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Sample GSM8282889 Query DataSets for GSM8282889
Status Public on May 21, 2024
Title AKPS in sgNT, ATAC, replicate 1
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 SAMN41472949
SRA SRX24621726

Supplementary file Size Download File type/resource
GSM8282889_NT1_atac_fragments.tsv.gz 1.8 Gb (ftp)(http) TSV
GSM8282889_NT1_atac_peaks.bed.gz 781.9 Kb (ftp)(http) BED
GSM8282889_NT1_per_barcode_metrics.csv.gz 18.7 Mb (ftp)(http) CSV
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Raw data are available in SRA

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