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 70

System / cell line: cdna ✕ Assay: time ✕ Clear

Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing.

PMID 34244540 · PMC8270970 · Scientific reports · 2021 · 8 claims · 5 setups

Has reproduction · 50

BoHV-1 infection causes substantial up- and down-regulation of host gene networks, including antiviral response and viral transcription/translation-associated genes

bovine direct amplified synthetic
Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer.

PMID 17868458 · PMC2375029 · Genome biology · 2007 · 8 claims · 8 setups

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Co-culture of certain breast cancer cell lines with stromal fibroblasts induces interferon-response genes (IRGs) in a subset of cancer cells

mda-mb231 epithelial breast early-stage cdna quantitative facs
Genomics of signaling crosstalk of estrogen receptor alpha in breast cancer cells.

PMID 18365014 · PMC2268000 · PloS one · 2008 · 7 claims · 6 setups

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Estrogen, growth factors and cAMP elicit surprisingly distinct ERα-dependent transcriptional responses in MCF7 cells

mcf7 promoter cdna quantitative computational
The effect of IL-13 and IL-13R130Q, a naturally occurring IL-13 polymorphism, on the gene expression of human airway smooth muscle cells.

PMID 15661077 · PMC548512 · Respiratory research · 2005 · 6 claims · 3 setups

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IL-13 and IL-13R130Q modulate the same set of genes in human airway smooth muscle cells (HASMC)

airway hasmc cdna taqman flow
CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.

PMID 17202170 · PMC1899094 · Nucleic acids research · 2007 · 7 claims · 4 setups

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Cyclonet is a web-based integrated database combining 'omics' and chemoinformatics data on mammalian cell cycle regulation in normal and pathological (cancer) states, built on a systems biology approach.

breast commercial vertebrate genes cdna activity computational
cDNA sequencing improves the detection of P53 missense mutations in colorectal cancer.

PMID 19671129 · PMC2731783 · BMC cancer · 2009 · 8 claims · 6 setups

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cDNA sequencing detects P53 missense mutations in colorectal cancer more frequently and reliably than DNA sequencing

colorectal paired sequencing cdna real-time
Novel SCN1A frameshift mutation with absence of truncated Nav1.1 protein in severe myoclonic epilepsy of infancy.

PMID 18680191 · PMC3708306 · American journal of medical genetics. Part A · 2008 · 8 claims · 3 setups

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A novel heterozygous SCN1A frameshift mutation, c.3608delA (p.Gln1203HisfsX4), was identified in a postmortem SMEI patient, located in the D2-D3 intracellular linker of NaV1.1.

postmortem cdna western quantitative
All systems GO for understanding mouse gene function.

PMID 15610553 · PMC549721 · Journal of biology · 2004 · 7 claims · 4 setups

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Quantitative, multivariate cross-tissue expression measurements are powerfully predictive of gene function

diverse tissues computational dye-swap reverse-transcription-coupled support
Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data.

PMID 24211736 · PMC3969109 · Methods (San Diego, Calif.) · 2014 · 8 claims · 6 setups

Has reproduction · 71

The 'hyb' pipeline detects, calls, folds and annotates chimeric reads from CLASH high-throughput sequencing data.

ago1 test clash multiplexed clash benchmarking demultiplexing
Lost in the world of functional genomics, systems biology, and translational research: is there life after the Milstein award?

PMID 17681845 · PMC1994668 · Cytokine & growth factor reviews · 2007 · 8 claims · 8 setups

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Genomic and proteomic approaches provide a comprehensive view of virus-host interactions and advance understanding of innate immunity and interferon/cytokine signaling

cd4+ hela influenza-infected liver cdna microarray mass
The 10 sea urchin receptor for egg jelly proteins (SpREJ) are members of the polycystic kidney disease-1 (PKD1) family.

