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| 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
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| 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.
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| 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.
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| Contributor(s) |
Zhao S, Su Y, Li H, Tang L, Wu W |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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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
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| Organization name |
Tsinghua University
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| Lab |
School of life science
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| Street address |
Tsinghua Road, Medical Building
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| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (14)
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| GSM5558180 |
WT intestinal organoids_scRNAseq |
| GSM5558181 |
Chgb-mCherry reporter organoids_scRNAseq |
| GSM5558182 |
DMSO-treated Chgb-mCherry reporter organoids_scRNAseq |
| GSM5558183 |
ISX-treated Chgb-mCherry reporter organoids_scRNAseq |
| GSM5558184 |
Intestinal stem cells, DMSO_RNA_rep1 |
| GSM5558185 |
Intestinal stem cells, DMSO_RNA_rep2 |
| GSM5558186 |
Intestinal stem cells, ISX_RNA_rep1 |
| GSM5558187 |
Intestinal stem cells, ISX_RNA_rep2 |
| GSM5558188 |
Intestinal stem cells, DMSO_ATAC_rep1 |
| GSM5558189 |
Intestinal stem cells, DMSO_ATAC_rep2 |
| GSM5558190 |
Intestinal stem cells, DMSO_ATAC_rep3 |
| GSM5558191 |
Intestinal stem cells, ISX_ATAC_rep1 |
| GSM5558192 |
Intestinal stem cells, ISX_ATAC_rep2 |
| GSM5558193 |
Intestinal stem cells, ISX_ATAC_rep3 |
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| Relations |
| BioProject |
PRJNA760929 |
| SRA |
SRP335749 |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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