Project description:Single-nucleus multiomic data was generated from human fetal cochleae across 11, 14, and 16 post-conceptual weeks (PCW) using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC+ Gene Expression platform. Snap-frozen tissues were minced and lysed in ice-cold Nuclei Lysis Buffer, followed by filtration through a 40 μm strainer and centrifugation. Nuclear integrity was confirmed via trypan blue staining prior to mild permeabilization using 0.1× Lysis Buffer. After quenching and washing, nuclei were resuspended in Diluted Nuclei Buffer and concentration was adjusted to 4,000–8,000 nuclei/μL. Libraries were prepared following the standard 10X Multiome protocol for simultaneous gene expression and chromatin accessibility profiling. Sequencing was performed on the Illumina platform, producing paired-end reads. Raw data were processed through the Cell Ranger ARC pipeline (v2.0.0) with alignment to the GRCh38 human genome. The final output comprises paired gene expression matrices and chromatin accessibility peaks, both linked to the same individual nuclei through shared barcodes.

2026-02-04 | E-MTAB-16331 | biostudies-arrayexpress

Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging [snATAC-Seq] [10X Multiome]

Project description:We performed single-nucleus ATAC-seq (snATAC-seq) to profile chromatin accessibility across eight brain regions from C57BL/6J male and female mice at 2, 9, and 18 months of age. Nuclei were isolated from frozen dissected brain regions, tagmented using barcoded Tn5, and sequenced using combinatorial barcoding or 10x Multiome (female samples). Our analysis reveals region- and age-dependent chromatin changes, highlighting regulatory programs associated with aging in specific brain cell types.

2025-05-02 | GSE294772 | GEO

mouse retina 10x Genomics Multiome ATAC+RNA data

Project description:Mouse retina is heterogeneous, composed of multiple neuronal and non-neuronal cell types. Among them, bipolar cells (BC), which connect photoreceptors (cones and rods) to inner retina, are traditionally dissected into rare subtypes of subtle functional and morphological differences. While high-resolution single-cell transcriptomic profiles of BCs are availabl, little is known about the corresponding single-cell chromatin landscapes. Although it is now possible to directly generate multiome data, there are often restrictions on cost, feasibility, and data quality. Therefore, integrating single-cell ATAC and RNA profiles obtained independently from the same retina sample may provide an exciting opportunity to comprehensively characterize these rare cell subtypes and discover transcription factors (TFs) important in establishing or maintaining the cell identities

2022-05-02 | GSE201402 | GEO

10x Multiome from Human Fetal Heart

Project description:10x Multiome from Human Fetal Heart

| PRJNA1162162 | ENA

10x Multiome from Human Fetal Heart

Project description:10x Multiome from Human Fetal Heart

| PRJNA1162163 | ENA

10X sc-multiome data of NCIH2170 cell line

Project description:NCIH2170 is a lung cancer cell line harboring a large amount of extrachromosomal DNA (ecDNA) with high cell-to-cell variation. We performed 10X sc-multiome sequencing on this cell line to study the pattern of gene expression and chromatin accessibility with the existence of ecDNA.

2025-05-12 | GSE293273 | GEO

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