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Series GSE183476 Query DataSets for GSE183476
Status Public on Sep 05, 2023
Title Isx-9 induces enteroendocrine cell differentiation in the intestinal organoids
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary We investigated the cell identity and cell proportion in the intestinal organoids treated by Isoxazole-9 (Isx-9) using single-cell transcriptome analysis. Isx-9 enriches enteroendocrine cells without altering the cell identity of other lineages. To investigate the mechanism of this process, we performed RNA-seq and ATAC-seq of Isx-9 treated intestinal stem cells. Based on the gene expression pattern and differential peaks of open chromatin, we found that Isx-9 upregulated neuroendocrine related genes, and elevated the chromatin accessibility at the promoter region of enteroendocrine related transcription factors.
 
Overall design Single-cell transcriptome profiles of 4 samples were generated, including WT intestinal organoids, Chgb-mCherry reporter organoids, and Chgb-mCherry reporter organoids treated by DMSO or Isx-9 for 6 days. In addition, RNA-seq and ATAC-seq of DMSO or Isx-9 treated intestinal stem cells were also performed.
 
Contributor(s) Zhao S, Su Y, Li H, Tang L, Wu W
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Submission date Sep 05, 2021
Last update date Sep 05, 2023
Contact name Wei Wu
E-mail(s) sj-zhao16@mails.tsinghua.edu.cn
Organization name Tsinghua University
Lab School of life science
Street address Tsinghua Road, Medical Building
City Beijing
ZIP/Postal code 100084
Country China
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (14)
GSM5558180 WT intestinal organoids_scRNAseq
GSM5558181 Chgb-mCherry reporter organoids_scRNAseq
GSM5558182 DMSO-treated Chgb-mCherry reporter organoids_scRNAseq
Relations
BioProject PRJNA760929
SRA SRP335749

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE183476_Bulk_RNA_seq_DEG_table.txt.gz 1.4 Mb (ftp)(http) TXT
GSE183476_RAW.tar 1.7 Gb (http)(custom) TAR (of BW, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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