|
Status |
Public on May 21, 2024 |
Title |
AKPS in PlexinB2 OE, ATAC, replicate 2 |
Sample type |
SRA |
|
|
Source name |
liver
|
Organism |
Mus musculus |
Characteristics |
tissue: liver genotype: AlbCre;dCas9SPH treatment: AAV8-sgPlxnb2-OE-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 |
SAMN41472947 |
SRA |
SRX24621728 |