Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Evaluation of a New Organization for Collecting Pre-chemotherapy Session Information

ABSTRACT: The primary objective of this study is to compare an experimental organization for chemotherapy session planning based on early, standardized, and prioritized means of data transmission via secure e-mail (laboratory results) and the use of a smart phone (for clinical toxicity data) compared to the regular organization, in terms of the rate of prescriptions of chemotherapy prepared at the latest the day before a session and then administered in full (over a 6-month observation period) among colorectal cancer patients in need of cancer treatment in an outpatient setting.

DISEASE(S): Colorectal Neoplasms

PROVIDER: 2247322 | ecrin-mdr-crc |

REPOSITORIES: ECRIN MDR

ACCESS DATA

Json Xml

Similar Datasets

Sequencing Universal Human Reference RNA by Smart-seq and early barcoding library preparation methods

Project description:Many library preparation methods are available for gene expression quantification. Here, we sequenced and analysed Universal Human Reference RNA (UHRR) prepared using Smart-Seq2, TruSeq (public data) and a protocol using unique molecular identifiers (UMIs) that all include the ERCC spike-in mRNAs to investigate the effects of amplification bias on expression quantification.

2016-05-13 | GSE75823 | GEO

Sequencing Universal Human Reference RNA by Smart-seq and early barcoding library preparation methods

2016-05-13 | E-GEOD-75823 | biostudies-arrayexpress

scNMT-seq of pancreatic organoids - RNA

Project description:Single-cell nucleosome, methylome and transcriptome (scNMT) sequencing is a recently developed method that allows multiomics profiling of single cells. In this scNMT protocol, we describe profiling of cells from mouse brain and pancreatic organoids, using liquid handling platforms to increase throughput from 96-well to 384-well plate format. Our approach miniaturizes reaction volumes and incorporates the latest Smart-seq3 protocol to obtain a higher number of detected genes and genomic DNA (gDNA) CpG sites per cell. We outline normalization steps to optimally distribute per-cell sequencing depth.

2022-08-12 | GSE210805 | GEO

scNMT-seq of pancreatic organoids - DNA methylation and chromatin accessibility

2022-08-12 | GSE210804 | GEO

Analysis of Transcriptome in hematopoietic stem cells after radiation injury with treatment of EGF or saline

Project description:Purpose: This study is designed to understand whether Epidermal Growth Factor treatment alters the transcriptome of hematopoietic stem cells after radiation injury Method: RNA was extracted from C57BL/6J mice at six weeks post 500cGy total body radiation and Epidermal Growth Factor or saline subcutaneous treatment. Libraries for RNA-Seq were prepared with Clontech kit. The data was sequenced on NextSeq500 for a paired-end 75bp read run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program. The Partek flow and Ingenuity Pathway Analysis (IPA) were used for bioinformatics methods and data analysis, respectively. The reads were mapped to the latest UCSC transcript set using STAR - 2.7.2a and GRCm38.97.

2020-07-29 | GSE146371 | GEO

Induction of meiosis by embryonic gonadal somatic cells differentiated from pluripotent stem cells

Project description:ESCs of bulk RNA-Seq were harvested and total RNA extracted using Qiagen RNeasy Mini kit, according to the manufacturers’ instruction, including a DNAse digestion. Single-cell library was prepared using smart-seq2 or the 10 × Genomics Chromium Single Cell 3′ Library and Gel Bead Kit v2 according to the manufacturer’s instructions.

2022-01-07 | GSE181501 | GEO

RNA-seq profiling of HSC, MPPs and HPC-1s from Phf6-deleted and Phf6-intact mice

Project description:The study profiled the effect of Phf6 deletion on gene expression in hematopoietic stem cells (HSCs), multipotent progenitor cells (MPPs) and hematopoietic progenitor cells (HPC-1). Phf6lox/Y;Tie2-creTg/+ mice were prepared on a C57BL/6 background so that Phf6 deletion could be selectively mediated by Tie2-cre. Cell populations were sorted from bone marrow samples using standard surface markers (Lin–SCA1+cKIT+(LSK) CD150+ CD48– for HSCs, Lin–SCA1+cKIT+(LSK) CD150– CD48– for MPPs and Lin–SCA1+cKIT+(LSK) CD150- CD48+ for HPC-1 cells). Phf6 intact and Phf6-delected cells of all three types were profiled by paired-end RNA-seq using an Illumina NextSeq 500 sequencer. RNA-seq libraries were prepared from the HPC-1 samples used a standard Illumina TruSeq library protocol whereas the libraries for the HSC and MPP samples used a SMART-seq ultra low input kit for cDNA synthesis and amplification. Statistical analysis of the TruSeq and SMART-seq samples was undertaken separately.

2019-02-20 | GSE126316 | GEO

Intermittent childhood hyperlipidaemia alters resident arterial macrophages and accelerates atherosclerosis

Project description:Mice deficient in the LDL receptor (LDLR KO mice) fed with high fat diet (HFD) feeding have been widely used as a model to mimic human atherosclerosis. RNA-seq using aortic macrophages to investigate the effects of aortic macrophages on the plaque size progression. LDLR KO mice, 6-8 weeks old, were used, and fed with either an alternative HFD or a regular HFD. After aorta macrophages were isolated, RNeasy Mini Kit (Qiagen) was used to isolate mRNA. Single end (50bp), unstranded, SMART-Seq v4 plus nextera (SMART-Seq v4 Ultra Low Input RNA Kit (Takara) ). The RNA-seq libraries were prepared with SMART-Seq v4 Ultra Low Input RNA Kit (Takara).

2024-07-31 | E-MTAB-12759 | biostudies-arrayexpress

Single cell RNA-sequencing of human tonsil Innate lymphoid cells (ILCs)

Project description:Single cell RNA-sequencing of human tonsil Innate lymphoid cells (ILCs) from three independent tonsil donors. Sequencing libraries were prepared from FACS sorted individual ILCs with the Smart-Seq2 protocol (Picelli et al. Nature Methods 2013)

2016-01-27 | E-GEOD-70580 | biostudies-arrayexpress

MetaDB a Data Processing Workflow in Untargeted MS-Based Metabolomics Experiments

Project description:This dataset reports the UPLC-QTof MS untargeted analysis of Vitis vinifera L. leaves, collected from Italy (Trentino) and Germany (Mecklenburg West-Pomerania), from two fungus-resistant grape varieties (PIWI), Regent and Phoenix. For each variety, 40 leaves were sampled from 10 plants (4 leaves/plant) in Italy, and other 40 with the same process in Germany. The leaves from each plant were homogenized and extracted separately, in the same day, under a randomized order. A quality control (QC) sample was prepared by pooling a small aliquot from each sample. </p> The aim of the project, was to use this sample/data set as an illustrative example for the use the pipeline MetaDB (https://github.com/rmylonas/MetaDB). MetaDB has been developed in order to combine, with a user-friendly web based, different bioinformatic tools used in metabolomics, which takes care a) metadata organization, b) creation of randomized sequences including QC sample, c) data quality evaluation, d) data storage organization, e) data analysis and f) submission to public repositories.

2014-11-09 | MTBLS137 | MetaboLights

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