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.
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.
Project description:As the light-sensing part of the visual system, the retina is comprised of five classes of neurons, including photoreceptors, horizontal, amacrine, bipolar, and retinal ganglion cells, along with several non-neuronal cell types such as Muller glia. These major cell classes can be further classified into hundreds of distinct cell subtypes. The development of the retina is under tight temporal control where multipotent progenitor cells differentiate into specific mature cell types in a sequential, but overlapping, order. Additionally, the developmental process is under tight spatial control, with cells at the central retina developing earlier than cells at the periphery. To provide a comprehensive view of the human fetal retina at the molecular level and investigate transcriptional regulatory mechanisms controlling the differentiation process, we profiled more than 300,000 single nuclei of the human fetal retina from 12 donors spanning post conception week 10 and 23 with Multiome RNA-seq and ATAC-seq.
Project description:We sequenced 2 heart samples from human fetal donors and detected the differential expressed mRNAs and lncRNAs. The network of significant differential expressed transcripts could be associated to developmental program. examination mRNA and lncRNA expression in heart tissues
