Project description:For single cell RNA sequencing analysis, whole cell population isolated from two breast cancer bone metastases and associated organoid models were analyzed by 10X genomic single cell RNA platform. Raw BCL files from Novaseq6000 was converted to FASTQ files with cellranger (Version: 3.1.0) mkfastq function. Cellranger count function was then applied for read alignment, barcode and UMI counting using GRCh38 as reference. scCB2 and DoubletFinder were used to predict and remove empty droplets and doublets of single cell data. Cells with number of features less 300 and more than 9000 were further filtered out based on the distribution of number of features. For bulk RNA sequencing, RNA were extracted from FFPE preserved primary tumor and bone metastasis. Library was prepared with TruSeq Stranded mRNA for FFPE kit, and sequenced by NextSeq 500 with high output 150 cycle kit.
Project description:This submission contains raw 10x Genomics Visium HD Spatial Gene Expression FASTQ files from three FFPE mucosa-associated lymphoid tissue lymphoma samples analyzed in the O2 marginal zone lymphoma study. Processed Space Ranger and downstream spatial transcriptomics files will be added before final GEO release. Submitter contact email: lcxujiadai@163.com.
Project description:Spatial gene expression profiling of mouse thoracic spine tissue using the 10x Genomics Visium platform (FFPE, probe-based chemistry). Library IVD2 was profiled on Visium slide V11A19-364 capture area D1. This capture area contains both mutant and control tissue regions. Raw FASTQs comprise two sequencing lanes (L001 and L002) of the same IVD2 library (8 files total).
Project description:This study used formalin-fixed paraffin-embedded (FFPE) human tissue collected for the Integrated teChnologies for Improved polyp SurveillancE (INCISE) collaborative from polypectomies performed within the Scottish BCSP in the NHS Greater Glasgow and Clyde health board between 2009-2016 in patients who underwent further colonoscopy between 6 months and 6 years after the index colonoscopy. The extracted DNA was then passed to the Genomics Innovation Alliance (formerly Glasgow Precision Oncology Laboratory; GPOL) for genomic sequencing using their bespoke Cancer Plus panel. The output from the sequencing is FASTQ files and VCF files.