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 Research Informatics Core (UICRIC).

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.

File Description Type
Sample1_summary.html Cellranger summary report for Sample1 result
Sample1_matrix/features.tsv.gz Gene features for Sample1 result
Sample1_matrix/barcodes.tsv.gz Feature list (cell barcodes) for Sample1 result
Sample1_matrix/matrix.mtx.gz Gene counts in sparse matrix format for Sample1 result
Sample1_matrix.h5 CellRanger H5 file for Sample1 result
Sample1.cloupe Cellranger Cloupe file for Sample1 result
Sample2_summary.html Cellranger summary report for Sample2 result
Sample2_matrix/features.tsv.gz Gene features for Sample2 result
Sample2_matrix/barcodes.tsv.gz Feature list (cell barcodes) for Sample2 result
Sample2_matrix/matrix.mtx.gz Gene counts in sparse matrix format for Sample2 result
Sample2_matrix.h5 CellRanger H5 file for Sample2 result
Sample2.cloupe Cellranger Cloupe file for Sample2 result
Sample3_summary.html Cellranger summary report for Sample3 result
Sample3_matrix/features.tsv.gz Gene features for Sample3 result
Sample3_matrix/barcodes.tsv.gz Feature list (cell barcodes) for Sample3 result
Sample3_matrix/matrix.mtx.gz Gene counts in sparse matrix format for Sample3 result
Sample3_matrix.h5 CellRanger H5 file for Sample3 result
Sample3.cloupe Cellranger Cloupe file for Sample3 result
Sample4_summary.html Cellranger summary report for Sample4 result
Sample4_matrix/features.tsv.gz Gene features for Sample4 result
Sample4_matrix/barcodes.tsv.gz Feature list (cell barcodes) for Sample4 result
Sample4_matrix/matrix.mtx.gz Gene counts in sparse matrix format for Sample4 result
Sample4_matrix.h5 CellRanger H5 file for Sample4 result
Sample4.cloupe Cellranger Cloupe file for Sample4 result

Sample list
Sample OriginalID
Library1 Library1

Method: Demultiplexing and gene expression quantification for 10X with CellRangerhttps://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger (version: 9.0.1)

Raw reads are mapped to the reference genome and demultiplexed into single cells using CellRanger.

Reference sequence database : hg38, v2024-Ahttps://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2024-A.tar.gz

CellRanger reference genome for human, hg38 v2024-A.

Figure 1 . Gene expression (GEX) summary by sample

Figure 2 . Gene expression (GEX) summary by capture library

Table 1 . Data processing summary statistics of gene expression by sample

Table 1 . Data processing summary statistics of gene expression by sample
Sample Library Cells Number of reads Confidently mapped to genome Confidently mapped to transcriptome Median UMI counts per cell Median genes per cell
Sample1 Library1 4,629 259,052,218 79.0% 63.1% 13,378 3,643
Sample2 Library1 5,958 337,191,931 83.7% 70.9% 13,900 3,556
Sample3 Library1 4,531 235,099,016 81.1% 67.5% 12,961 3,307
Sample4 Library1 5,048 164,735,238 82.1% 68.3% 8,305 2,652

Table 2 . Data processing summary statistics of gene expression by capture library

Table 2 . Data processing summary statistics of gene expression by capture library
Sample Cells Number of reads Confidently mapped to genome Confidently mapped to transcriptome Sequencing saturation
Library1 20,166 1,079,471,941 80.5% 66.5% 56.3%

Citations