PMID 17629917 · PMC1934368 · BMC genomics · 2007 · 8 claims · 5 setups

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Sea urchins possess 10 SpREJ (PKD1 family) genes, compared to five in humans, all defined by possession of a ~600 residue REJ domain

strongylocentrotus sprej purpuratus full-length cdna secondary real-time
Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes.

PMID 18776137 · PMC2584123 · Diabetes · 2008 · 6 claims · 7 setups

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Lymphocytes (but not monocytes) from type 1 diabetic patients show a distinct subset of genes with significantly increased H3K9me2 compared with healthy controls.

blood pooled gene chip-chip conventional quantitative
Mutations in the C-terminus of the X protein of hepatitis B virus regulate Wnt-5a expression in hepatoma Huh7 cells: cDNA microarray and proteomic analyses.

PMID 18477650 · PMC2443277 · Carcinogenesis · 2008 · 8 claims · 7 setups

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HBx C-terminal deletion mutants (HBx3'-30 and HBx3'-40) produce differentially expressed gene and protein profiles in transfected Huh7 HCC cells, mostly involving transcriptional regulation, oncogenes/tumor suppressors, cell junctions, signal transduction, metabolism and immune response

huh7 frozen hcc genomic cdna two-dimensional western
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
Expanding CEP290 mutational spectrum in ciliopathies.

PMID 19764032 · PMC4340070 · American journal of medical genetics. Part A · 2009 · 7 claims · 4 setups

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A large heterozygous genomic deletion spanning the CEP290 C-terminus (exons 42-54) was identified in a JSRD-COR patient previously known to carry only one CEP290 point mutation.

peripheral genomic quantitative cdna pcr
Identification of herpesvirus transcripts from genomic regions around the replication origins.

PMID 37773348 · PMC10541914 · Scientific reports · 2023 · 8 claims · 8 setups

Has reproduction · 59

Herpesviruses display distinct patterns of transcriptional overlaps near or at the replication origins (Oris)

nine same vzv prv direct cage-seq qrt-pcr
Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

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XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

hct116 macaque cos-7 genomic cdna est molecular
GoMiner: a resource for biological interpretation of genomic and proteomic data.

PMID 12702209 · PMC154579 · Genome biology · 2003 · 8 claims · 4 setups

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GoMiner organizes 'interesting' gene lists (e.g., differentially expressed genes) into the Gene Ontology hierarchy for biological interpretation, displaying results as both a tree and a directed acyclic graph (DAG).

du145 gene gominer cdna flow category
Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

PMID 16914452 · PMC1557807 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Analysis of 56,419 full-length cDNAs identified 6877 alternative splicing genes encoding 18,297 alternative splicing variants made of 37,670 exons.

full-length deduced alternative panel cdna-to-genome manual motif
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

Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing.

Characterization of heterotypic interaction effects in vitro to deconvolute global gene expression profiles in cancer.

Genomics of signaling crosstalk of estrogen receptor alpha in breast cancer cells.

The effect of IL-13 and IL-13R130Q, a naturally occurring IL-13 polymorphism, on the gene expression of human airway smooth muscle cells.

CYCLONET--an integrated database on cell cycle regulation and carcinogenesis.

cDNA sequencing improves the detection of P53 missense mutations in colorectal cancer.

Novel SCN1A frameshift mutation with absence of truncated Nav1.1 protein in severe myoclonic epilepsy of infancy.

All systems GO for understanding mouse gene function.

Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data.

Lost in the world of functional genomics, systems biology, and translational research: is there life after the Milstein award?

The 10 sea urchin receptor for egg jelly proteins (SpREJ) are members of the polycystic kidney disease-1 (PKD1) family.

Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes.

Mutations in the C-terminus of the X protein of hepatitis B virus regulate Wnt-5a expression in hepatoma Huh7 cells: cDNA microarray and proteomic analyses.

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

Expanding CEP290 mutational spectrum in ciliopathies.

Identification of herpesvirus transcripts from genomic regions around the replication origins.

Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

GoMiner: a resource for biological interpretation of genomic and proteomic data.

Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs.

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