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Sample GSM7173299 Query DataSets for GSM7173299
Status Public on Jan 16, 2024
Title intermittent fasted, p53 KO [HFD-IF-KO]
Sample type SRA
Source name eWAT
Organism Mus musculus
Characteristics tissue: eWAT
strain: BL6J
cell type: Adipoq-CreERT2 x p53-floxed
genotype: KO
treatment: intermittent fasted
Extracted molecule total RNA
Extraction protocol eWAT depots were immediately flash frozen in liquid nitrogen after harvesting. Frozen tissues were thawn, carefully minced in lysis Buffer (10 mM Tris-Hcl, 146 mM NaCl, 21 mM MgCl2, 1 mM CaCl2, 0.1 % CHAPs pH=7.4) and grinded by using a tight douncer (Thermo Fisher Scientific, Waltham, MA, United States) on ice. Homogenized tissue was filtered through a 40 µm sieve (Corning, Massachusetts, United States), centrifuged at 500 x g for 5 min at 4 °C to pellet the nuclei and resuspended in buffer supplemented with 1 % BSA and 0.2 U/µl RNAnase inhibitor.
10X-based libraries were generated following manufacture’s protocol (10X Genomics, Pleasanton, CA, United States). Briefly, 1000 nuclei/ µl suspension was loaded to 10X chromium with a V3 kit. Sequencing was performed using a S1 Novaseq Flowcell (Illumina, Eindhoven, Netherlands).
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description 10X genomics
Data processing Demultiplexing, barcode processing, gene counting using the Cell Ranger software v5.0.0
Cellbender, to distinguish cell-containing droplets
DoubletFinder, to exclude potential droplets
Seurat pipeline for batch-correction, clustering and signature gene identification
Cellchat, for Ligand-receptor interactions
Assembly: GRCm38.p6 GENCODE Release M23
Supplementary files format and content: Tab-separated values files and matrix files
Submission date Apr 13, 2023
Last update date Jan 16, 2024
Contact name Genome Informatics
Organization name ETH ZURICH / University of Zurich
Department Functional Genomics Center Zurich (FGCZ)
Street address Winterthurerstrasse 190
City Zurich
ZIP/Postal code 8057
Country Switzerland
Platform ID GPL24247
Series (1)
GSE229690 Adipocyte p53 coordinates the adipose tissue immune cell landscape upon intermittent fasting
SRA SRX19962287
BioSample SAMN34176156

Supplementary file Size Download File type/resource
GSM7173299_146677-barcodes.tsv.gz 112.6 Kb (ftp)(http) TSV
GSM7173299_146677-features.tsv.gz 374.7 Kb (ftp)(http) TSV
GSM7173299_146677-matrix.mtx.gz 179.8 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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