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.

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File Description Type
Sample1_cellranger_files.zip ZIP file of CellRanger output for Sample1 result
Sample1_summary.html Cellranger summary report for Sample1 result
Sample1.cloupe Cellranger Cloupe file for Sample1 result
Sample2_cellranger_files.zip ZIP file of CellRanger output for Sample2 result
Sample2_summary.html Cellranger summary report for Sample2 result
Sample2.cloupe Cellranger Cloupe file for Sample2 result
Sample3_cellranger_files.zip ZIP file of CellRanger output for Sample3 result
Sample3_summary.html Cellranger summary report for Sample3 result
Sample3.cloupe Cellranger Cloupe file for Sample3 result
Sample4_cellranger_files.zip ZIP file of CellRanger output for Sample4 result
Sample4_summary.html Cellranger summary report for Sample4 result
Sample4.cloupe Cellranger Cloupe file for Sample4 result

Sample list
Sample OriginalID
20k_Mouse_PBMC_Splenocyte_5p_gem-x_multiplex_BCR 20k_Mouse_PBMC_Splenocyte_5p_gem-x_multiplex_BCR
20k_Mouse_PBMC_Splenocyte_5p_gem-x_multiplex_GEX 20k_Mouse_PBMC_Splenocyte_5p_gem-x_multiplex_GEX
20k_Mouse_PBMC_Splenocyte_5p_gem-x_multiplex_TCR 20k_Mouse_PBMC_Splenocyte_5p_gem-x_multiplex_TCR

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: cellranger 10.0.0)

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

Figure 1 . Gene expression (GEX) summary by sample

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

Figure 3 . VDJ summary by sample

Figure 4 . VDJ 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 4415 102595479 0.8572416139311558 0.7244679953197548 7045 2607
Sample2 Library1 5770 133316936 0.8744798110271601 0.7377039403305818 7147 2747
Sample3 Library1 4871 123322757 0.8407543791775592 0.6930443746080053 7404 2664
Sample4 Library1 5139 112371821 0.8733557232288689 0.7371562128551783 6876 2717

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 20195 584109020 0.8215036295792865 0.6251008912685512 0.5058704677204019

Table 3 . Data processing summary statistics of VDJ data by sample

Table 3 . Data processing summary statistics of VDJ data by sample
Sample Library Library Type Reads mapped to IGH Reads mapped to IGK Reads mapped to IGL Cells Reads mapped to TRA Reads mapped to TRB
Sample1 Library1 VDJ B 0.2459843247615746 0.4155297700375907 0.24119202506950535 2271
Sample1 Library1 VDJ T 742 0.2081728221798966 0.6267381746838706
Sample2 Library1 VDJ B 0.25265142587791656 0.3936986600598978 0.28371550272184315 3140
Sample2 Library1 VDJ T 1418 0.22683323510321624 0.6221137131730318
Sample3 Library1 VDJ B 0.2527336842215409 0.4257222681469545 0.2210491069092888 2473
Sample3 Library1 VDJ T 806 0.1926877353000558 0.6174273464685692
Sample4 Library1 VDJ B 0.2468500582641323 0.39493113915278494 0.29653002086117 2784
Sample4 Library1 VDJ T 1189 0.2290741194165588 0.6195889527940317

Table 4 . Data processing summary statistics of VDJ data by capture library

Table 4 . Data processing summary statistics of VDJ data by capture library
Sample Library Type Number of reads Reads mapped to IGH Reads mapped to IGK Reads mapped to IGL Cells Reads mapped to TRA Reads mapped to TRB
Library1 VDJ B 156048766 0.24270967415141115 0.38555372807017546 0.26375083428680396 10668
Library1 VDJ T 144886269 4155 0.18499300493737103 0.5333786969042085

Citations