CellRanger
Generated by: Mark Maienschein-Cline
Report date: March 27, 2020
Overview
When you publish manuscripts based on data generated at our facility, we would greatly appreciate an acknowledgement of our efforts. Please cite our facility as follows (for example):
Basic processing of the raw data were performed by the University of Illinois at Chicago Core for Research Informatics (UICCRI).
We adhere to a general policy for acknowledgements and authorship as established by the Association for Biomolecular Resource Facilities (ABRF) , and we support the following statement from the ABRF.
The existence of core facilities depends in part on proper acknowledgment in publications. This is an important metric of the value of most core facilities. Proper acknowledgment of core facilities enables them to obtain financial and other support so that they may continue to provide their essential services in the best ways possible. It also helps core personnel to advance in their careers, adding to the overall health of the core facility.
Please contact us for assistance in drafting manuscripts.
Details
- Method: Demultiplexing and gene expression quantification for 10X with CellRanger
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Raw reads are mapped to the reference genome and demultiplexed into single cells using CellRanger.
- Reference sequence database : mm10
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CellRanger reference genome for mouse mm10.
Table 1. Data processing summary statistics Download table data
| Stats | Estimated Number of Cells | Median UMI Counts per Cell | Median Genes per Cell | Number of Reads | Sequencing Saturation | Valid Barcodes | Reads Mapped Confidently to Genome | Reads Mapped Confidently to Transcriptome |
|---|---|---|---|---|---|---|---|---|
| sample1 | 1967 | 99 | 85 | 717367 | 0.8% | 65.3% | 75.6% | 54.4% |
| sample2 | 5401 | 50 | 45 | 1036378 | 0.5% | 65.0% | 77.7% | 48.8% |