characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2023-10-12T22:00:08Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2023-10-12T22:00:08Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA113602115
characteristics.characteristic: External Id
characteristics.text: Laboratory of Translational Research, AULS-IIRCCS di Reggio Emilia
characteristics.characteristic: INSDC center name
characteristics.text: 2023-10-12T22:00:08Z
characteristics.characteristic: INSDC first public
characteristics.text: 2023-10-12T22:00:08Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS15596496
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-13069:BIN_3 | 010 | CK
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.characteristic: broker name
characteristics.text: not collected
characteristics.characteristic: collection date
characteristics.text: human
characteristics.characteristic: common name
characteristics.text: Protocols: Spatial Transcriptomic was performed using the GeoMx DSP® (Nanostring technologies, Seattle, WA, USA) starting from slides of 5μm FFPE diagnostic biopsies. In order to perform spatial selection, slides were stained with GeoMx Solid Tumor TME Morphology Kit (Nanostring technologies) including antibodies against CytoKeratin (CK), CD45 and SYTO-13 as nuclear stain. On each slide, the pathologist designed regions of interest (ROIs) representative of the tumor and tumor microenvironment. CK+ regions were classified as tumor, CK- regions were classified as tumor microenvironment. Microenvironment regions were further subdivided in CD45+ (immune-compartment) and CD45- (stroma). The slides were hybridized with the GeoMx® Cancer Transcriptome Atlas panel according to manufacturer protocol. After AOIs selection and photo-cleavage GeoMx RNA probes were sequenced Hybridized RNA-probes were collected from each of the selected AOIs, and libraries for NGS sequencing were constructed by GeoMx® Seq Code Pack (Nanostring technologies). Libraries were pooled according to AOIs dimension, purified by AMPure XP beads (Beckman Coulter, Brea, Cali-fornia, USA) clean up and finally resuspended in a volume proportional to the number of pooled AOIs. The quality and quantity of library pools were evaluated by Agilent Bioanalyzer.
characteristics.characteristic: description
characteristics.text: adult
characteristics.characteristic: developmental stage
characteristics.text: triple-negative breast cancer
characteristics.characteristic: disease
characteristics.text: not collected
characteristics.characteristic: geographic location (country and/or sea)
characteristics.text: 15-pCR
characteristics.characteristic: individual
characteristics.text: not applicable
characteristics.characteristic: isolate
characteristics.text: CK+
characteristics.characteristic: markers
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: breast
characteristics.characteristic: organism part
characteristics.text: pathological complete response
characteristics.characteristic: response to treatment
characteristics.text: tumor
characteristics.characteristic: sampling site
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: female
characteristics.characteristic: sex
characteristics.text: BIN_3 | 010 | CK
characteristics.characteristic: title