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| Status |
Public on Sep 27, 2023 |
| Title |
Lexis_snRNA-seq_WT |
| Sample type |
SRA |
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| Source name |
iWAT
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| Organism |
Mus musculus |
| Characteristics |
tissue: iWAT
genotype: Lexis WT
treatment: Western diet
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| Treatment protocol |
Western diet
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| Extracted molecule |
total RNA |
| Extraction protocol |
We isolated the nuclei of iWAT from western diet fed male mice using a protocol slightly modified from recent publication (Sarvari et al., 2021; Van Hauwaert et al., 2021). Briefly, iWAT from 3 mice of Lexis-AdWT group or Lexis-AdWT group were isolated (without lymph node) pooled (according to group) and minced. 2 ml NIB buffer (250 mM Sucrose, 10 mM HEPES, 1.5 mM MgCl2, 10 mM KCl, 0.001% IGEPAL CA-630, 0.2 mM DTT, 0.5 U/µL RNase inhibitor) were added to 400 mg pooled iWAT, then homogenized with 2 ml glass dounce homogenizer. After filtering through 70 µm cell strainer, another 2 ml NIB was added to the filtered homogenate and centrifuged at 1000 g× 10 min× 4 °C. The lipid layer was aspirated, pellet was resuspended in the remaining supernatant and then transferred to a new pre-cooled 5 ml DNA low binding tube on ice and added 2 ml NIB. Nuclei were pelleted by centrifuging at 500 g × 10 min× 4 °C, resuspended in 100 µL NRB (1% BSA in PBS, 0.04 U/ µL RNase inhibitor) and filtered through a 40 µm tip strainer. 15,000 nuclei were taken out and resuspended in NRB as previous protocol described (Sarvari et al., 2021; Van Hauwaert et al., 2021).
We performed 10x Genomics single-nucleus RNA sequencing at USC Norris Molecular Genomics Core immediately after nuclei isolation. Single cell RNA sequencing was prepared using 10x Genomics 3' v3.1 (Cat number: 1000092) following manufacturer's protocol. Samples were parsed into single nuclei using 10x Genomics Chromium Controller and libraries were simultaneously prepared. Prepared single cell RNA sequencing libraries were sequenced on the Illumina Novaseq6000 platform at a read length of 28x90 and read depth of 50,000 reads/cell for 5000-7000 cells.
Prepared single cell RNA sequencing libraries were sequenced on the Illumina Novaseq6000 platform at a read length of 28x90 and read depth of 50,000 reads/cell for 5000-7000 cells.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
single-nucleus RNA sequencing
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| Data processing |
Sequencing data was package and analyzed using 10x Genomics Cell Ranger analysis tool. The R package Seurat (V4) was used to cluster the cells in the merged matrix (Hao et al., 2021).
Assembly: mm10
Supplementary files format and content: TSV; MTX: Matrix files
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| Submission date |
Oct 26, 2022 |
| Last update date |
Sep 27, 2023 |
| Contact name |
Zhengyi Zhang |
| E-mail(s) |
zhengyizhang@mednet.ucla.edu
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| Organization name |
UCLA
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| Street address |
Westwood
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| City |
Los Angeles |
| ZIP/Postal code |
90055 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE216608 |
A PPARγ-lncRNA axis modulates thermoneutral remodeling of white adipose tissue [snRNA-seq] |
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| Relations |
| BioSample |
SAMN31460306 |
| SRA |
SRX18028428 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6681145_KO_barcodes.tsv.gz |
21.9 Kb |
(ftp)(http) |
TSV |
| GSM6681145_KO_features.tsv.gz |
244.7 Kb |
(ftp)(http) |
TSV |
| GSM6681145_KO_matrix.mtx.gz |
14.0 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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