biostudies-arrayexpressHelga BergholtzHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16918This experiment includes GeoMx spatial transcriptomic analyses of FFPE tissue from breast ductal carcinoma in situ lesions from 16 patients. All lesions were subject to ER, PR, HER2 and Ki67 immunohistochemistry and assigned a molecular subtype. The main aim was to compare DCIS of the two subtypes Triple Negative and Luminal A. From each patient sample, multiple regions of interest (ROIs) were selected and the synthetics nucleotide oligos attached to RNA probes were sequenced separately. Tumor areas and stromal areas were sequenced separately. The data provided is the raw (unnormalized) count matrix, and Q3 normalized data from tumor and stroma areas separetely in addition to corresponding metadata files to enable linking between patient ID and ROI.biostudies-arrayexpressSample Collection - 5µm FFPE tissue sections were placed in Leica Bond Plus slides and prepared according to the vendors instructions. Tissue were stained with PanCK, SMA and CD45 antibodies. Regions of interests were selected with under guidance of a pathologist, including areas with intraductal cancer cell growth and periductal stromal areas. Segments from cancer cells and stroma were analyzed separately. Stromal segments were segmented based on CD45 status (CD45+ and CD45-).Sequencing - Paired-end sequencing was performed using NovaSeq 6000 sequencer with an S4 v1.5 35-cycle flow cell (Illumina).Nucleic Acid Extraction - In the GeoMX method, probes are attached to RNA within the tissue section. After ROI selection, oligo tags attached to probes are cleaved off and sequenced. This was performed according to Bruker's protocol: https://www.brukerspatialbiology.com/wp-content/uploads/2022/06/MAN-10153-01-GeoMx-DSP-NGS-Readout-User-Manual.pdfLibrary Construction - Library preparation and PCR were performed according to the manufacturer’s instructions, and the samples were purified twice using AMPure XP Beads (Beckman Coulter) at a 1.2X bead-to-sample ratio.MIAME ScoreOrganizationAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Quality control and normalization were performed using the GeoMX software separately for cancer cell ROIs and stromal ROIs. Genes expressed above limit of detection (>2) in more than one ROI were included. ROIs with fewer than 10% of targets above the limit of detection were removed (four CD45+ ROIs). The final cancer cell dataset included 72 ROIs and gene expression data for 9554 genes, and the final stroma dataset included 65 CD45-negative ROIs and 60 CD45-positive ROIs with gene expression data for 11266 genes. Normalization was performed using the third quantile (Q3) method.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000spatial transcriptomics by high-throughput sequencingHomo sapiensImmune cell landscape and metabolic gene activity distinguish triple negative from luminal A-like Ductal Carcinoma In SituHelga BergholtzJens Henrik NorumTherese SørlieJens Henrik Norum, Hossein Schandiz, Torill Sauer, Jürgen Geisler, Lorant Farkas, Neda Hekmati, Carina Strell, Helga Bergholtz, Therese SørliefalseSpatial transcriptomic analyses of triple negative and luminal A breast ductal carcinoma in situThis experiment includes GeoMx spatial transcriptomic analyses of FFPE tissue from breast ductal carcinoma in situ lesions from 16 patients. All lesions were subject to ER, PR, HER2 and Ki67 immunohistochemistry and assigned a molecular subtype. The main aim was to compare DCIS of the two subtypes Triple Negative and Luminal A. From each patient sample, multiple regions of interest (ROIs) were selected and the synthetics nucleotide oligos attached to RNA probes were sequenced separately. Tumor areas and stromal areas were sequenced separately. The data provided is the raw (unnormalized) count matrix, and Q3 normalized data from tumor and stroma areas separetely in addition to corresponding metadata files to enable linking between patient ID and ROI.2026-06-26T00:00:00Z2026-06-26T07:38:21.084Z2026-04-15T13:36:46.349ZE-MTAB-16918EFO_0002944EFO_0004170EFO_0030005EFO_0005518EFO_0003816EFO_0004184