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The raw data of chemoproteomics related to IDRB-Probe-2 for validating the effectiveness of iTarget.

ABSTRACT: The eight raw files starting with 'AGTRAP-P' represent the chemoproteomic experiment of multiple concentrations of IDRB-Probe-2 in HEK-293. Each concentration includes three measurements taken from distinct samples.126, 127N and 127C represent the data of 0.5 μM IDRB-Probe-2. 128N, 128C and 129N represent the data of 1.5 μM IDRB-Probe-2. 129C, 130N and 130C represent the data of 5 μM IDRB-Probe-2. 131N, 131C and 132N represent the data of 15 μM IDRB-Probe-2. 132C, 133N and 133C represent the data of 50 μM IDRB-Probe-2. 134N, 134C and 135N represent the data of 100 μM IDRB-Probe-2. The eight raw files starting with 'AGTRAP-CRF' represent the chemoproteomic experiment of multiple concentrations of IDRB-CRP in HEK-293. Each concentration includes three measurements taken from distinct samples. 134N, 134C and 135N represent the data of 0.5 μM IDRB-CRP. 132C, 133N and 133C represent the data of 1.5 μM IDRB-CRP. 131N, 131C and 132N represent the data of 5 μM IDRB-CRP. 129C, 130N and 130C represent the data of 15 μM IDRB-CRP. 128N, 128C and 129N represent the data of 50 μM IDRB-CRP. 126, 127N and 127C represent the data of 100 μM IDRB-CRP.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

DISEASE(S): Colon Cancer

SUBMITTER: Minjie Mou

LAB HEAD: Minjie Mou

PROVIDER: PXD077137 | Pride | 2026-05-06

REPOSITORIES: Pride

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Project description:Transcription factors play diverse roles during embryonic development, combinatorially controlling multiple cellular states in a spatially and temporally defined manner. Resolving the dynamic transcriptional profiles that underlie these patterning processes is essential for understanding embryogenesis at the molecular level. Here we show how temporal, tissue-specific changes in embryonic transcription factor function can be discerned by integrating caged morpholinos (cMOs) with photoactivatable fluorophores, fluorescence-activated cell sorting (FACS), and microarray technologies. As a proof of principle, we have dynamically profiled No tail-a (Ntla)-dependent genes at different stages of axial mesoderm development in zebrafish, discovering and characterizing discrete sets of transcripts that are coincident with either notochord cell fate commitment or differentiation. Our studies demonstrate how optically controlled chemical tools can be use to probe developmental processes with spatiotemporal precision and reveal the sequential activation of distinct transcriptomes within a cell lineage by a single transcriptional factor. Zebrafish zygotes were injected with a mixture of ntla caged morpholino (cMO) and caged fluorescein dextran (cFD), and a 100 µm-diameter region of the posterior chordamesoderm 125 μm anterior to the center of Kupffer’s vesicle was UV-irradiated at 12 hours post fertilization (hpf). The UV irradiation generated an active morpholino targeting the ntla 5'UTR and simultaneously labeled the cells with green fluorescence. By 36 hpf, the irradiated, green-fluorescent cells contributed to both notochord and floor plate, but the notochord cells were partially vacuolated and disorganized. Combining these caged reagents with microarray analysis identified transcriptional changes coincident with loss of ntla at 16 hpf and subsequent notochord differentiation. Zebrafish zygotes were injected with a mixture of ntla cMO/cFD, and a 100 µm-diameter region of the posterior chordamesoderm 125 μm anterior to the center of Kupffer’s vesicle was UV-irradiated at 12 hpf. Control embryos were injected with cFD and similarly irradiated at 12 hpf. Experimental and control sets of embryos were enzymatically dissociated at 16 hpf, green-fluorescent cells were isolated by FACS, and collected in trizol. Thirty embryos were used for each experiment or controls, each yielding approximately 8,000 green fluorescent cells. Five biological replicates were performed along with five paired controls. Total RNA was isolated from each sample, reverse transcribed, and amplified using WTA2 TransPlex Complete Whole Transcriptome Amplification kit (Sigma) using a miniaturized procedure and manufacturer-recommended incubation steps. The synthesized cDNA was sent to Nimblegen for dye labeling and hybridization. Samples were hybridized to the Nimblegen 2007 (Zv 7) Danio rerio Gene Expression Array chip using one dye per chip. Raw probe data (.pair file) was subjected to RMA, normalization, background correction, and generation of gene expression summary (.calls file) by Nimblegen. Processed data was analyzed in ArrayStar software (DNAStar). Significantly affected genes (fold change > 2 and p-value < 0.10) were identified using a moderated t-test.

			Action	DRS
	AGTRAP-CRF-1.raw	Raw
	AGTRAP-CRF-2.raw	Raw
	AGTRAP-CRF-3.raw	Raw
	AGTRAP-CRF-4.raw	Raw
	AGTRAP-CRF-5.raw	Raw

Dataset Information

The raw data of chemoproteomics related to IDRB-Probe-2 for validating the effectiveness of iTarget.

Dataset's files

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