Raw sequencing data was acquired from the McDermott Sequencing Core at UT Southwestern in the form of binary base call (BCL) files. BC files were de-multiplexed with the 10X Genomics i7 index (used during library preparation) using Illumina’s bcl2fastq v2.19.1 and the mkfastq command from 10X Genomics CellRanger v3.0.2 suite. Resulting FASTQ files were checked for quality using FASTQC (v0.11.5).99 A reference mouse genome-annotation index was built using mouse genome (GRCm38p6) and Gencode annotation (vM17) with mkref command from 10X Genomics CellRanger v3.0.2 suite. Extracted and quality passed Extracted FASTQ reads were then aligned to reference mouse genome-annotation index and raw count tables were generated using count command from 10X Genomics CellRanger v3.0.2 suite. Cellbender was then run on the raw unfiltered count tables to discard potential ambient RNA.100 (link) Potential doublets were identified with DoubletFinder using filtered count tables generated by CellBender.101 (link) This produced an expression matrix containing cells as rows and genes as columns which was used for downstream analysis.
Genomics cellranger v3
Manufactured by 10x Genomics
CellRanger v3.0.2 is a software suite developed by 10x Genomics for processing single-cell RNA sequencing data. It performs tasks such as demultiplexing, barcode processing, and gene expression quantification.
Automatically generated - may contain errors
Lab products found in correlation
2 protocols using genomics cellranger v3
1
Single-cell RNA-seq pipeline for mouse
2
Single-cell RNA-seq Workflow for Transcriptome Analysis
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Raw sequencing data were acquired from the North Texas Genome Center at the University of Texas at Arlington and McDermott Sequencing Core at UT Southwestern in the form of binary base call (BCL) files. Raw BCL files were then demultiplexed with 10x Genomics i7 indices (used during library preparation) using Illumina’s bcl2fastq v2.19.1 and “cellranger mkfastq” from 10x Genomics CellRanger v3.0.2 tools. Extracted paired-end reads (28 bp long R1–16 bp 10x cell barcode and 12 bp UMI sequence information, 124 bp long R2—transcript sequence information from cDNA fragment) were first checked for read quality using FastQC v0.11.5 (FastQC, Babraham Bioinformatics, URL: FastQC">https://www.bioinformatics.babraham.ac.uk/projects/FastQC ). Extracted paired-end reads were then aligned to the reference human genome (GRCh38.p12) from University of California Santa Cruz (UCSC) genome browser and reference human annotation (Gencode v28) and counted using “cellranger count” from 10x Genomics CellRanger v3.0.2 tools. Since the nuclear transcriptome contained unspliced transcripts, reads mapping to a pre-mRNA reference file were counted. The resulting raw UMI count matrix contains genes as rows and nuclei as columns and was further used for downstream analysis.
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