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Tagmentation (CUT&Tag) assay for ATF4 in HCT116 (Human colorectal cancer) cells

ABSTRACT: Tagmentation (CUT&Tag) assay for ATF4 in HCT116 (Human colorectal cancer) cells

PROVIDER: PRJNA904318 | ENA |

REPOSITORIES: ENA

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Tagmentation (CUT&Tag) assay for ATF4 in HCT116 (Human colorectal cancer) cells

Project description:To determine the biological function of ATF4 in the modulation of downstream target genes, we performed Tagmentation (CUT&Tag) assay in HCT 116 (Human colorectal cancer) cells

2022-11-29 | GSE218559 | GEO

CUT&Tag assay for ATF4 in C57BL/6 primarily cultured neurons.

Project description:To elucidate the biological role of ATF4 in regulating downstream target genes, we conducted a CUT&Tag assay in primarily cultured neurons.

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CUT&Tag assay for ATF4 in C57BL/6 primarily cultured neurons.

Project description:CUT&Tag assay for ATF4 in C57BL/6 primarily cultured neurons.

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RNA sequencing analysis of isoginkgetin and thapsigargin treated HCT116 and HCT116 ATF4 deficient cells

Project description:Activating transcription factor 4 (ATF4) is activated during cellular stress through a pathway called the integrated stress response (ISR). We had previously reported that the splicing inhibitor isoginkgetin (IGG) activates ATF4 and ATF4-dependent transcripts. To determine the role of ATF4 in the transcriptional response to IGG, we used tandem CRISPR cas9 gene editing to create an ATF4 deficient HCT116 (colon cancer) cell line. We completed RNA sequencing on HCT116 parental and HCT116 ATF4 deficient cells treated with IGG, and thapsigargin (Tg), a positive control for ATF4 activation. We found that IGG led to the differential expression of 76 transcripts, and 58 of these were dependent on ATF4. Tg led to a far more robust transcriptional response, which appeared to be less ATF4 dependent.

2024-10-09 | GSE249009 | GEO

CUT&Tag of mouse primary B cells transduced Pbx1 overexpression plasmid.

Project description:We performed the cleavage under targets and tagmentation (Cut & tag) assay followed by sequencing enriched DNA fragments to reveal the direct downstream targets of Pbx1. Firstly, we overexpressed Pbx1b with Pbx1b-IRES-GFP retrovirus in murine peripheral B cells to ensure the yields of DNA fragments. CUT & tag libraries were generated following instructions of the manufacturer’s protocol (Vazyme; cat TD901-01) and the Pbx1 antibody (CST; cat 4342) was used for signal enrichment.

2023-03-26 | E-MTAB-12769 | biostudies-arrayexpress

Different proteins expression were dectected by iTRAQ assay in NGB/HCT116 and Vector/HCT116

Project description:Different proteins expression were dectected by iTRAQ assay in HCT116 cell line over-expression NGB or not.

2023-05-10 | PXD038420 | Pride

RNA sequencing analysis of isoginkgetin and thapsigargin treated HCT116 and HCT116 ATF4 deficient cells

Project description:RNA sequencing analysis of isoginkgetin and thapsigargin treated HCT116 and HCT116 ATF4 deficient cells

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High-throughput reporter assay for human genetic variants overlapping ATF4 binding sites

Project description:Activating Transcription Factor 4 (ATF4) is a transcription factor that regulates cellular responses to nutrient deficiency, endoplasmic reticulum stress and oxidative stress. At the organism level, it is implicated in processes such as hematopoiesis, skeletogenesis, eye development, memory, muscle atrophy, and carbohydrate and lipid metabolism. Here, we carried out a massively parallel reporter assay (MPRA) to identify allelic regulatory effects of human genetic variants that reside in ATF4 binding sites identified in ChIP-Seq experiments.

2023-12-01 | GSE225216 | GEO

Cut&Run Analysis of ATF4 genomic occupancy in HCT116 colon carcinoma cell lines after treatment with DMSO, etoposide, tunicamycin, or histidinol

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Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation.

Project description:Whereas techniques to map chromatin-bound proteins are well-developed, mapping chromatin-associated RNAs remains a challenge. Here we describe Reverse Transcribe & Tagment (RT&Tag), in which RNAs associated with a chromatin epitope are targeted by an antibody followed by a protein A-Tn5 transposome. Localized reverse transcription generates and the Tn5 transposase tagments RNA/cDNA hybrids. We demonstrate the utility of RT&Tag in Drosophila cells for capturing the noncoding RNA roX2 with the dosage compensation complex and maturing transcripts associated with silencing histone modifications. We also show that RT&Tag can detect N6-methyladenosine (m6A)-modified mRNAs, and show that genes producing methylated transcripts are characterized by extensive promoter pausing of RNA polymerase II. The high efficiency of in situ antibody tethering and tagmentation makes RT&Tag especially suitable for rapid low-cost profiling chromatin-associated RNAs from small samples.

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