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TranscriptomicsProfiling the transcriptome of Thalassiosira pseudonana under silicon replete and deplete growth.
T. pseudonana tiling arrays were used to validate gene models and to predict new genes in the genome of this diatom. The tiling array data validated transcription of about 41% (4,653) of the 11,390 computationally predicted genes. An additional 1,132 transcripts were identified that did not correspo...
ORGANISM(S): Thalassiosira pseudonana CCMP1335 
2010-05-26 | E-GEOD-9661 | biostudies-arrayexpress
ProteomicsA mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides
Less than half of all MS/MS spectra acquired in shotgun proteomics typically result in a confident peptide match. Here we present an ultra-tolerant Sequest database search that allowed peptide matching even with modifications of unknown masses up to ±500 Da. From an HEK293 cell proteome-wide datas...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-06-19 | MSV000079841 | MassIVE
TranscriptomicsProfiling the transcriptome of Thalassiosira pseudonana under environmentally relevant growth conditions
T. pseudonana gene-specific arrays were used for differential gene expression. Seven hundred nine genes were differentially expressed by more than 2-fold (Bayesian t-test, p< 0.001) under at least one growth-limiting condition relative to nutrient-replete conditions. A striking result of the hierarc...
ORGANISM(S): Thalassiosira pseudonana CCMP1335 
2010-05-26 | E-GEOD-9660 | biostudies-arrayexpress
Proteomics,MultiomicsDefining the effects of genetic variation on a proteome-wide scale
Genetic variation governs protein expression through both transcriptional and post-transcriptional processes. To investigate this relationship, we combined a multiplexed, mass spectrometry-based method for protein quantification with an emerging mouse model harboring extensive genetic variation fro...
ORGANISM(S): Mus Musculus (ncbitaxon:10090) 
2017-11-08 | MSV000081696 | MassIVE
ProteomicsEffect of Kinase Inhibitors on Intraerythrocytic Plasmodium falciparum Phosphoproteome
Three flasks of asynchronous blood stage P. falciparum Dd2 culture were grown to ~15% parasitemia, 4% hematocrit using the Trager- Jensen method. Per biological replicate, parasites were treated with 5 x EC50 or EC90 of compound depending on the slope of the EC50 curve for 3 hours. Compounds are DC-...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Plasmodium Falciparum Dd2 (ncbitaxon:57267) 
2023-04-03 | MSV000091619 | MassIVE
ProteomicsSample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression
Targeted proteomics enables hypothesis-driven research by measuring the cellular expression of protein cohorts related by function, disease, or class after perturbation. Here, we present a pathway-centric approach and an assay builder resource for targeting entire pathways of proteins selected from ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090) 
2022-08-11 | MSV000090110 | MassIVE
ProteomicsBioplex 3 AP-MS Dataset for Library Construction
The BioPlex (biophysical interactions of ORFeome-based complexes) network is the result of creating thousands of cell lines with each expressing a tagged version of a protein from the ORFeome collection. Immunopurification of the tagged protein and detection of associated proteins by mass spectromet...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2021-12-13 | MSV000088555 | MassIVE
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