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MetabolomicsExperimental and computational approaches for deep metabolome annotation with application to the ecotoxicological model organism Daphnia magna

Identifying metabolomes with greater coverage and confidence is a critical step towards interpreting the metabolic basis of human and environmental health. Yet for over two decades the field of metabolomics has been inhibited by limited metabolite identification. To address this, we developed the...

MTBLS2273 | MetaboLights
MetabolomicsWT 2.0: Unveiling the “dark matter” in the metabolome using all-ion stepwise fragmentation acquisition mode (ASFAM) and deep learning-based feature extraction

Current metabolomics methods often miss low-abundance compounds and yield incomplete or ambiguous MS2 spectra, resulting in the presence of “dark matter” within the metabolome. Here, we introduce WT 2.0, which employs an all-ion stepwise fragmentation acquisition mode (ASFAM) to acquire comprehe...

2025-09-23 | MTBLS13023 | MetaboLights
TranscriptomicsRNA-seq of A431 cell line after gefitinib treatment
RNA sequencing of A431 cell line samples before and after gefitinib treatment, at 0, 2, 6 and 24 hours, was performed in order to characterize the cell line's early and late response to this drug, and to compare against proteomics (mass spectrometry) characterization of the cell line using the same ...
ORGANISM(S): Homo sapiens 
2016-12-01 | E-MTAB-5285 | biostudies-arrayexpress
GenomicsDeep sequencing analyzed the coverage of sgRNA in haploid stem cells.
Deep sequencing analyzed the coverage of sgRNA in haploid stem cells.
PRJNA473519 | ENA
ProteomicsHigh-Coverage Four-Dimensional Data-Independent Acquisition Proteomics and Phosphoproteomics Enabled by Deep Learning-Driven Multi-Dimensional Prediction
Here, a workflow of 4D DIA proteomics by using the predicted multi-dimensional in silico library was established. A deep learning model Deep4D that could high-accurately predict the CCS and RT of both the unmodified and phosphorylated peptides was developed, which is the model based on self-attentio...
ORGANISM(S): Homo Sapiens Mus Musculus Saccharomyces Cerevisiae 
PXD034553 |
OtherDeep sequencing analyzed the coverage of sgRNA in haploid stem cells.
We used the deep sequencing to analyze the sgRNA coverage of Dnd1 library in 4B2N1-DP1 and 4B2N1-DP2 cell lines. The amplicon obtained from PCR reaction from genome using high-fidelity DNA polymerase. By obtaining over 10 million reads of each sample from deep sequencing, we mapped the reads to the ...
ORGANISM(S): Mus musculus 
2018-08-06 | GSE115015 | GEO
TranscriptomicsCharacterization of the Imprinting Signature of Mouse Embryo Fibroblasts by RNA Deep Sequencing
Mouse embryo fibroblasts (MEFs) closely resemble mouse embryos and are convenient sources for biochemical studies when cell number may be limiting from mouse embryos. To derive the imprinting signature of MEFs and potentially detect novel imprinted genes we characterized them using strand- and allel...
ORGANISM(S): Mus musculus 
2013-11-18 | E-GEOD-49538 | biostudies-arrayexpress
ProteomicsDeep proteome coverage of microglia using a streamlined data independent acquisition-based proteomic workflow: method consideration for a phenotypically diverse cell type
As the immune cells of the brain, microglia play a key role in various homeostatic and disease-related processes. In order to carry out their numerous functions, microglia are able to adopt a wide range of phenotypic states. The proteomic landscape represents a more accurate molecular representation...
ORGANISM(S): Mus musculus (Mouse) 
2025-03-31 | PXD056436 | Pride
Dia-pasef Dda library generation Deep proteomics Microglia Dia methods development 
TranscriptomicsA Comparative Profile of the MicroRNA Transcriptome in Immature and Mature Porcine Testes using Solexa Deep Sequencing
MicroRNAs (miRNAs) are small non-coding regulatory RNAs that play key roles in many diverse biological processes such as spermatogenesis. However, no study has been performed on the miRNA transcriptome of developing porcine testes. Here, we employed Solexa deep sequencing technology to extend the re...
ORGANISM(S): Sus scrofa 
2011-09-23 | E-GEOD-28169 | biostudies-arrayexpress
ProteomicsExpanding proteome coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) combined with broad specificity proteolysis
The "deep" proteome has been accessible by mass spectrometry for some time. However, the number of proteins identified in cells of the same type has plateaued at ~8,000-10,000 without ID transfer from reference proteomes/data. Moreover, limited sequence coverage hampers the discrimination of protein...
ORGANISM(S): Homo sapiens (Human) 
2017-02-07 | PXD003977 | Pride
Fusion lumos Deep proteome 
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