Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole transcriptome sequencing of papillary thyroid cancer of Indian origin

ABSTRACT: The study involves whole transcriptome sequencing of 40 orphan FFPE tumors obtained from papillary thyroid carcinoma patients of Indian origin. With this, we aim to describe the expression profile, fusion genes and pathogen profile of this specific subset of papillary thyroid cancer patients. This knowledge will further allow us to gain an insight into transcriptomic alterations prevalent in Indian papillary thyroid carcinoma.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER:

PROVIDER: E-MTAB-12476 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): ERP143361

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Whole transcriptome sequencing of anaplastic thyroid cancer of Indian origin

Project description:The study involves whole transcriptome sequencing of 30 orphan FFPE tumors obtained from anaplastic thyroid carcinoma patients of Indian origin. With this, we aim to describe the expression profile, fusion genes and pathogen profile of this specific subset of anaplastic thyroid cancer patients. This knowledge will further allow us to gain an insight into transcriptomic alterations prevalent in Indian anaplastic thyroid carcinoma.

2025-11-09 | E-MTAB-12479 | biostudies-arrayexpress

Targeted sequencing of anaplastic thyroid cancer genome of Indian origin

Project description:The study involves targeted sequencing of 30 orphan FFPE tumors obtained from anaplastic thyroid carcinoma patients of Indian origin. With this, we aim to describe the mutation profile of this specific subset of anaplastic thyroid cancer patients. This knowledge will further allow us to gain an insight into genomic alterations prevalent in Indian anaplastic thyroid carcinoma.

2025-07-01 | E-MTAB-13774 | biostudies-arrayexpress

Whole exome sequencing of anaplastic thyroid cancer of Indian origin

Project description:The study involves whole exome sequencing of 38 orphan primary tumors obtained from anaplastic thyroid carcinoma patients of Indian origin. With this, we aim to describe the mutational profile of this specific subset of anaplastic thyroid cancer patients. This knowledge will further allow us to gain an insight into potentially actionable genomic alterations prevalent in Indian anaplastic thyroid carcinoma.

2025-07-01 | E-MTAB-13697 | biostudies-arrayexpress

Whole exome sequencing of human tumours and cell lines to investigate how ERBB2 and KRAS Alterations mediate response to EGFR inhibitors in early stage Gallbladder Cancer

Project description:Purpose: The uncommonness of gallbladder cancer in the developed world has contributed to the generally poor understanding of the disease. The development of new and effective treatment has been and continues to be a major public health imperative. Methods: We report mutational and copy number analysis of 44 predominantly early-staged gallbladder tumors and 5-gallbladder cancer cell lines by a combination of directed and whole exome sequencing at an average coverage of 100X and above. Using gallbladder cancer cell lines and xenograft mouse models we performed phospho-proteome array profiling, followed by an in-depth functional characterization. Results: We describe recurrent activating ERBB2 somatic mutation in 6 of 44 gallbladder primary tumors with an overall mutation frequency of 13%, along with KRAS activating mutations in 3 of 44 samples. Consistent with whole exome findings, a phospho-proteomic array profile of 49-tyrosine kinase revealed constitutive phosphorylation of ERBB2 and EGFR that were found to heterodimerize. We demonstrate that treatment with ERBB2-specific, EGFR-specific shRNA or with covalent EGFR family inhibitor BIBW-2992 inhibits transformation, survival, migration, invasion, and tumor forming characteristics of gallbladder cancer cells harboring wild type or KRAS (G13D) but not KRAS (G12V) mutation. Furthermore, we show in vivo reduction in tumor size is paralleled by a reduction in the amounts of phospho-ERK in KRAS (G13D) but not in KRAS (G12V) xenografts, validating the in vitro findings Conclusion: Findings from this study implicate ERBB2 as an important therapeutic target in early stage gallbladder cancer. We also present the first evidence that the presence of KRAS (G12V), but not KRAS (G13D) mutation, may preclude gallbladder cancer patients to respond to anti-EGFR treatment, similar to the clinical algorithm commonly practiced to opt for anti-EGFR treatment in colorectal cancer.

2018-12-29 | E-MTAB-6619 | biostudies-arrayexpress

Prognostic significance of the proteome profile of well differentiated papillary thyroid carcinoma

Project description:This research will evaluate the role of tissue proteome profile in regional metastatic disease. Considering that one of the main factors of survival in patients with papillary thyroid carcinoma is the presence of regional or distant metastatic disease, this research will focus on the difference in the proteome profiles between papillary thyroid carcinomas which had regional metastatic disease present at the time of surgery, and ones that did not have regional metastatic disease in neck lymph nodes at the time of surgery. In this study, 10 samples of papillary thyroid carcinomas without regional metastatic disease and 10 samples of well-differentiated papillary thyroid carcinomas with regional metastatic disease will be analyzed. The goal of this research is to try to identifiy certain differences in tissue proteomic profiles of papillary thyroid carcinoma depending on the presence of regional metastatic disease in neck lymph nodes.

2025-07-21 | PXD042415 | Pride

Whole exome sequencing of Lung Squamous Carcinoma Patients of Indian Origin

Project description:The study involves whole exome sequencing of 20 primary tumors obtained from lung squamous carcinoma patients of Indian origin. With this, we aim to describe the mutational profile of this specific subset of lung cancer patients. This knowledge will further allow us to gain an insight into potentially actionable genomic alterations prevalent in Indian lung squamous carcinoma.

2022-02-11 | E-MTAB-8801 | biostudies-arrayexpress

Cervical Adenocarcinoma Whole Exome sequencing

Project description:Raw data of exome sequencing of 17 paired samples and 1 orphan tumor sample, total 18 samples

2022-02-12 | E-MTAB-9766 | biostudies-arrayexpress

Proteomics of thyroid tumours - Proteomics of thyroid tumours provides new insights into their molecular composition and changes associated with malignancy

Project description:Although most thyroid tumours are benign, thyroid cancer represents the most common malignancy of the endocrine system, comprising mainly follicular and papillary thyroid carcinomas (FTC and PTC, respectively). Previous studies have shed some light on the molecular pathogenesis of thyroid cancer but there have not been any comprehensive mass spectrometry-based proteomic studies to reveal protein expression differences between thyroid tumours and the molecular alterations associated with tumour malignancy. We applied a label-free quantitative mass spectrometry analysis to compare normal thyroid tissue with the three most common tumours of the thyroid gland: follicular adenoma, follicular carcinoma and papillary carcinoma.

2017-05-03 | PXD002732 | Pride

Whole exome sequencing of EGFR-TKI naive and EGFR-TKI resistant lung adenocarcinoma samples

Project description:Whole exome sequencing was performed on set of 48 DNA samples obtained from 16 EGFR mutated NSCLC patients whose tumors progressed following EGFR-TKI treatment. The DNA samples included baseline biopsy, rebiopsy and blood from the same patient. By comparing the variants in rebiopsy tumors and baseline tumors we aim to understand the genomic alterations responsible for the development of EGFR-TKI resistance in NSCLC patients.

2022-02-11 | E-MTAB-11404 | biostudies-arrayexpress

Sequencing results of FTO overexpressing in papillary thyroid cells [RNA-seq]

Project description:We tried to analyze the effect of FTO on papillary thyroid carcinoma. We constructed a FTO overexpression stable cell line of papillary thyroid carcinoma cells. We performed meRIP-seq sequencing analysis of the FTO overexpression stable transfer cell line to try to assess which genes were changed at the m6A level in papillary thyroid cancer cells by overexpressing FTO.

2022-05-06 | GSE199206 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data