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Differential gene expression upon shRNA-mediated silencing of APC in HT-29 colorectal cancer cells

ABSTRACT: Differential gene expression upon shRNA-mediated silencing of APC in HT-29 colorectal cancer cells

PROVIDER: PRJNA544079 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9102880.fastq.gz	Fastqsanger.gz
	SRR9102881.fastq.gz	Fastqsanger.gz
	SRR9102882.fastq.gz	Fastqsanger.gz
	SRR9102883.fastq.gz	Fastqsanger.gz

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Differential gene expression upon shRNA-mediated silencing of APC in HT-29 colorectal cancer cells

Project description:Wnt signaling plays a pivotal role in colorectal cancer. Intrinsic activation of Wnt by mutational events, such as mutations in the tumor suppressor gene APC, represents the most frequent initiating event in this disease background. Long truncated versions of APC retain partial functionality, which leads to a sub-maximal, “just right” activation state of Wnt signaling supposed to be beneficial for disease initiation. In order to study the transcriptomic alterations of an over-stimulated Wnt signaling pathway, conditional shRNA-mediated silencing of APC was performed in chromosomal instable HT-29 CRC cells which express a 1555 amino acid variant of APC protein able to bind and partially inactivate β-catenin. To achieve this, cells were stably transduced with lentiviral particles encoding for a doxycyline-inducible shRNA directed against APC, or, as a control, a non-silencing shRNA (pTRIPZ inducible shRNA vectors, RHS4740-EG324, Horizon Dharmacon, CO, USA). 72 hours after APC silencing, total RNA was isolated and quality controlled for subsequent RNA-Seq Analysis (DKFZ Heidelberg, Genomic and Proteomic Core Facility) on a HiSeq 2000 instrument (Illumina). Overall, we observed bona-fide Wnt target genes, such as NKD1, AXIN2, PTK7, ASCL2, and SMOC2, and additional putative direct or indirect targets of Wnt signaling up-regulated upon shRNA-mediated APC silencing.

2020-06-25 | GSE131575 | GEO

Human colon cancer HT-29 and LS174T cells: stably transfected with shRNA-Ascl2/EGFP vs. stably transfected with shRNA-Control/EGFP

Project description:Achaete scute-like 2 (Ascl2), a basic helix-loop-helix (bHLH) transcription factor, controls the fate of intestinal stem cells. However, the role of Ascl2 in colon cancer progenitor cells remains unknown. The cell lines HT-29 (47.5-95% of CD133+ population) and LS174T (0.45% of CD133+ population) were chosen for functional evaluation of Ascl2 in colon cancer progenitor cells after gene knockdown by RNA interference. The microRNA (miRNA) microarrays identified 26 two-fold up-regulated miRNAs and 58 two-fold down-regulated miRNAs in shRNA-Ascl2/HT-29 cells and 178 two-fold up-regulated miRNAs and 172 two-fold down-regulated miRNAs in shRNA-Ascl2/LS174T cells. Two-condition experiment: shRNA-Ascl2/HT-29 cells vs. shRNA-Ctr/HT-29 cells, and shRNA-Ascl2/LS174T cells vs. shRNA-Ctr/LS174T cells. Biological replicates: 1 HT-29 cells stably transfected with shRNA-Ascl2/EGFP, 1 LS174T cells stably transfected with shRNA-Ascl2/EGFP, 1 HT-29 cells stably transfected with shRNA-Control/EGFP, and 1 LS174T cells stably transfected with shRNA-Control/EGFP, independently grown and harvested. One replicate per array.

2012-01-07 | E-GEOD-34926 | biostudies-arrayexpress

Human colon cancer HT-29 and LS174T cells: stably transfected with shRNA-Ascl2/EGFP vs. stably transfected with shRNA-Control/EGFP

2012-01-07 | GSE34926 | GEO

Gene expression analysis of BRD4 knockdown in HT-29 and HCT116 cells

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Project description:Colorectal cancer HT-29 cell line is a comonly-used human cancer cell line. We have used this cell line for examining the effect of various anticancer compounds on gene expression and we obtained gene expression data of untreated HT-29 cells as a control data for the analysis.

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Peripheral regions and central regions from HT-29 tumors

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Effect of sodium butyrate on colorectal cancer cell line HT-29

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2016-12-31 | GSE61429 | GEO

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