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Series GSE256434 Query DataSets for GSE256434
Status Public on Feb 28, 2024
Title Flexible and high-throughput simultaneous profiling of gene expression and chromatin accessibility in single cells
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Gene expression and chromatin accessibility are highly interconnected processes. Disentangling one without the other provides an incomplete picture of gene regulation. However, simultaneous measurements of RNA and accessible chromatin are technically challenging, especially when studying complex organs with rare cell-types. Here, we present easySHARE-seq, an elaboration of SHARE-seq, providing simultaneous measurements of ATAC- and RNA-seq within single cells, enabling identification of cell-type specific cis-regulatory elements (CREs). easySHARE-seq retains high scalability, improves RNA-seq data quality while also allowing for flexible study design. Using 19,664 joint profiles from murine liver nuclei, we linked CREs to their target genes and uncovered complex regulation of key genes such as Gata4. We further identify de-novo genes and cis-regulatory elements displaying zonation in Liver sinusoidal epithelial cells (LSECs), a challenging cell type with low mRNA levels, demonstrating the power of multimodal measurements. EasySHARE-seq therefore provides a flexible platform for investigating gene regulation across cell types and scale.
Overall design easySHARE-seq to profile gene expression and chromatin accessibility in cell lines (HEK, OP-9) and murine liver nuclei
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Contributor(s) Soltys V, Chan YF
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Submission date Feb 23, 2024
Last update date Feb 29, 2024
Contact name Volker Soltys
Organization name Friedrich Miescher Laboratory of the Max Planck Society
Lab Chan Lab
Street address Max-Planck Ring 9
City Tübingen
ZIP/Postal code 72076
Country Germany
Platforms (2)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL25526 Illumina NovaSeq 6000 (Homo sapiens; Mus musculus)
Samples (4)
GSM8098531 Mouse Liver Nuclei (ATAC-seq)
GSM8098532 Mouse Liver Nuclei (RNA-seq)
GSM8098533 Species Mixing (ATAC-seq)
BioProject PRJNA1079667

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Supplementary file Size Download File type/resource
GSE256434_Metadata_Liver.txt.gz 72.2 Kb (ftp)(http) TXT
GSE256434_RAW.tar 972.9 Mb (http)(custom) TAR (of BED, MTX, NARROWPEAK, TXT)
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