|
| Status |
Public on May 21, 2024 |
| Title |
AKPS in sgNT, ATAC, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
genotype: AlbCre;dCas9SPH
treatment: AAV8-sgNT-EF1a-EGFP
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For each sample (2 sgNT and 2 sgPlxnb2 OE livers), three 50 μm liver sections were transferred into a pre-chilled gentleMACS C-tube (Miltenyi) and homogenized in the gentleMACS™ Octo Dissociator with 2 mL nuclei extraction buffer (Miltenyi). The nuclei suspension was filtered through a 70 µm SmartStrainer into a DNA-low binding 5 mL Tube (Eppendorf) and spun down at 150g for 3 minutes, at 4 °C. The pellet was resuspended in 5 mL 1% BSA in PBS and strained through a 30 µm SmartStrainer into a new tube. Upon centrifugation, the pellet was washed again in 5 mL 1% BSA in PBS. Nuclei were resuspended in 500 µL 1% BSA in PBS, counted and visually inspected.
16’000 nuclei per sample were profiled with the Chromium Single Cell Multiome ATAC + Gene Expression kit (10x) according to manufacturer’s instructions. Libraries were quality controlled and sequenced as described above.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
BCL files were demultiplexed using Bcl2fastq v2.20.0.422 from Illumina, then single nucleus count matrices were generated using Cell Ranger Arc (10X Genomics) with GRCm38 v2020-A gene code
Assembly: GRCm38
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files.
Library strategy: Single Cell Multiome ATAC + Gene Expression
|
| |
|
| Submission date |
May 21, 2024 |
| Last update date |
May 21, 2024 |
| Contact name |
Costanza Borrelli |
| E-mail(s) |
costanza.borrelli@bsse.ethz.ch
|
| Organization name |
ETH Zurich
|
| Street address |
Mattenstrasse 26
|
| City |
Basel |
| ZIP/Postal code |
4028 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE267982 |
In vivo interaction screening reveals liver-derived constraints to metastasis [Single Cell Multiome ATAC + Gene Expression] |
|
| Relations |
| BioSample |
SAMN41472945 |
| SRA |
SRX24621730 |
