Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

POPCOL: population-based colonoscopy.

ABSTRACT: PopCol is a cohort study in Stockholm, Sweden that includes a data-rich set of individuals with data available from bowel symptoms questionnaires, gastroenterology visits and biospecimens (genotype and 16S sequencing from blood and stool samples, respectively). Genotyping was carried out using the Illumina HumanOmniExpressExome-8v1 arrays at the SciLifeLab NGI facility in Uppsala, Sweden. Fecal DNA was extracted from samples kept at -80Ã‚Â°C using Qiagen 5 QIAamp DNA Stool Mini Kits and analyzed using 16S rRNA gene amplicon sequencing (in the V1-V2 hypervariable region). This was performed on the Illumina MiSeq platform at the Institute of Clinical Molecular Biology (IKMB) in Kiel, Germany. Of these, six PopCol participants were PPI users and 12 used antibiotics. The study was approved by the local Committee of Research Ethics (ForskningskommittÃƒÂ© Syd) at Karolinska Institutet, Stockholm, in November 2001. Written informed consent was obtained from all participants

PROVIDER: EGAS00001004869 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Similar Datasets

c8be300c-3791-4ebe-b44a-202025b9d721 - samples

Project description:PopCol is a cohort study in Stockholm, Sweden that includes a data-rich set of individuals with data available from bowel symptoms questionnaires, gastroenterology visits and biospecimens (genotype and 16S sequencing from blood and stool samples, respectively). Genotyping was carried out using the Illumina HumanOmniExpressExome-8v1 arrays at the SciLifeLab NGI facility in Uppsala, Sweden. Fecal DNA was extracted from samples kept at -80Ã‚Â°C using Qiagen 5 QIAamp DNA Stool Mini Kits and analyzed using 16S rRNA gene amplicon sequencing (in the V1-V2 hypervariable region). This was performed on the Illumina MiSeq platform at the Institute of Clinical Molecular Biology (IKMB) in Kiel, Germany. Of these, six PopCol participants were PPI users and 12 used antibiotics. The study was approved by the local Committee of Research Ethics (ForskningskommittÃƒÂ© Syd) at Karolinska Institutet, Stockholm, in November 2001. Written informed consent was obtained from all participants

| EGAD00001007071 | EGA

In-depth serum proteomics of hospitalized COVID-19 patients and PCR-negative healthy controls with HiRIEF LC-MS/MS

Project description:We performed in-depth MS-based plasma-proteome profiling in 20 hospitalised patients with COVID-19 and 7 healthy controls (PCR- and sero-negative for SARS-CoV-2) by high-resolution isoelectric focusing (HiRIEF) coupled with liquid chromatography and mass-spectrometry (LC-MS/MS). The SARS‐CoV‐2 PCR‐confirmed patients from Karolinska University Hospital in Stockholm, Sweden, were included in the study in April 2020. Data from the cohort and methodology of clinical and immunological assays has been previously described in detail elsewhere (Varnaitė et al., 2020). The study was approved by the Regional Ethical Review Board in Stockholm, Sweden and by the Swedish Ethical Review Authority, and is in accordance with the Declaration of Helsinki. All COVID-19 patients and healthy controls included in this study provided written informed consent. The cohort is described in detail elsewhere (Varnaitė et al., 2020) Reference: Varnaitė, R., García, M., Glans, H., Maleki, K.T., Sandberg, J.T., Tynell, J., Christ, W., Lagerqvist, N., Asgeirsson, H., Ljunggren, H.-G., et al. (2020). Expansion of SARS-CoV-2-Specific Antibody-Secreting Cells and Generation of Neutralizing Antibodies in Hospitalized COVID-19 Patients. J. Immunol. 205, 2437–2446.

2023-09-01 | PXD037486 | Pride

β-Actin-dependent global chromatin organization and gene expression programs control cellular identity.

