The output Illumina base call files from both sequencing runs were merged and converted to FASTQ files using Cell Ranger software v2.0.1, which included Illumina’s bcl2fastq v2.19.1.403. FASTQ files of each mouse sample were converted to count matrices using Cell Ranger software, based on transcriptome reference of Mus musculus (mm10 1.2.0). Barcodes (25,707) were identified as cells, according to Cell Ranger’s algorithm of calling cell barcodes. This algorithm takes as input the expected number of recovered cells, which was set to 3000 cells in our study. It then orders all barcodes by their unique molecular identifier (UMI) content and computes the number of UMIs at the 99th percentile. All barcodes whose total UMI count was at most 1/10 of this number were referred to as low-quality cells and discarded.

Note: The content above has been extracted from a research article, so it may not display correctly.

Please log in to submit your questions online.
Your question will be posted on the Bio-101 website. We will send your questions to the authors of this protocol and Bio-protocol community members who are experienced with this method. you will be informed using the email address associated with your Bio-protocol account.

We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.