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 21

System / cell line: normalized ✕ Assay: antibody ✕ Clear

Antibody protein array analysis of the tear film cytokines.

PMID 18677223 · PMC3786218 · Optometry and vision science : official publication of the American Academy of Optometry · 2008 · 7 claims · 4 setups

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Tear fluid contains factors with affinity for plastic, capture antibodies, and IgG that create matrix effects profoundly impacting dot ELISA/array reliability

tear normalized antibody 12-plex two-step
Key regulatory molecules of cartilage destruction in rheumatoid arthritis: an in vitro study.

PMID 18205922 · PMC2374452 · Arthritis research & therapy · 2008 · 7 claims · 4 setups

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A standardized 3D in vitro alginate bead model of chondrocytes stimulated with synovial fibroblast supernatants can be used to profile RA-related cartilage destruction genes

sv40 articular differentially antibody-based oligonucleotide real-time
beta- Catenin mutations and aberrant nuclear expression during endometrial tumorigenesis.

PMID 11161379 · PMC2363713 · British journal of cancer · 2001 · 7 claims · 4 setups

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Cell membrane β-catenin immunoreactivity shows a stepwise decrease from normal endometrium, through atypical hyperplasia, to grade 3 carcinoma.

endometrial immunohistochemistry rt-pcr pcr
Proteomic analysis of mechanisms of hypoxia-induced apoptosis in trophoblastic cells.

PMID 17299580 · PMC1796955 · International journal of medical sciences · 2006 · 8 claims · 7 setups

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Hypoxia induces apoptosis in JAR trophoblastic cells, shown by time-dependent increase in internucleosomal DNA fragmentation

jar powerblot mtt death
A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells.

PMID 34426512 · PMC8415381 · Genome research · 2021 · 8 claims · 8 setups

Has reproduction · 57

About 5% of tested PCRP antibodies showed high-confidence cognate-target enrichment in at least one assay and are strong candidates for further validation.

k562 hct116 subset chip-exo chip-seq western
Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

PMID 16519801 · PMC1421398 · BMC biotechnology · 2006 · 8 claims · 8 setups

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The Creator Splice system (5' intron splicing) significantly increases protein expression levels compared to the standard Creator system

hek293t mammalian coli vector immunoblot fluorescence bacterial
Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups

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Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.

blood platelets platelet-rich platelet whole-genome quantitative flow
Three assays show differences in binding of wild-type and mutant p53 to unique gene sequences.

PMID 19925028 · PMC2917581 · Technology in cancer research & treatment · 2009 · 7 claims · 6 setups

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Three different DNA binding assays (EMSA, SPA, streptavidin magnetic bead assay) show differences in binding of wild-type and mutant p53 to unique gene sequences

nuclear wro electrophoretic binding streptavidin
Enforced MYC expression directs a distinct transcriptional state during plasma cell differentiation.

PMID 40721291 · PMC12305944 · Life science alliance · 2025 · 8 claims · 7 setups

Has reproduction · 74

Acute MYC (T58I) and BCL2 overexpression drives an aberrant B-cell differentiation phenotype with altered surface marker expression while functional antibody secretion is retained

peripheral rna-seq flow edu antibody
Endogenous retroviral elements LTR8B and MER65 rewire PSG9 regulation to control trophoblast syncytialization and pre-eclampsia risk.

PMID 41796334 · PMC12969887 · Genome biology · 2026 · 8 claims · 8 setups

Has reproduction · 68

Retrovirus-derived LTR8B acts as a trophoblast-specific cis-regulatory element within the PSG array, with LTR8B at PSG9 influencing other PSG family members as a master regulator

sghpl-4 trophoblast placenta bewo chip-exonuclease crispr-cas9 chromatin
Characterization of ALTO-encoding circular RNAs expressed by Merkel cell polyomavirus and trichodysplasia spinulosa polyomavirus.

PMID 33999949 · PMC8158866 · PLoS pathogens · 2021 · 8 claims · 8 setups

Has reproduction · 80

MCPyV generates two circular RNAs (circALTO1, circALTO2) spanning the early region/ALTO ORF, detectable in VP-MCC cell lines and patient tumors

mcpyv-infected vp-mcc waga mcc rna-seq inverse qrt-pcr
Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo.

