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| Status |
Public on Jul 06, 2023 |
| Title |
Liver, 5-months post engraftment, replicate2, snRNA-seq (dataset II) |
| Sample type |
SRA |
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| Source name |
Liver
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| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
tissue: Liver
cell type: Hepatocytes
treatment: 5-months post-engraftment
sample type: 5-months post engraftment
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| Extracted molecule |
total RNA |
| Extraction protocol |
To identify and characterize cell states associated with AAV transduction in human heptocytes, we employed a droplet-based (10x chromium) single nucleus transcriptomics approach. Hepatic nuclei were isolated and profiled from (a) human hepatocytes before engraftment, (b) liver samples from FRG mice engrafted with human hepatocytes, and (c) liver samples from FRG mice engrafted with human hepatocytes, treated with two AAV vectors (LLK03, REDH).
Libraries were prepared from single nucei. Breifly, nuclei were isoalted from flash-frozen chunks of tissue, which were homogenized using a Kimble Dounce tissue grinder, followed by straining with a 40 μm cell strainers, two rounds of centrifugation at 500g. Nuclei were stained with DAPI and proridium iodide, followed by FACS sorting to isolate PI-positive nuclei. Libraries were then prepared using a 10x Genomics Chromium Single Cell 3’v3 Reagent Kits were used according to manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Nuclear RNA
high2
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: Combined GRCh38, mm10, AAV reference
Supplementary files format and content: Tab-separated values files and matrix files
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| Submission date |
Jul 08, 2022 |
| Last update date |
Jul 06, 2023 |
| Contact name |
Marti Cabanes-Creus |
| E-mail(s) |
mcabanescreus@cmri.org.au
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| Organization name |
Children's Medical Research Institute
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| Street address |
214 Hawkesbury Rd
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| City |
Westmead |
| State/province |
NSW |
| ZIP/Postal code |
2145 |
| Country |
Australia |
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| Platform ID |
GPL25526 |
| Series (1) |
| GSE207809 |
Development of an AAV-LK03 variant with improved liver lobular biodistribution in the humanised FRG model II |
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| Relations |
| BioSample |
SAMN29617762 |
| SRA |
SRX16105369 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6319632_ROD_C5_barcodes.tsv.gz |
29.7 Kb |
(ftp)(http) |
TSV |
| GSM6319632_ROD_C5_features.tsv.gz |
680.6 Kb |
(ftp)(http) |
TSV |
| GSM6319632_ROD_C5_matrix.mtx.gz |
61.0 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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