Project description:Purpose: The goals of this study are to use NGS to perform transcriptome profiling (RNA-seq) to find the difference of the gene expression programs among Wild Type (Wt), Actb+/- (Hetero) and Actb-/- (KNO) Mouse Embryonic Fibroblasts Methods: Total RNA was extracted from 70% confluent cells using TRI Reagent according to the manufacturer protocol (Sigma-Aldrich). Quality of total RNA was evaluated at SciLIfe lab (Stockholm, Sweden) using Qubit and Bioanalyzer respectively, samples which pass the QC were used for library construction according to the SciLife lab guideline using TruSeq Stranded mRNA Library Prep Kit (Illumina). Deep sequencing was performed at Science for Life Laboratory, the National Genomics Infrastructure, NGI, Karolinska Institute, Stockholm. Data was processed through the standard RNAseq analysis pipeline at NYUAD. Read aligmnet was performed using tophat2 v2.1.0 against Mus musculus GRCm38.p4 genome version. Cufflinks v2.2.1 was used to derive expression (FPKM) values. Cuffdiff was used to identify differential gene expression. Results: Using an optimized data analysis workflow, we identified genes differentially expressed between Wild Type and Actb+/-, WT and Actb-/-, Actb+/- and Actb-/- Mouse Embryonic Fibroblasts. Selected differentially expressed genes were confirmed by qRT-PCR. Gene ontology analysis further identified biological processes, cellular components and molecular functions that were overrepresented in the differentially expressed genes. Conclusions: Our study shows that there are gene programs differentially regulated among Wild Type, Actb+/- and Actb-/- Mouse Embryonic Fibroblasts

2017-03-09 | GSE95830 | GEO

16S profile of stool from conventional unifected and C.rodentium infected mice

Project description:We aim to determine if mice in our mouse colony had similar of different microbiomes. To do this, we perfromed 16S sequencing of stool from unifected mice of the gentotypes listed below. We also looked at how infection causes dysbiosis of the mircobiome, measuring 16S sequencing over a C.rodentium infection timecourse.

2018-07-03 | GSE116491 | GEO

Evaluating the gut microbiota shifts caused by two diets based on ancient grains

Project description:Total DNA was extracted from stool specimens, amplified to collect amplicons of variable V3–V4 regions of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.

2022-08-24 | GSE206807 | GEO

16S rRNA gene sequences aw6 p4, p5, p9, p10, p11, p12, p13, p14

Project description:Hypervariable regions V3-V5 of bacterial 16S rRNA genes. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

2014-03-14 | E-ERAD-254 | biostudies-arrayexpress

Comparing the microbiota composition between Cocaine addicted and Healthy subjects and the corresponding shift caused by rTMS treatment.

Project description:Total DNA was extracted from saliva and stool of the patients, amplified to collect amplicons of variable V3–V4 regions of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.

2023-05-31 | GSE206765 | GEO

Comparing the microbiota composition between HPV positive and negative patients with CRC

Project description:Total DNA was extracted from the stool of the patients, amplified to collect amplicons of variable V3–V4 regions (primers 341F and 805R) of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.

2023-10-15 | GSE216589 | GEO

High-throughput sequencing for microRNAs in uninjured and regenerating newt hearts

Project description:We have developed a standardized and reproducible heart resection/regeneration model system in the red-spotted newt. In order to ascertain the involvement of microRNAs in this amazing process, we made and sequenced cDNA libraries for microRNAs in order to provide sequence data that we could use in further quantitative and qualitative studies. We constructed small RNA cDNA libraries for uninjured (Uninj), 7dpi and 21dpi heart samples, which were sequenced using Illumina-Solexa technology at SciLifeLabs (Stockholm, Sweden).

2013-09-24 | E-GEOD-46527 | biostudies-arrayexpress

Microbiota and Complications in Kidney Transplant Recipients

Project description:<p>In this study, we investigated the role of the gut microbiota on the development of complications in kidney transplant recipients. We collected serial fecal specimens from 168 kidney transplant recipients within the first 3 months after transplantation. We performed 16S rRNA gene sequencing of the V4-V5 hypervariable region and examined whether the relative gut abundance of pathogenic bacteria was associated with future development of complications like bacteriuria and urinary tract infections. In a subset of samples, we performed metagenomic sequencing of stool and urine supernatant specimens to determine strain level analysis. </p>

| phs001879 | dbGaP

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