title: GSM8416609: F_7_carcinoma_7d; Homo sapiens; OTHER
library_construction_protocol: Sections were deparaffinized and subjected to heat-induced protein epitope retrieval (using retrieval buffer at pH 9, Thermo Fisher Scientific, 00-4956-58) for 15 minutes at 100°C using a steam cooker. Retrieval for mRNA was performed using proteinase K (Thermo Fisher Scientific, 25530049) at 1µg/ml for 15 minutes. Slides were incubated with the human Whole Transcriptome Atlas (WTA) probe panel (Nanostring, NA-GMX-RNA-NGS-HuWTA-4, Lot HWTA21003) at 37°C in a humidified environment overnight. Sections were washed according to standard protocols and direct immunofluorescence was performed with antibodies against CD34 conjugated to Alexa-647 (Novus Biologicals, clone QBEnd-10, NBP2-34713AF647), Pan-cytokeratin conjugated to to Alexa532 (Novus Biologicals, clone AE1/AE3, NBP2-33200), CD45 conjugated to Alexa594 (clone 2B11 + PD7/26, Novus Biologicals, NBP2-34528), and a nuclear counterstain (Syto-13, Nanostring). DSP device run was performed according to the manufacturer's protocol (https://university.nanostring.com/geomx-dsp-ngs-readout-user-manual). Library preparation and sequencing were performed according to the manufacturers' protocol (https://university.nanostring.com/geomx-dsp-ngs-readout-user-manual). The library was sequenced using an Illumina NextSeq 550 sequencer with the specifications provided by Nanostring (paired-end reads at length 27, index length 8, PhiX 5%) at a final library concentration of 1.6 pM using a NextSeq 550 High Output 75-cycle kit (Illumina, 20024906).