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H3K27ac ChIP-seq and RNA-seq of papillary thyroid carcinoma patient's tissues and paired normal tissues

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE224357 | GEO | 2025/05/26

REPOSITORIES: GEO

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CHIP-seq analysis of H3K27ac in papillary thyroid carcinoma patient's tissues and paired normal tissues

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2025-05-27 | GSE224355 | GEO

RNA-seq of papillary thyroid carcinoma (PTC) patient's tissues and paired normal tissues

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CHIP-seq analysis of H3K27ac in papillary thyroid carcinoma patient's tissues and paired normal tissues

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H3K27ac ChIP-seq and RNA-seq of papillary thyroid carcinoma patient's tissues and paired normal tissues

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RNA-seq of papillary thyroid carcinoma (PTC) patient's tissues and paired normal tissues

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Transcription profiling of human papillary thyroid carcinoma and paired normal tissues

Project description:We analyzed the gene expression profiles of 7 papillary thyroid carcinoma samples compared to 7 paired normal samples using Affymetrix tools and dChip software. The objective was to find potential molecular markers for this disease

2007-07-03 | E-GEOD-3678 | biostudies-arrayexpress

Transcriptome analysis discloses dysregulated genes in normal appearing tumor-adjacent thyroid tissues from patients with papillary thyroid carcinoma.

Project description:Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. The molecular characteristics of histologically normal appearing tissue adjacent to the tumor (NAT) from PTC patients are not well characterized. The aim of this study was to characterize the global gene expression profile of NAT and compare it with those of normal and tumor thyroid tissues. We performed total RNA sequencing with fresh frozen thyroid tissues from a cohort of three categories of samples including NAT, normal thyroid (N), and PTC tumor (T). Transcriptome analysis shows that NAT presents a unique gene expression profile, which was not associated with sex or the presence of lymphocytic thyroiditis. Among the differentially expressed genes (DEGs) of NAT vs N, 256 coding genes and 5 noncoding genes have been reported as cancer genes involved in cell proliferation, apoptosis, and/or tumorigenesis. Bioinformatics analysis with Ingenuity Pathway Analysis software revealed that "Cancer, Organismal Injury and Abnormalities, Cellular Response to Therapeutics, and Cellular Movement" were major dysregulated pathways in the NAT tissues. This study provides improved insight into the complexity of gene expression changes in the thyroid glands of patients with PTC.

| S-EPMC8266864 | biostudies-literature

microRNA expression profiling of papillary thyroid carcinoma (PTC) and matched adjacent normal thyroid tissues

Project description:We profiled the microRNA expression of 5 pairs of PTC and normal thyroid tissues. All the tissues were immediately snap-frozen in liquid nitrogen and confirmed as papillary thyroid carcinoma by expert pathologists. Numerous deregulated mature microRNAs were identified comparing PTC tissues versus normal thyroid tissues. Details about the clinical-pathological characteristics of the samples are also provided.

2019-03-06 | GSE113629 | GEO

Dataset of differential gene expression between total normal human thyroid and histologically normal thyroid adjacent to papillary thyroid carcinoma.

Project description:This article contains further data and information from our published manuscript [1]. We aim to identify significant transcriptome alterations of total normal human thyroid vs. histologically normal thyroid adjacent to papillary thyroid carcinoma. We performed a systematic meta-analysis of all the available gene expression profiles for the whole organ also collecting gene expression data for the normal thyroid adjacent to papillary thyroid carcinoma. A differential quantitative transcriptome reference map was generated by using TRAM (Transcriptome Mapper) software able to combine, normalize and integrate a total of 35 datasets from total normal thyroid and 40 datasets from histologically normal thyroid adjacent to papillary thyroid carcinoma from different sources. This analysis identified genes and genome segments that significantly discriminated the two groups of samples. Differentially expressed genes were grouped and enrichment function analyses were performed identifying the main features of the differentially expressed genes between total normal thyroid and histologically normal thyroid adjacent to papillary thyroid carcinoma. The search for housekeeping genes retrieved 414 loci.

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In-depth characterization of the microRNA transcriptome in normal thyroid and papillary thyroid carcinoma.

Project description:ContextA single microRNA gene may give rise to several mature products that differ in length, called isomiRs. IsomiRs are known to be tissue specific and functionally relevant. The microRNA sequence heterogeneity of the thyroid gland has yet to be determined.ObjectiveThe objective of the study was to provide a comprehensive view of the microRNA transcriptome in normal thyroid and papillary thyroid carcinoma (PTC).DesignWe used next-generation deep sequencing to analyze microRNA length heterogeneity and expression profiles of PTC tumors (n = 14), unaffected tissue adjacent to tumors (n = 14), and control, noncancerous thyroid tissue (n = 14). The results were validated with a microarray on an additional set of 9 PTC tumor/normal tissue pairs.ResultsEighty-nine microRNAs were significantly deregulated in PTC compared with normal thyroid tissue (false discovery rate < 0.05, fold change 0.13-20.7). Top deregulated miRNAs included miR-146b-5p, miR-221-3p, miR-7-3p, miR-551b-3p, miR-486-3p, and miR-144-3p, confirming previous microarray profiling. The expression of miRNAs did not depend on the BRAF mutation status. Interestingly, 85% of the most abundant microRNAs consisted of isoforms that differed from the standard reference sequence deposited in miRBase. Moreover, the reference microRNAs were completely absent in 42.4% and 35.9% of the microRNAs expressed in normal thyroid and PTC tumors, respectively. Numerous isomiRs had altered seed sequences, which led to a different set of target genes. For highly deregulated miR-146b-5p, we detected 6 isoforms (tumor/normal fold change 14.4-28.7, false discovery rate < 0.002) that varied at their 5' ends with a 1-nt difference that created 2 alternative seeds. The target genes for those 2 seeds overlapped in only 13.1% of genes.ConclusionsAlmost all microRNAs exhibit isoforms of variable length and potentially distinct function in thyroid tumorigenesis.

| S-EPMC5399477 | biostudies-literature

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