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| Status |
Public on Jan 12, 2024 |
| Title |
SAT_33 |
| Sample type |
SRA |
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| Source name |
Subcutaneous adipose
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Subcutaneous adipose
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Frozen tissue biopsies from 4 donors were combined prior to isolation. The tissue was minced over dry ice and incubated in ice-cold lysis buffer consisting of 0.1% IGEPAL, 10 mM Tris-HCl, 10 mM NaCl, and 3 mM MgCl2. After a 10-min incubation, the lysate was filtered through a MACS 30-um smart strainer (Miltenyi Biotec #130-110-915). Nuclei were centrifuged at 500 x g for 5 minutes at 4C, and gently re-suspended in 1 mL of wash buffer consisting of 1X PBS, 1.0% BSA, and 0.2 U/ul RNase inhibitor (Sigma #3335402001). Nuclei were filtered again through a 40 um flowmi tip strainer (Sigma Aldrich # BAH136800040). Finally, nuclei were centrifuged at 500 x g for 5 minutes at 4C, re-suspended, and submitted for library preparation.
Libraries were prepared using the 10X Single Cell 3' v3.1 protocol and the 10X Chromium platform. The 21 resulting libraries were sequenced using an Illumina NovaSeq S4 targeting 200 million reads per sample.
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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 3' v3.1
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| Data processing |
Reads were aligned to the GRCh38 primary human genome with Gencode v24 gene annotations. STARSolo v2.7.3a was used for alignment with the --soloFeatures GeneFull argument to include intronic regions for UMI counting. Demuxlet, implemented in the popscle v0.1-beta software package, was used for assigning droplets to the one of the 4 pooled donors for each library.
Assembly: GRCh38
Supplementary files format and content: Matrix market format for gene counts.
Supplementary files format and content: Tab-separated text file for meta data, barcodes (column names), and gene names (row names).
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| Submission date |
Nov 30, 2023 |
| Last update date |
Jan 12, 2024 |
| Contact name |
Marcus Alvarez |
| E-mail(s) |
malvarez@mednet.ucla.edu
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| Organization name |
UCLA
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| Department |
Human Genetics
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| Lab |
Pajukanta
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| Street address |
695 Charles E Young Dr South, Gonda 6335
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE249089 |
Single-nucleus RNA-sequencing of human subcutaneous adipose tissue biopsies from 84 Finnish participants. |
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| Supplementary data files not provided |
| Raw data are available in SRA |
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