Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Time course analysis of colon cancer samples (part 2)

ABSTRACT: The study outcome was to evaluate the effect of the time on tumor samples and possibly select specific genes whose expression is time-related, that could be used as detectors of tissue degradation. RNA extracted from specimens of 14 patients at four time points after surgery was analyzed for gene expression on high-density oligonucleotide microarrays. A mixed-effects model implemented by considering the factor time (T0, T1, T2, T3) as fixed and the factor patient as random was used to identify probes with different expression means across the four different time points. The p-values of the model were adjusted with the Bonferroni method (p<0. 05).

ORGANISM(S): Homo sapiens

SUBMITTER: Maurizio Callari

PROVIDER: E-GEOD-37178 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Time course analysis of colon cancer samples (part 1)

Project description:The study outcome was to evaluate the effect of the time on normal colon mucosa samples and possibly select specific genes whose expression is time-related, that could be used as detectors of tissue degradation. RNA extracted from specimens of 15 patients at four time points after surgery was analyzed for gene expression on high-density oligonucleotide microarrays. A mixed-effects model implemented by considering the factor time (T0, T1, T2, T3) as fixed and the factor patient as random was used to identify probes with different expression means across the four different time points. The p-values of the model were adjusted with the Bonferroni method (p<0. 05).

2013-02-01 | E-GEOD-37175 | biostudies-arrayexpress

Liver Chromatin accessibility landscapes during onset of salmon maturation

Project description:We sequenced 12 ATAC-Seq lbraries from four biological replicates before (T1) and after the onset of maturation (T2, T3, T4) from liver. To characterise changes in chromatin state following long light initiation, we defined differentially accessible regions (DARs) where mapping counts differed significantly between T1 and other time points. This revealed a strong early remodelling in the chromatin state landscape, as most DARs were observed at T2 (n=1501) before decreasing in stepwise fashion at T3 (n=477) and T4. The majority of DARs (n=1036 or 57%) exhibit reduced accessibility at T2 compared with T1 and subsequently remained unchanged at later time points (Fig. 5a; Supplementary Figure S14). Similarly, regions that gained accessibility at T2 (n=696 or 38%) also remained unchanged at later timepoints. This left less than 10% of DARs (n=99) that displayed an oscillating pattern following the onset of the maturation. Together, this revealed the ATAC-seq signatures were predominantly stable chromatin state changes.

2020-08-28 | GSE156998 | GEO

Epigenome-wide analysis of healthy obese individuals during a one-year weightloss intervention

Project description:Genome wide DNA methylation profiling of healthy obese individuals during a one-year weight loss intervention. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,000 CpGs. Adipose tissue biopsies were collected at three time points, baseline (T0), Fifth month (T1) and Twelfth month (T2).

2017-11-08 | GSE103768 | GEO

Genomic responses in blood during acute human anaphylaxis

Project description:Gene expression was profiled in peripheral blood samples collected over three time points from patients during acute anaphylaxis and from healthy controls. Patients presented to the Emergency Department (ED) at Royal Perth Hospital with acute, moderately severe anaphylaxis. Samples were collected at ED arrival (T0), 1 hour later (T1), and 3 hours post arrival (T2).

2014-07-02 | GSE47655 | GEO

Gluten-free microbiome study UMCG

Project description:Gluten-free diet intervention: 11 individuals, 3 time points (T1: 1 week before intervention, T2: at the intervention; T3: 5 weeks after intervention. Fecal samples taken at each time point were sujbject of VLP enrichment and routine metagenomics sequencing

| EGAS00001005225 | EGA

FBLN1 and FABP4 are drivers of resistance to fleece rot in Australian Merino sheep

Project description:Transcriptional profiling of Ovine skin samples comparing resistant (RES) to susceptible (SUS) animals following fleece rot induction. Two condition experiment, RES vs SUS biopsies, over 3 time points. 31 RES 31 SUS T0: Prior to commencment of treatment T1: 2-3 days post commencment T2: 11 days post commencment The first skin biopsies were taken on the first day (T0) prior to commencement of the five day regime of simulated rainfall. Subsequent skin biopsies were taken 2-3 days into the wetting regime (T1) and following a recovery period of 11 days from the time that the wetting regime had begun (T2).

2010-06-05 | E-GEOD-21022 | biostudies-arrayexpress

RNASeq of murine choroid plexus following one (T1), three (T3) and three days of DSS treatment followed by two days of water (T5)

Project description:To evaluate, at the molecular level, potential pathways involved in changes of PVB permeability, we dissected lateral CP tissues at all time points (T0, T1, T3, or T5) and performed transcriptional profiling by deep RNA-sequencing. We used a regression model-based method for the classification of co-regulated genes based on their temporal expression profiles and the identification of differentially expressed genes (DEGs).

2021-10-26 | GSE178750 | GEO

Chimeric RNA profiling demonstrates an association of alveolar rhabdomyosarcoma with specific stages of normal myogenesis

Project description:Total RNA extracted from differentiated mesenchymal stem cells at four time points (T1,T2,T3,T4) and sequenced using Illumina Hi-seq 2000 platform to generate RNA sequencing with 101bp in read length. Nearly 50 million raw reads were yielded from each sample respectively. We used FastQC to confirm the quality of raw fastq sequencing data, and SOAPfuse software to detect fusion transcripts.

2016-02-09 | GSE64032 | GEO

Nivolumab treatment for relapsed/refractory Epstein-Barr virus-associated hemophagocytic lymphohistocytosis in adults

Project description:Single cell RNA sequencing (scRNA-seq) was performed with peripheral blood cells before (Day 0, T0), during nivolumab treatment (Day 7, T1; Day 21, T2), and when plasma EBV turned negative (Day 76, T3) in 1 patient (patient 7). scRNA-seq libraries were generated following the recommended protocol of the 3’ scRNA-seq 10X genomics platform and using v2 chemistry, and sequenced data was collected by illumina NovaSeq 6000 sequencing.

2019-10-07 | GSE138504 | GEO

Vein and Intervein Drought RNAseq

Project description:We report here the RNAseq data generated from a drought experiment using tomato leaves (Solanum lycopersicum), in which three timepoints and two treatments were collected. More specifically, RNAseq was generated from tomato plants prior to drought (T0), during a period of drought (T1) and after a period of recovery from drought (T2). At timepoints 1 and 2 (T1 & T2), a control set of plants that were continuously watered are also included. Furthermore, at each timepoint, each leaf was dissected into two parts, including the vein and intervein. The samples are therefore named as Tissue/Timepoint/Treatment, and include VT0W (vein, T0, watered), VT1W (vein, T1, watered), VT1D (vein, T1, drought), VT2D, VT2W and IVT0W (intervein, T0, Watered), IVT1D, IVT1W, IVT2D, IVT2W. Note that VT2D and IVT2D, while named "drought", were actually recovered from drought.

2020-10-31 | GSE156402 | 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