Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Screening of plasma exosomal RNAs as a diagnostic marker for cervical cancer: analysis of patients who underwent primary chemoradiotherapy

ABSTRACT: 1. The expression of plasma exosomal ncRNAs and mRNAs was compared a group of 12 samples from healthy individuals (normal group) with a group of 30 samples from cervical cancer patients before primary concurrent chemoradiotherpay (cancer group) using differentially expressed gene (DEG) analysis. The RNAs with both |log2FC| >2 and P values < 0.05 2. We prepared for log2 fold change values of plasma exosomal RNAs for 30 patients from 30 samples in second week during CCRT compared with those before treatment to screen secondary biological function of primarily selected DEGs. We analyzed the association between non-coding RNA (ncRNA)-mRNA network and cancer using ingenuity pathway analysis after secondary selection according to the number and correlation of mRNAs (or ncRNAs) relevant to log2FC in the expression of primarily selected ncRNAs (or mRNAs) before and after CCRT. The raw NGS data of 58 samples from 29 patients were uploaded in E-MTAB-10215. Here we will upload raw RNA sequencing data of 12 samples from 12 healthy individuals and 2 samples from one cervical cancer patient.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Oyeon Cho

PROVIDER: E-MTAB-10930 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA seq from plasma exosome before and after chemoradiotherapy for cervical cancer patients

Project description:We sequenced plasma exosomal RNA obtained from 58 blood samples from 29 cervical cancer patients treated with concurrent chemoradiotherapy (CCRT) followed by intracavitary brachytherapy. The patients with 2018 International Federation of Gynecology and Obstetrics [FIGO] stage IB-IVB at diagnosis were included. The 29 cervical cancer patients had two blood samples for each patient drawn before and after CCRT. Next generation sequencing data from plasma exosome included small RNAs, long non-coding RNAs, and mRNAs, of which miRNAs and mRNAs were used for analysis. The log2 fold change values were calculated between the two samples from each patient to detect miRNAs as predictors of early progression and metastasis. We analysed their biological functions through miRNA-mRNA network analysis after selecting several potential exosomal miRNAs associated with clinical results.

2021-05-23 | E-MTAB-10215 | biostudies-arrayexpress

The exponential slope from absolute lymphocyte counts during radiochemotherapy can predict an aggressive course of cervical cancer.

Project description:We sequenced plasma exosomal RNA obtained from 24 blood samples from 12 cervical cancer patients treated with concurrent chemoradiotherapy (CCRT) followed by intracavitary brachytherapy. The patients with 2018 International Federation of Gynecology and Obstetrics [FIGO] stage IB-3C2 at diagnosis were included. The 12 cervical cancer patients had two blood samples for each patient drawn before and after CCRT. Next generation sequencing data from plasma exosome included small RNAs, long non-coding RNAs, and mRNAs, of which miRNAs and mRNAs were used for analysis. The log2 fold change values were calculated between the two samples from each patient to detect mRNAs as predictors of slope of function estimated from ALCs and survival. We selected several potential exosomal mRNAs associated with clinical results.

2023-08-13 | E-MTAB-12187 | biostudies-arrayexpress

microRNA profiling of female and male mouse pituitary gland across pubertal transition

Project description:The pituitary gland exhibits sex differences in its function. Diseases associated with dysregulation of the pituitary are also sex-biased in prevalence. Previous qPCR profiling of puberty-related genes in the pituitary gland revealed increasingly sex-biased expression of genes profiled across pubertal transition. Here, we performed small RNA-seq on total RNA extracted from C57BL/6J mouse pituitary gland of both sexes mice at 4 ages spanning pubertal transition (postnatal days 12, 22, 27, 32) (6 replicates per sex at each age) to examine microRNA (miRNA) regulation of sex differences in gene expression observed. Total RNA was sent to SickKids TCAG core to construct small RNA-seq libraries using NEBNext Small RNA Library Prep Kit according to manufacterer’s protocol. Resulting single-end libraries were sequenced at TCAG core on the Illumina HiSeq 2500 v4 flow cell with SR50 bp. Data obtained was processed using miRDeep2 pipeline to align small RNA-seq reads to the mouse genome (mm10) and to filter for miRNAs.

2022-10-12 | E-MTAB-9460 | biostudies-arrayexpress

Short and Long RNA sequencing of human mature erythrocytes

Project description:We employed high-throughput sequencing of both short (~18-24nt) and long (>200nt) RNAs in human erythrocytes. We obtained blood from five healthy individuals for the short (small) RNA-seq library preparations and blood from three individuals for the long RNA-seq library preparations. We identified an abundant, diverse population of RNAs. Both polyadenylated and nonpolyadenlated long RNAs were identified. Additionally, known and novel microRNAs were identified in the short RNA dataset using the probabalistic modeling algorithm miRDeep. These RNAs lend insight into erythrocyte biology and provide utility as potential biomarkers. To determine both shared and unique aspects of the erythrocyte long RNA transcriptome, we compared this transcriptome with that of the PBMC and CD34+ erythroid progenitor transcriptomes. Sequencing of RNAs from mature erythrocytes of healthy individuals

2015-11-19 | E-GEOD-63703 | biostudies-arrayexpress

microRNA profiling of fetal lamb heart treated with coiled implantation in left atrium against untreated controls

Project description:We created a fetal lamb model of hypoplastic left heart syndrome (HLHS), by implanting coils in the left atrium in mid-gestation. We performed bulk RNA sequencing of left ventricles (LV), right ventricles (RV), ascending aortae (AAo) and pulmonary arteries (PA). Single nucleus RNA sequencing was performed on LV free wall tissue (n = 4 coiled samples, n = 3 controls).

