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| Status |
Public on Apr 15, 2024 |
| Title |
Ad-Lib, PM1, scRNA-seq |
| Sample type |
SRA |
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| Source name |
iWAT
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| Organism |
Mus musculus |
| Characteristics |
cell type: SVF
tissue: iWAT
strain: C57BL/6
age: 8 weeks old
treatment: Ad-Lib
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| Extracted molecule |
total RNA |
| Extraction protocol |
The fourth inguinal white adipose tissue (iWAT) depot from Ad-Lib or TAN mice were dissected and placed on a sterile 6-well tissue culture plate with ice-cold 1X DPBS. Excess liquid was removed from fat pads by blotting. Each tissue was cut and minced with scissors and then placed in 15 ml conical tubes containing digestion buffer (2 ml DPBS and Collagenase II at 3 mg/ml; Worthington Biochemical, Lakewood, NJ, USA) for 40 min of incubation at 37°C with gentle shaking at 100 rpm. Following tissue digestion, enzyme activity was stopped with 8 ml of resuspension media (DMEM/F12 with glutamax supplemented with 15%FBS and 1% pen/strep; Thermo Scientific, CA). The digestion mixture was passed through 100 μm cell strainer and centrifuged at 150 x g for 8 min at room temperature. To remove red blood cells, the pellet was resuspended and incubated in RBC lysis buffer (Thermo Scientific, CA) for 3 min at room temperature, followed by centrifugation at 150 x g for 8 min. The pellet was then resuspended in resuspension media and again spun down at 150 x g for 8 min. The cell pellet was resuspended in 1 ml of 0.01% BSA (in DPBS) and passed through a 40 μm cell strainer (Fisher Scientific, Hampton, NH, USA) to discard debris. Cell number was counted for 10X Genomics single cell application.
To yield an expected recovery of 4000-7000 single cells, an estimated 10,000 single cells per channel were loaded onto Single Cell 3’ Chip (10X Genomics, CA). The Single Cell 3’ Chip was placed on a 10X Genomics instrument to generate single cell gel beads in emulsion (GEMs). Chromium Single Cell 3’ v3 Library and Cell Bead Kits were used according to the manufacturer’s instructions to prepare single cell RNA-Seq libraries.
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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 |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10 (GRCm38)
Supplementary files format and content: Digital gene expression matrices (genes x cells) in sparse matrix format. Compressed, flat text files with tab delimiters. File format is compatible with the R package Seurat. Requires the corresponding features (genes) and barcodes (cell names) files.
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| Submission date |
Apr 12, 2024 |
| Last update date |
Apr 15, 2024 |
| Contact name |
Prashant Rajbhandari |
| E-mail(s) |
prashant.rajbhandari@gmail.com
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| Phone |
5172316099
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| Organization name |
Icahn School of Medicine at Mount Sinai
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| Street address |
1468 Madison Ave, Annenberg 18-10
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE263899 |
Insulin and leptin oscillations license food-entrained browning and metabolic flexibility |
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| Relations |
| BioSample |
SAMN40947912 |
| SRA |
SRX24239940 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8206972_PM1.barcodes.tsv.gz |
29.1 Kb |
(ftp)(http) |
TSV |
| GSM8206972_PM1.features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
| GSM8206972_PM1.matrix.mtx.gz |
39.8 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
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