73. The RNAseq dataset contains fastq files for 234 samples corresponding to 134 patients. There are 208 breast cancer samples, taken at screening (N=136) or week 6 (N=76). In addition, there are 26 lymph node samples taken at screening.	DNBSEQ-T7	234
EGAD50000003198	This dataset contains raw sequencing data from spatial transcriptomic profiling of 86 treatment-naive primary hormone receptor-positive, HER2-negative breast tumors from 85 patients. Libraries were generated using the 10x Genomics Visium Spatial Gene Expression workflow and sequenced on an Illumina NovaSeq 6000. The dataset comprises the FASTQ files associated with the spatial transcriptomic experiments included in this study.	Illumina NovaSeq 6000	87