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| Status |
Public on Jan 08, 2025 |
| Title |
Control GEX Sample 2 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
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| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Nuclei were isolated from approximately 20 mg of frozen mouse liver harvested from control (TCF7L2LoxP/LoxP) and liver-specific TCF7L2 mutant mice (Hep-TCF7L2ΔDBD). 10X Genomics Chromium single nuclei multiome gene expression and Assay for Transposase-Accessible Chromatin (ATAC) libraries were prepared from approximately 5000 nuclei/mice at the Genome Sequencing Facility at the University of Texas Health at San Antonio (UTHSA). Liver samples were processed in pairs (one control and one mutant) on three consecutive days to minimize batch effects. Library quality and quantity were assessed using the 2100 Bioanalyzer and were sequenced on a NovaSeq 6000 (Illumina, CA, USA).
Starting with frozen tissue, a wide range of sample types can be dissociated with the Chromium Nuclei Isolation Kit. The resulting single nuclei suspension is transposed in bulk before partitioning into GEMs on the Chromium instrument. DNA fragments and the 3’ ends of mRNA from individual nuclei are identified with unique 10x Barcodes. Two complementary libraries are generated from each sample, followed by sequencing and data analysis. 10x Barcodes are used to associate reads back to cells of origin, and gene expression and open chromatin profiles are linked with certainty
10X Single Cell Multiome ATAC + Gene Expression
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
2645-C_GEX
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| Data processing |
Gene counting, peak calling, barcode processing, and aggregation were done using the Cell Ranger Arc v2.0.2 software (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files
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| Submission date |
Jul 27, 2023 |
| Last update date |
Jan 08, 2025 |
| Contact name |
Luke Norton |
| E-mail(s) |
nortonl@uthscsa.edu
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| Organization name |
UTHSCSA
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| Street address |
7703 Floyd Curl Dr
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| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE239480 |
The Role of TCF7L2 in Hepatic Metabolic Zonation |
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| Relations |
| SRA |
SRX21130844 |
| BioSample |
SAMN36687917 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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