biostudies-arrayexpressLesang ShenHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17604This experiment was designed to characterize tumor microenvironmental cell states associated with differential lymph node metastatic propensity in breast cancer. FFPE primary breast tumor specimens from 14 patients were analyzed, including 7 Aggressive cases with primary tumors ≤2 cm and ≥4 metastatic lymph nodes and 7 Mild cases with primary tumors ≥3.5 cm and no lymph node involvement. Single-nucleus transcriptomic libraries were generated using the snRandom-seq workflow with random-primer-based RNA capture and sequenced on an Illumina NovaSeq 6000 platform.biostudies-arrayexpressSequencing - The resulting snRandom-seq libraries were sequenced on an Illumina NovaSeq 6000 platform. Raw sequencing reads were generated for subsequent quality control, alignment to the human reference genome, and generation of feature-barcode expression matrices.Sample Collection - Formalin-fixed paraffin-embedded (FFPE) primary breast tumor specimens were retrospectively obtained from patients who underwent curative surgery at the Second Affiliated Hospital, Zhejiang University School of Medicine, between 2021 and 2022. Patients were stratified using an extreme-phenotype design according to primary tumor size and lymph node involvement. Seven Aggressive cases, defined as primary tumors ≤2 cm with ≥4 metastatic lymph nodes, and seven Mild cases, defined as primary tumors ≥3.5 cm without lymph node involvement, were selected for snRandom-seq. All samples were collected with informed consent under approval of the institutional ethics committee.Nucleic Acid Extraction - Single nuclei were prepared from FFPE breast tumor specimens according to established snRandom-seq protocols and the manufacturer's instructions. The resulting single-nucleus suspensions were processed using the VITAcruizer Single-Cell Preparation System v1.0 (M20 Genomics) for subsequent nucleic acid capture.Library Construction - Single-nucleus total RNA libraries were generated using snRandom-seq. Droplet formation, single-nucleus encapsulation and nucleic acid capture were performed using the VITAcruizer Single-Cell Preparation System v1.0, followed by library construction and purification using the VITApilote High-Throughput Eukaryotic Single-Cell Transcriptome (Paraffin) Kit (M20 Genomics). Libraries contained P5 and P7 sequencing adapters.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Raw sequencing reads were processed using fastp with default parameters to remove adapter sequences and low-quality reads. The filtered reads were aligned to the human reference genome GRCh38-2020-A using VITASEER v1.0 to generate feature-barcode matrices. Nuclei expressing more than 100 genes and with a mitochondrial UMI fraction below 20% were retained for downstream analysis.Data Transformation - UMI count matrices were library-size normalized and log-transformed using Scanpy v1.9.3. Data were scaled after regression of total UMI counts and mitochondrial UMI percentage.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RAN-seq of total RNA from single cellsHomo sapiensLesang ShenfalseSingle-nucleus RNA sequencing of FFPE breast cancer tissues with contrasting lymph node metastatic propensityThis experiment was designed to characterize tumor microenvironmental cell states associated with differential lymph node metastatic propensity in breast cancer. FFPE primary breast tumor specimens from 14 patients were analyzed, including 7 Aggressive cases with primary tumors ≤2 cm and ≥4 metastatic lymph nodes and 7 Mild cases with primary tumors ≥3.5 cm and no lymph node involvement. Single-nucleus transcriptomic libraries were generated using the snRandom-seq workflow with random-primer-based RNA capture and sequenced on an Illumina NovaSeq 6000 platform.2026-09-20T00:00:00Z2026-09-20T01:00:38.965Z2026-09-10T10:34:19.395ZE-MTAB-17604ERP205754EFO_0002944EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0004184