Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 768

System / cell line: relative ✕ Clear

RPS4Y gene family evolution in primates.

PMID 18477388 · PMC2397393 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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The duplication event giving rise to RPS4Y2 occurred after the divergence of New World monkeys, about 35 million years ago.

primate chromosomes rps4x concatenated pcr fluorescence repeat
Contributions of proteomics to understanding phagosome maturation.

PMID 18331591 · PMC2613258 · Cellular microbiology · 2008 · 8 claims · 8 setups

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Proteomic studies across many species have identified hundreds of proteins associated with phagosomes, revealing conserved functional classes (vATPase subunits, GTPases, hydrolases, SNAREs, Rabs, cytoskeletal proteins).

macrophage dictyostelium drosophila entamoeba quantitative 2dge prefractionation
Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

PMID 18267968 · PMC2367719 · Nucleic acids research · 2008 · 6 claims · 8 setups

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The seed arm (guide strand positions 2-8), its complementary passenger-strand sequence, the 5' end of the guide strand, and the 3' overhang of the passenger strand can be simultaneously replaced with DNA without substantial loss of gene-silencing activity.

cho-k1 e14tg2a recombinant hela dual-luciferase rt-pcr electrophoresis
A genome-wide screen for noncoding elements important in primate evolution.

PMID 18215302 · PMC2242780 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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A new likelihood ratio test (LRT) method, using nearby ancestral repeats to control for local mutation rate, can identify noncoding elements with lineage-specific accelerated substitution rates.

phastcons global genome accelerated comparative targeted fisher's
Band 3 Courcouronnes (Ser667Phe): a trafficking mutant differentially rescued by wild-type band 3 and glycophorin A.

PMID 18174378 · PMC2605348 · Blood · 2008 · 7 claims · 8 setups

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Homozygous SLC4A1 Ser667Phe mutation causes both hereditary spherocytosis and incomplete distal renal tubular acidosis in the proband

erythrocyte genomic erythrocytes xenopus sds-page sscp dids
The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice.

PMID 20368178 · PMC2894525 · Science translational medicine · 2009 · 7 claims · 6 setups

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Germ-free C57BL/6J mice can be stably and heritably colonized with a human fecal microbiota, reproducing much of the donor's bacterial diversity.

fecal postnatal luminal pooled 16s shotgun body
Immunohistochemical and proteomic evaluation of nuclear ubiquitous casein and cyclin-dependent kinases substrate in invasive ductal carcinoma of the breast.

PMID 20069058 · PMC2801467 · Journal of biomedicine & biotechnology · 2009 · 7 claims · 5 setups

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NUCKS is highly overexpressed in invasive ductal carcinoma (IDC) of the breast compared to matched normal tissue.

matched idc nucks rabbits lc-ms sds-page western
Identification of beta-secretase (BACE1) substrates using quantitative proteomics.

PMID 20041192 · PMC2793532 · PloS one · 2009 · 7 claims · 5 setups

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Quantitative proteomics of conditioned medium from BACE1-overexpressing HEK and HeLa cells identified 68 putative β-secretase substrates

hek293 hela hek concentrated silac western sds-page
Mesotrypsin promotes malignant growth of breast cancer cells through shedding of CD109.

PMID 20035377 · PMC2929293 · Breast cancer research and treatment · 2010 · 8 claims · 8 setups

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Serine protease inhibitors (aprotinin, SBTI) cause morphological reversion of malignant T4-2 breast cancer cells in 3D culture, restoring acinar structure and basal polarity

hmt-3522 organotypic quantitative lentiviral
A global view of protein expression in human cells, tissues, and organs.

PMID 20029370 · PMC2824494 · Molecular systems biology · 2009 · 7 claims · 6 setups

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A high fraction (>65%) of proteins is expressed in most human cells and tissues, while very few proteins (<2%) are detected in any single cell type.

normal computational hepatocytes same immunohistochemistry immunofluorescence unsupervised
A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

PMID 20012890 · PMC2797846 · Behavior genetics · 2010 · 6 claims · 4 setups

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SNP Microarrays and Pooling (SNP-MaP) is a valid economical method for genome-wide screening of quantitative trait extremes using pooled DNA on microarrays

teds diagnosed ceph snp individual transmission
Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements.

