GSM9076815: Bulk RNA-sequencing of bulk tumour for patient 11642; Homo sapiens; RNA-Seq
WGS: For FT organoids and PBMC samples, the Genomic DNA (gDNA) was extracted with the DNeasy Blood & Tissue Kits (Qiagen), and quantified by Qubit. Tumor bulk RNA seq:Tumor cells around 5,000-20,000 cells were sorted by Epcam+ by FACS. The RNA was extracted by GenElute Single Cell RNA Purification Kit (Sigma-Aldrich) , and quantified by Agilent RNA 6000 Pico Kit. The WGS libraries were prepared by Novogenes company and sequenced pair-ended on Illumina Novaseq X plus. For the tumor sample, tumor cells were sorted by Epcam+ by FACS, and the DNA was extracted by REPLI-g Advanced DNA Single Cell Kit and quantified by SpectraMax® Quant™ AccuBlue™ Pico dsDNA Assay Kit Cat. We used our in-house method DigiPico to construct the library. Tumor bulk RNA seq:The SMARTer Stranded Total RNA-Seq kit v2 - Pico Input (Takara) was used to prepare sequencing libraries which were indexed, enriched by 15 cycles of amplification, assessed using the Agilent TapeStation, and then quantified by Qubit. Sequenced pair-ended on Illumina Novaseq X plus