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Series GSE188212 Query DataSets for GSE188212
Status Public on Nov 15, 2022
Title Comprehensive microRNA analysis across genome-edited colorectal cancer organoid models reveals miR-24 as a candidate regulator of cell survival
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
Summary Colorectal cancer (CRC) is the third most diagnosed cancer and the second leading cause of cancer-related death worldwide Unique mutational combinations can result in distinct changes to gene regulatory mechanisms leading to variability in the efficacy of available therapeutics. To work toward novel therapeutic strategies, it is important to understand the mechanisms by which unique combinations of mutations affect gene regulatory mechanisms. To that end, in this study, we generated RNA- and small RNA-seq data from Apc (A; n=3), Apc/Kras/p53 (AKP; n=1), B-catenin (B; n=5), B-catenin/Kras/p53 (BKP; n=1), Kras/Rspo3/p53 (KRP; n=2), Kras/Rspo3/p53/Smad4 (KRPS; n=4), Kras/Rspo3/Smad4 (KRS; n=3), Rspo3 (R; n=2) mutant mouse enteroids, and wild-type (WT; n=2) controls. From this analysis, we found that miR-24-3p is upregulated master miRNA regulator across mutational contexts. Functional studies identified miR-24-3p as a regulator of cell survival. Utilizing RNA- and leChRO-seq from HCT116 cells treated with a miR-24-3p inhibitor (n=3) or scramble control (n=3), we identified HMOX1 and PRSS8 as candidate miR-24-3p targets subject to post-transcriptional regulation by miR-24-3p.
 
Overall design RNA- and small RNA-seq comparison between genetically modified mouse enteroid models and WT control. RNA- and ChRO-seq comparison between HCT116 cells treated with a miR-24-3p inhibitor or scramble control.
Web link https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-09018-1
 
Contributor(s) Sethupathy P, Villanueva JW
Citation(s) 36457077
Submission date Nov 04, 2021
Last update date May 01, 2023
Contact name Praveen Sethupathy
Organization name Cornell University
Department Biomedical Science
Street address Cornell University College of Veterinary Medicine, Box 17
City Ithaca
State/province NY
ZIP/Postal code 14853
Country USA
 
Platforms (3)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (58)
GSM5672380 Apc mutant enteroid smRNA-seq sample #1
GSM5672381 Apc mutant enteroid smRNA-seq sample #2
GSM5672382 Apc mutant enteroid smRNA-seq sample #3
Relations
BioProject PRJNA777927
SRA SRP344610

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Supplementary file Size Download File type/resource
GSE188212_ChRO_GSE188212_DESeq_normalized_counts27SEP21.csv.gz 1.1 Mb (ftp)(http) CSV
GSE188212_DESeq_normalized_counts_nMk.csv.gz 1.5 Mb (ftp)(http) CSV
GSE188212_RNA_RLOG-LIMMA_normalized_counts.csv.gz 5.9 Mb (ftp)(http) CSV
GSE188212_smRNA_RLOG-LIMMA_normalized_counts.csv.gz 237.4 Kb (ftp)(http) CSV
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Processed data are available on Series record

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