PMID 20008508 · PMC2836564 · Nucleic acids research · 2010 · 8 claims · 6 setups

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Most TEs insert within specific 'hotspots' along the targeted TE rather than uniformly.

genome sequences unique nested chi-square position-specific
Reduced transcription of TCOF1 in adult cells of Treacher Collins syndrome patients.

PMID 20003452 · PMC2801500 · BMC medical genetics · 2009 · 8 claims · 5 setups

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TCOF1 transcript levels are significantly reduced (~18%) in leucocytes of TCS patients compared to controls

leucocytes mesenchymal leucocyte real-time direct flow
A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.

PMID 19997597 · PMC2781549 · PloS one · 2009 · 8 claims · 7 setups

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The majority of proteins expressed in growing and non-growing S. aureus cells can be identified and quantified by a metabolic labeling proteomic approach

aureus 2-d 1-d gelc-ms
Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival.

PMID 19924232 · PMC2773120 · PloS one · 2009 · 8 claims · 5 setups

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37 miRNAs are significantly differentially expressed between MYCN-amplified (MNA) and non-MNA neuroblastoma tumors, suggesting direct or indirect regulation by MYCN

neuroblastoma shep-tet21 stem-loop array tlda
Evidence for a novel gene associated with human influenza A viruses.

PMID 19917120 · PMC2780412 · Virology journal · 2009 · 8 claims · 8 setups

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A 167-codon ORF (NEG8) on the negative-sense genomic strand of segment 8 is associated with early-20th-century human influenza A isolates

influenza pre-1950 avian neg8 comparative neighbour-joining fixed
Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ).

PMID 19902006 · PMC2774473 · Journal of biomedicine & biotechnology · 2010 · 8 claims · 5 setups

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iTRAQ labelling combined with 4800 MALDI TOF/TOF can detect quantitative differences in the maternal plasma proteome between DS and euploid pregnancies

maternal tryptic scx-fractionated identified itraq immunodepletion strong
MEROPS: the peptidase database.

PMID 19892822 · PMC2808883 · Nucleic acids research · 2010 · 8 claims · 5 setups

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MEROPS is a manually curated hierarchical classification of peptidases and protein inhibitors organized into protein species, families, and clans based on sequence and structural homology.

archaean holotype c-x-c proteins comparative domain substrate
Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.

PMID 25520726 · PMC4251292 · Frontiers in plant science · 2014 · 8 claims · 8 setups

Has reproduction · 93

24 h of waterlogging significantly alters mRNA abundance of 1968 genes in Jatropha roots (931 up, 1037 down).

jatropha geo bulk semi-quantitative quantitative
Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and titanium amplicon pyrosequencing and metagenomic approaches.

PMID 19860898 · PMC2773781 · BMC microbiology · 2009 · 7 claims · 5 setups

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VLU infections are polymicrobial with no single bacterium colonizing the wounds

individual pooled second btefap quantitative bulk

Experiments

RPS4Y gene family evolution in primates.

Contributions of proteomics to understanding phagosome maturation.

Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

A genome-wide screen for noncoding elements important in primate evolution.

Band 3 Courcouronnes (Ser667Phe): a trafficking mutant differentially rescued by wild-type band 3 and glycophorin A.

The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice.

Immunohistochemical and proteomic evaluation of nuclear ubiquitous casein and cyclin-dependent kinases substrate in invasive ductal carcinoma of the breast.

Identification of beta-secretase (BACE1) substrates using quantitative proteomics.

Mesotrypsin promotes malignant growth of breast cancer cells through shedding of CD109.

A global view of protein expression in human cells, tissues, and organs.

A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

Large-scale discovery of insertion hotspots and preferential integration sites of human transposed elements.

Reduced transcription of TCOF1 in adult cells of Treacher Collins syndrome patients.

A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.

Widespread dysregulation of MiRNAs by MYCN amplification and chromosomal imbalances in neuroblastoma: association of miRNA expression with survival.

Evidence for a novel gene associated with human influenza A viruses.

Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ).

MEROPS: the peptidase database.

Elucidation of the molecular responses to waterlogging in Jatropha roots by transcriptome profiling.

Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and titanium amplicon pyrosequencing and metagenomic approaches.