2023-05-31 | E-MTAB-12230 | biostudies-arrayexpress

The porcine microRNA transcriptome response to transmissible gastroenteritis virus infection

Project description:Transmissible gastroenteritis virus (TGEV; Coronaviridae family) causes huge economic losses to the swine industry. MicroRNAs (miRNAs) play a regulatory role in viral infection and may be involved in the mammalian immune response. Here, we report a comprehensive analysis of host miRNA expression in TGEV-infected swine testis (ST) cells. Deep sequencing generated 3,704,353 and 2,763,665 reads from uninfected ST cells and infected ST cells, respectively. The reads were aligned to known Sus scrofa pre-miRNAs in miRBase 19, identifying 284 annotated miRNAs. Certain miRNAs were differentially regulated during TGEV infection, which confirmed the hypothesis that specific miRNAs play a regulatory role in virus-host interactions. 59 unique miRNAs displayed significant differentially expression between the normal and TGEV-infected ST cell samples: 15 miRNAs were significantly up-regulated and 44 were significantly down-regulated. Stem-loop RT-PCR was carried out to determine the expression levels of specific miRNAs in the two samples, and the results were consistent with those of sequencing. Gene ontology enrichment analysis of host target genes demonstrated that the differentially expressed miRNAs are involved in regulatory networks, including cellular process, metabolic process, immune system process. This is the first report of the identification of ST cell miRNAs and the comprehensive analysis of the miRNA regulatory mechanism during TGEV infection, which revealed the miRNA molecular regulatory mechanisms for the viral infection, expression of viral genes and the expression of immune-related genes. The results presented here will aid research on the prevention and treatment of viral diseases. 2 ST(Porcine testicular cells) cell samples, ST: normal ST cell sample (contro sample), TGEV: TGEV (Transmissible gastroenteritis virus) infected ST cell samples

2015-01-08 | E-GEOD-64737 | biostudies-arrayexpress

The porcine microRNA transcriptome response to porcine cytomegalovirus infection

Project description:Porcine cytomegalovirus (PCMV; genus Cytomegalovirus, subfamily Betaherpesvirinae, family Herpesviridae) is an immunosuppressive virus that mainly inhibits the immune function of T lymphocytes and macrophages, which has caused great distress to the farming industry. In this study, we obtained the miRNA expression profiles of PCMV-infected and control porcine macrophages, PCMV-infected and control porcine tissues via high-throughput sequencing. The comprehensive analysis of miRNA profiles showed that 306 miRNA database annotated and 295 novel pig-encoded miRNAs were detected. Gene Ontology (GO) analysis of the target genes of miRNAs in PCMV infected porcine macrophages showed that the differentially expressed miRNAs are mainly involved in immune and metabolic process. This is the first report of the miRNA transcriptome in PCMV infected porcine macrophages and PCMV infected tissues and the analysis of the miRNA regulatory mechanism during PCMV infection. Further research into the regulatory mechanisms of miRNAs during immunosuppressive viral infections will contribute to the treatment and prevention of immunosuppressive viruses. miRNA expression profiling of PCMV-infected and control porcine macrophages; PCMV-infected and control porcine tissues via high-throughput sequencing.

2015-12-19 | E-GEOD-76156 | biostudies-arrayexpress

Genome-wide miRNA profile of MCF7 cells overexpressing wild-type and mutant miR-222

Project description:MCF7 cells were infected with retrovirus to overexpress wild-type and mutant miR-222 Measure miRNA expression level in MCF7 cells after overexpressing wild-type and mutant miR-222

2015-02-05 | E-GEOD-64363 | biostudies-arrayexpress

Short RNAs expression profiling in SET2 cells.

Project description:We report the application of Illumina short RNA sequencing for characterization and discovery of miRNAs and moRNAs in SET2 cells carrying JAK2 V617F mutation. Short RNAs sequencing for miRNA quantification, discovery and characterisation.

2012-02-08 | E-GEOD-30672 | biostudies-arrayexpress

Deep sequencing of small RNA facilitates tissue and sex associated microRNA discovery in zebrafish

Project description:The role of microRNAs in gene regulation has been well established. The extent of miRNA regulation also increases with increasing genome complexity. Though the number of genes appear to be equal between human and zebrafish, substantially less microRNAs have been discovered in zebrafish compared to human (Release 19). It appears that most of the miRNAs in zebrafish are yet to be discovered. We sequenced small RNAs from brain, gut, liver, ovary, testis, eye, heart and embryo of zebrafish. In brain, gut and liver sequencing was done in male and female separately. Majority of the sequenced reads (16-62%) mapped to known miRNAs, with the exception of ovary (5.7%) and testis (7.8%). Using the miRNA discovery tool (miRDeep2), we discovered novel miRNAs from the un-annotated reads that ranged from 7.6 to 23.0%, with exceptions of ovary (51.4%) and testis (55.2%). The prediction tool identified a total of 459 novel pre-miRNAs. We compared expression of miRNAs between different tissues and between males and females to identify tissue associated and sex associated miRNAs respectively. These miRNAs could serve as putative biomarkers for these tissues. The brain and liver had highest number of tissue associated (22) and sex associated (34) miRNAs, respectively. This study comprehensively identifies tissue and sex associated miRNAs in zebrafish. Further, we have discovered 459 novel pre-miRNAs (~30% seed homology to human miRNA) as a genomic resource which can facilitate further investigations to understand miRNA-mRNA gene regulatory networks in zebrafish which will have implications in understanding the function of human homologs. Known miRNA profiling, novel miRNA discovery and identification of tissue associated and sex associated miRNAs from sRNA deep sequencing data of different tissues and embryo of zebrafish (in triplicate) was carried out using the Illumina HiSeq 2000 platform.

2015-10-16 | E-GEOD-57169 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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