Project description:In a cross-site study we evaluated the performance of ribosomal RNA removal kits from Illumina, Takara/Clontech, Kapa Biosystems, Lexogen, New England Biolabs and Qiagen on intact and degraded RNA samples. We found that all of the kits were capable of performing significant ribosomal depletion, though there were differences in their ease of use. All kits were able to remove ribosomal RNA to below 20% with intact RNA and identify ~14,000 protein coding genes from the Universal Human Reference RNA sample at >1FPKM. Analysis of differentially detected genes among kits suggested that transcript length may be a key factor in library production efficiency. These results provide a roadmap for labs on the strengths of each of these methods and how best to utilize them.

2018-02-01 | GSE100127 | GEO

Comprehensive human serum spectral library

Project description:For a comprehensive analysis of the human serum proteome, we constructed a spectral library for DIA-MS. Our spectral library contained information on 20,303 peptides derived from 1,597 human serum proteins. We believe that the constructed spectral library will be useful for proteomic analysis of human serum by DIA-MS.

2024-04-10 | PXD041558 | JPOST Repository

Comprehensive Arabidopsis Proteome Spectral Library

Project description:We constructed a comprehensive Arabidopsis Spectral Assay library that is useful for DIA/SWATH-MS quantitative proteome analysis.

2019-11-06 | PXD012708 | Pride

Selection of RNA-seq library preparation protocol for a comprehensive transcriptome analysis in T acute lymphoblastic leukemia (T-ALL)

Project description:The aim of this study was to compare two different library preparation protocols: Illumina TruSeq Stranded mRNA (referred to as PA) and TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat (RD) each with two different variants of the fragmentation step: standard fragmentation conditions (94°C for 8 minutes; further described as P1) and modified conditions (90°C for 2 minutes; further described as P2). The modification was expected to produce longer fragments. Each of the 5 tested T-ALL samples was sequenced using a combination of 4 different protocols: PA_P1, RD_P1, PA_P2, RD_P2 (for PA_P2 we performed two technical replicates). All 25 libraries were sequenced on Illumina NovaSeq6000 platform, in 2x150 mode, with a coverage of 150M reads/sample. High number of reads obtained for each of the samples allowed us to carry out a comprehensive comparison using various analysis methods aimed at identifying differentially expressed genes, alternative splicing events, gene fusions, somatic mutations and indels.

2021-11-23 | E-MTAB-10253 | biostudies-arrayexpress

SARS-CoV-2 library prep comparison

Project description:Comparing library preparation methods for SARS-CoV-2 multiplex amplicon sequencing on the Illumina MiSeq platform

| PRJEB38369 | ENA

A comprehensive library of human transcription factors for cell fate engineering

Project description:A comprehensive library of human transcription factors for cell fate engineering

| PRJNA670483 | ENA

Comprehensive comparative analysis of strand-specific RNA sequencing methods

Project description:Strand-specific massively-parallel cDNA sequencing (RNA-Seq) is a powerful tool for novel transcript discovery, genome annotation, and expression profiling. Despite multiple published methods for strand-specific RNA-Seq, no consensus exists as to how to choose between them. Here, we developed a comprehensive computational pipeline for the comparison of library quality metrics from any RNA-Seq method. Using the well-annotated Saccharomyces cerevisiae transcriptome as a benchmark, we compared seven library construction protocols, including both published and our own novel methods. We found marked differences in complexity, strand-specificity, evenness and continuity of coverage, agreement with known annotations, and accuracy for expression profiling. Weighing each method’s performance and ease, we identify the dUTP second strand marking and the Illumina RNA ligation methods as the leading protocols, with the former benefitting from the availability of paired-end sequencing. Our analysis provides a comprehensive benchmark, and our computational pipeline is applicable for assessment of future protocols in any organism.

2010-08-15 | GSE21739 | GEO

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