PMID 16231974 · PMC1262628 · PLoS biology · 2005 · 8 claims · 8 setups

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Distinct combinations of pre-mRNA splicing factors are recruited to sites of alternatively spliced transcripts in intact cells, providing the first in vivo evidence for differential splicing factor association.

cos-1 cos-7 tau10-1 rt-pcr quantitative rna-fish
Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 7 claims · 8 setups

Has reproduction · 71

Two distinct RNA modification patterns exist among BCa samples with radically different clinical outcomes and biological characteristics.

bca meta-geo tcga-blca tcga bulk rna-seq somatic
High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis.

PMID 23222129 · PMC3553938 · Nucleic acids research · 2013 · 8 claims · 7 setups

Has reproduction · 69

NusA interacts with RNAP ubiquitously throughout the M. tuberculosis chromosome and its ChIP-seq profile mirrors RNAP distribution in both exponential and stationary phase, despite NusA not binding DNA directly.

mycobacterium tuberculosis chip-seq input strand-specific
Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

PMID 17175541 · PMC1802633 · Nucleic acids research · 2007 · 7 claims · 7 setups

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A typical MHC-II-like S-Y module is present upstream of the RAB4B transcription start site, identified by genome-wide profile scanning

genomic raji monocyte-derived rj2.2.5 computational chip-on-chip chromatin
Functional analysis of human mutations in homeodomain transcription factor PITX3.

PMID 17888164 · PMC2093940 · BMC molecular biology · 2007 · 7 claims · 5 setups

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Both S13N and G219fs mutants show partial loss-of-function in DNA-binding and/or transactivation activity, with G219fs more severely affected than S13N

lens western immunocytochemistry electrophoretic
Point mutations in GLI3 lead to misregulation of its subcellular localization.

PMID 19829694 · PMC2758996 · PloS one · 2009 · 6 claims · 8 setups

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The MID1-α4-PP2A complex regulates the subcellular localization and transcriptional activity of GLI3.

hela immunofluorescence real-time luciferase
Transcription factor binding sites in the pol gene intragenic regulatory region of HIV-1 are important for virus infectivity.

PMID 16061936 · PMC1182164 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Oct-1, Oct-2, PU.1, Sp1 and Sp3 interact in vitro with the pol gene HS7 region

nuclear spodoptera hiv-infected nih3t3 electrophoretic supershift emsa
Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 6 setups

Has reproduction

Expression stability in CHO cell lines is controlled at three levels: choice of integration site, integrity/concatemerization pattern of the transgene, and stress-related cellular processes.

horizon six cho-k1 cho genome rna-seq targeted
Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

PMID 17705821 · PMC2045109 · BMC molecular biology · 2007 · 8 claims · 8 setups

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Multiple alternatively spliced 5'-UTR isoforms of human PPARdelta mRNA differ in translation efficiency

placenta five lines huh7 5'-race rt-pcr real-time

Experiments

Antibody protein array analysis of the tear film cytokines.

Key regulatory molecules of cartilage destruction in rheumatoid arthritis: an in vitro study.

beta- Catenin mutations and aberrant nuclear expression during endometrial tumorigenesis.

Proteomic analysis of mechanisms of hypoxia-induced apoptosis in trophoblastic cells.

A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells.

Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

Three assays show differences in binding of wild-type and mutant p53 to unique gene sequences.

Enforced MYC expression directs a distinct transcriptional state during plasma cell differentiation.

Endogenous retroviral elements LTR8B and MER65 rewire PSG9 regulation to control trophoblast syncytialization and pre-eclampsia risk.

Characterization of ALTO-encoding circular RNAs expressed by Merkel cell polyomavirus and trichodysplasia spinulosa polyomavirus.

Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo.

Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis.

Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

Functional analysis of human mutations in homeodomain transcription factor PITX3.

Point mutations in GLI3 lead to misregulation of its subcellular localization.

Transcription factor binding sites in the pol gene intragenic regulatory region of HIV-1 are important for virus infectivity.

Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.