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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Output Files

File Description Type
sc5p_v2_mm_balbc_T_1k_5gex_matrix/features.tsv.gz Gene features for sc5p_v2_mm_balbc_T_1k_5gex result
sc5p_v2_mm_balbc_T_1k_5gex_matrix/barcodes.tsv.gz Feature list (cell barcodes) for sc5p_v2_mm_balbc_T_1k_5gex result
sc5p_v2_mm_balbc_T_1k_5gex_matrix/matrix.mtx.gz Gene counts in sparse matrix format for sc5p_v2_mm_balbc_T_1k_5gex result
sc5p_v2_mm_balbc_T_1k_5gex.cloupe Cellranger Cloupe file for sc5p_v2_mm_balbc_T_1k_5gex result
sc5p_v2_mm_balbc_T_1k_t_airr_rearrangement.tsv Annotated contigs and consensus sequences of VDJ rearrangements in the AIRR format for sc5p_v2_mm_balbc_T_1k_t result
sc5p_v2_mm_balbc_T_1k_t_all_contig_annotations.csv High-level and detailed annotations of each contig for sc5p_v2_mm_balbc_T_1k_t result
sc5p_v2_mm_balbc_T_1k_t_all_contig_fasta.gz Sequences for assembled VD(J) contigs for sc5p_v2_mm_balbc_T_1k_t result
sc5p_v2_mm_balbc_T_1k_t_consensus_annotations.csv High-level and detailed annotations of each clonotype consensus sequence for sc5p_v2_mm_balbc_T_1k_t result
sc5p_v2_mm_balbc_T_1k_t_clonotypes.csv High-level descriptions of each clonotype for sc5p_v2_mm_balbc_T_1k_t result
sc5p_v2_mm_balbc_T_1k_t_filtered_contig_annotations.csv High-level annotations of each high-confidence, cellular contig for sc5p_v2_mm_balbc_T_1k_t result
sc5p_v2_mm_balbc_T_1k_t.cloupe Cellranger Vloupe file for sc5p_v2_mm_balbc_T_1k_t result

Details

Method: Demultiplexing and gene expression quantification for 10X with CellRanger

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

FiguresReturn to top

Figure 1. Gene expression (GEX) sample summary

TablesReturn to top

Table 1. Data processing summary statistics of gene expression samples Download table data

Sample 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
sc5p_v2_mm_balbc_T_1k_5gex 992 3976 1649 97505715 91.9% 94.4% 85.1% 65.6%

Additional filesReturn to top

Details

Method: Demultiplexing and VD(J) region quantification for 10X with CellRanger

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

FiguresReturn to top

Figure 1. VDJ sample summary

TablesReturn to top

Table 1. Data processing summary statistics of VDJ samples Download table data

Sample Estimated Number of Cells Number of Cells With Productive V-J Spanning Pair Median TRA UMIs per Cell Median TRB UMIs per Cell Number of Read Pairs Valid Barcodes Reads Mapped to Any V(D)J Gene Reads Mapped to TRA Reads Mapped to TRB
sc5p_v2_mm_balbc_T_1k_t 785 618 5 11 6289407 97.4% 94.2% 21.0% 73.1%

Additional filesReturn to top

Citations