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 333

System / cell line: normalized ✕ Clear

Tumor suppressor in lung cancer 1 (TSLC1) alters tumorigenic growth properties and gene expression.

PMID 16083501 · PMC1208945 · Molecular cancer · 2005 · 8 claims · 8 setups

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Restoration of TSLC1 expression in A549 cells (yielding the 12.2 line) suppresses tumorigenic growth, markedly reducing cell expansion/proliferation rate.

a549 nsclc expansion wst-1 flow
Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups

Has reproduction · 67

Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.

single methanol-fixed reads slice mrna-seq light-microscopy read
Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

PMID 15804358 · PMC1079825 · BMC genomics · 2005 · 8 claims · 8 setups

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Human, mouse, and rat SPAM1/Spam1 transcripts initiate within an ERV1 pol (internal coding) region rather than within an LTR

testis panel genome 5'-race non-quantitative
Speeding disease gene discovery by sequence based candidate prioritization.

PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups

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Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.

ensembl training same hgmd comparative machine tenfold
Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

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Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

liver genomic tissues embryos rt-pcr genomic secondary
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
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
Antibody binding loop insertions as diversity elements.

PMID 17023486 · PMC1635297 · Nucleic acids research · 2006 · 7 claims · 8 setups

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A lysozyme-binding VHH CDR3 loop can be grafted into two surface-exposed loops of superfolder GFP, conferring lysozyme-binding activity while the protein remains fluorescent.

gfp-anti-lysozyme coli full-length gfp-hcdr3 elisa flow surface
Serum diagnosis of diffuse large B-cell lymphomas and further identification of response to therapy using SELDI-TOF-MS and tree analysis patterning.

PMID 18163913 · PMC2242801 · BMC cancer · 2007 · 8 claims · 8 setups

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SELDI-TOF-MS serum proteomic patterns analyzed by decision tree classification (Biomarker Pattern Software) can discriminate DLBCL patients from healthy controls with high sensitivity and specificity.

serum seldi dlbcl pooled seldi-tof-ms proteinchip decision
Metatranscriptomics of the human oral microbiome during health and disease.

PMID 24692635 · PMC3977359 · mBio · 2014 · 8 claims · 8 setups

Has reproduction · 62

Disease-associated periodontal communities display conserved community-level metabolic gene expression profiles between patients, whereas the metabolic gene expression of individual species is highly variable between patients.

patient-matched subset health rna-seq rrna comparison metatranscriptomics
Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

PMID 18036263 · PMC2246181 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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Revised multifactorial likelihood analysis incorporating ER, CK5/6, and CK14 tumor immunohistochemistry improves classification of BRCA1 unclassified variants

archival kconfab myriad lymphoblastoid immunohistochemistry multifactorial co-occurrence
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
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
Persistence of attenuated HIV-1 rev alleles in an epidemiologically linked cohort of long-term survivors infected with nef-deleted virus.

PMID 17601342 · PMC1933581 · Retrovirology · 2007 · 7 claims · 6 setups

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Dominant, persistent rev alleles from SBBC subjects D36 and C64 show ~90% reduced Rev/RRE binding compared to HIV-1 NL4-3, C18, and C98 Revs.

pbmc his-tagged cem mammalian pcr electrophoretic western
Activation-induced cytidine deaminase acts as a mutator in BCR-ABL1-transformed acute lymphoblastic leukemia cells.

PMID 17485517 · PMC2118573 · The Journal of experimental medicine · 2007 · 8 claims · 8 setups

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AID mRNA is aberrantly expressed in Ph+ ALL but largely absent in Ph- ALL

normal ph+ semiquantitative western rt-pcr
Evaluation of the OPTC gene in primary open angle glaucoma: functional significance of a silent change.

PMID 17359525 · PMC1838427 · BMC molecular biology · 2007 · 8 claims · 8 setups

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OPTC is a candidate gene involved in POAG pathogenesis

genomic pcr optc retinal pcr-sscp dhplc sequencing
Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1).

PMID 19133980 · PMC4303606 · British journal of haematology · 2009 · 7 claims · 6 setups

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Downregulation of GR mRNA in the resistant myeloma cell line is caused by a block to transcriptional elongation within intron B of the GR gene

mm.1s pcr demethylating quantitative
Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.

PMID 19115125 · PMC2947716 · Journal of neurovirology · 2009 · 7 claims · 5 setups

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HIV-1 isolates from CI patients induce a distinct macrophage proteome signature compared to isolates from NC patients and SF162

monocyte-derived mdm mdms western p24 seldi-tof sds-page
Mutations in UCP2 in congenital hyperinsulinism reveal a role for regulation of insulin secretion.

PMID 19065272 · PMC2588657 · PloS one · 2008 · 6 claims · 5 setups

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Heterozygous UCP2 coding variants (parentally inherited) were identified in 2 of 10 CHI patients with no mutations in known CHI genes

peripheral saccharomyces yeast ins-1e dhplc proton western
Alterations in candidate genes PHF2, FANCC, PTCH1 and XPA at chromosomal 9q22.3 region: pathological significance in early- and late-onset breast carcinoma.

PMID 18990233 · PMC2633285 · Molecular cancer · 2008 · 8 claims · 5 setups

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PHF2, FANCC and PTCH1 show high frequency of alterations (deletion/methylation) compared to XPA in both early- and late-onset breast carcinoma groups

invasive breast normal microsatellite methylation sscp

Experiments

Tumor suppressor in lung cancer 1 (TSLC1) alters tumorigenic growth properties and gene expression.

Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

Speeding disease gene discovery by sequence based candidate prioritization.

Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

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

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

Antibody binding loop insertions as diversity elements.

Serum diagnosis of diffuse large B-cell lymphomas and further identification of response to therapy using SELDI-TOF-MS and tree analysis patterning.

Metatranscriptomics of the human oral microbiome during health and disease.

Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

Functional analysis of human mutations in homeodomain transcription factor PITX3.

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

Persistence of attenuated HIV-1 rev alleles in an epidemiologically linked cohort of long-term survivors infected with nef-deleted virus.

Activation-induced cytidine deaminase acts as a mutator in BCR-ABL1-transformed acute lymphoblastic leukemia cells.

Evaluation of the OPTC gene in primary open angle glaucoma: functional significance of a silent change.

Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1).

Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.

Mutations in UCP2 in congenital hyperinsulinism reveal a role for regulation of insulin secretion.

Alterations in candidate genes PHF2, FANCC, PTCH1 and XPA at chromosomal 9q22.3 region: pathological significance in early- and late-onset breast carcinoma.