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| Status |
Public on Jan 16, 2024 |
| Title |
ad libitum fed, ctrl [HFD-AL] |
| Sample type |
SRA |
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| Source name |
eWAT
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| Organism |
Mus musculus |
| Characteristics |
tissue: eWAT
strain: BL6J
cell type: p53 floxed
genotype: Ctrl
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| 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).
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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 |
10X genomics
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| 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
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| Submission date |
Apr 13, 2023 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Genome Informatics |
| E-mail(s) |
fgcz.gi@gmail.com
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| Organization name |
ETH ZURICH / University of Zurich
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| Department |
Functional Genomics Center Zurich (FGCZ)
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| Street address |
Winterthurerstrasse 190
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| City |
Zurich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE229690 |
Adipocyte p53 coordinates the adipose tissue immune cell landscape upon intermittent fasting |
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| Relations |
| SRA |
SRX19962286 |
| BioSample |
SAMN34176157 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7173298_146676-barcodes.tsv.gz |
125.0 Kb |
(ftp)(http) |
TSV |
| GSM7173298_146676-features.tsv.gz |
374.7 Kb |
(ftp)(http) |
TSV |
| GSM7173298_146676-matrix.mtx.gz |
226.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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