Single-cell DNA methylome and 3D genome atlas of human subcutaneous adipose tissue [snm3C-seq3]

We performed single-nucleus RNA-seq and single-nucleus methyl-3C seq on subcutaneous adipose tissue (SAT) biopsies from Finnish women who underwent abdominal SAT liposuction at Tilkka Hospital, Helsinki, Finland. The purpose of this study was to understand the epigenomic, 3D topology, and transcriptomic dynamics across the SAT cell-types. We performed snRNA-seq on subcutaneous adipose tissue (SAT) biopsies from eight participants, and snm3C-seq3 on five of the eight SAT biopsies. snm3C-seq3: An Arima Genomics Arima-HiC Kit was used for the in situ chromatin conformation capture (3C), the fluorescence-activated nuclei sorting (FANS) and library preparation were performed using the snm3C-seq3 workflow, and libraries were sequenced using the Illumina NovaSeq 6000 instrument with S4 flow cells generating 150 bp paired-end reads. snRNA-seq: The single-nucleus sequencing libraries were either constructed using the Chromium Single Cell 3’ v3.1 chemistry and sequenced on an Illumina NovaSeq S4 with a target sequencing depth of 600 million read pairs (n=6), or constructed using the Single Cell Multiome ATAC + Gene Expression Reagent Kit and sequenced on an Illumina NovaSeq SP with a target sequencing depth of 400 million reads (n=5). *************************************************************** Raw files for human/patient samples were not submitted to GEO due to concerns about submitting personally identifiable sequence data for open access. ***************************************************************

本研究针对芬兰赫尔辛基蒂尔卡医院接受腹部皮下脂肪抽吸术的芬兰女性受试者的皮下脂肪组织（subcutaneous adipose tissue, SAT）活检样本，开展了单细胞核RNA测序（single-nucleus RNA-seq）与单细胞核甲基化3C测序（single-nucleus methyl-3C seq）。本研究旨在阐明皮下脂肪组织各类细胞的表观基因组、三维拓扑结构及转录组动态变化。
我们对8名受试者的皮下脂肪组织活检样本进行了单细胞核RNA测序（snRNA-seq），并对其中5份样本开展了单细胞核甲基化3C测序3（snm3C-seq3）。
snm3C-seq3实验流程：采用Arima Genomics公司的Arima-HiC试剂盒完成原位染色质构象捕获（3C），利用snm3C-seq3标准流程完成荧光激活细胞核分选（fluorescence-activated nuclei sorting, FANS）与文库制备，随后使用搭载S4流动槽的Illumina NovaSeq 6000测序仪进行测序，生成150bp双端读长序列。
snRNA-seq实验：单细胞核测序文库分别采用两种方案构建：其一为使用Chromium Single Cell 3’ v3.1 试剂盒构建文库，随后在Illumina NovaSeq S4测序仪上完成测序，目标测序深度为6亿读对（n=6）；其二为使用Single Cell Multiome ATAC + Gene Expression Reagent Kit 构建文库，在Illumina NovaSeq SP测序仪上测序，目标测序深度为4亿读段（n=5）。
****************************************************************
由于担心将包含个人可识别信息的测序数据提交至开放获取数据库，人类/患者样本的原始测序文件未上传至基因表达汇编（Gene Expression Omnibus, GEO）。
****************************************************************