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 278

System / cell line: tissues ✕ Clear

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

PMID 18833279 · PMC3682493 · Nature · 2008 · 7 claims · 8 setups

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Recovered and characterized HIV-1 sequences (DRC60) from a 1960 Bouin's-fixed paraffin-embedded lymph node biopsy from Léopoldville, Belgian Congo

archival hiv-1-positive cdna concatenated rt-pcr quantitative pcr
GeneSpeed Beta Cell: an online genomics data repository and analysis resource tailored for the islet cell biologist.

PMID 18795106 · PMC2532782 · Experimental diabetes research · 2008 · 6 claims · 4 setups

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GeneSpeed Beta Cell is an online genomics data repository allowing simultaneous multiexperiment viewing and multidimensional (Boolean intersection/union) querying of pancreas- and islet-relevant datasets, integrated with GeneSpeed's domain-based gene categorization.

embryonic pancreatic panel pituitary affymetrix
Gene structure and mutant alleles of PCDH15: nonsyndromic deafness DFNB23 and type 1 Usher syndrome.

PMID 18719945 · PMC2716558 · Human genetics · 2008 · 8 claims · 6 setups

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PCDH15 has an updated gene structure with four additional exons beyond the previously reported 35, producing isoforms in four classes with three alternative cytoplasmic domains (CD1, CD2, CD3).

genomic retina cdna protocadherin str pcr rt-pcr
Genotypic analysis of two hypervariable human cytomegalovirus genes.

PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups

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UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.

hcmv clinical pcr ul146 pcr nested molecular
Identifying alternative hyper-splicing signatures in MG-thymoma by exon arrays.

PMID 18545673 · PMC2409220 · PloS one · 2008 · 8 claims · 6 setups

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An integrative ad-hoc functional GO analysis combining threshold-based (Fisher exact/hypergeometric) and threshold-free (Kolmogorov-Smirnov) statistics, plus term-to-parent comparisons, detects disease-relevant splicing events from exon array data.

mg-thymoma colon exon fluorescent reverse
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

user-supplied ranked gene fasta-formatted functional gene novo
Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

PMID 18366763 · PMC2292204 · BMC molecular biology · 2008 · 8 claims · 8 setups

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Transcription start sites of human DYRK1A are distributed over an 800 bp region within an unmethylated CpG island

pc3 saos2 resting phoenix 5'-race-pcr rt-pcr chip-seq
Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups

Has reproduction · 50

330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.

brassica r500 rapa genomic bulk reference-based snp
Characterization of novel isoforms and evaluation of SNF2L/SMARCA1 as a candidate gene for X-linked mental retardation in 12 families linked to Xq25-26.

PMID 18302774 · PMC2266716 · BMC medical genetics · 2008 · 8 claims · 4 setups

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The SNF2L gene spans 77 kb and is encoded by 25 exons that undergo alternative splicing to generate multiple distinct transcripts.

lines genomic 293hek rt-pcr genomic indirect
Genome-wide census and expression profiling of chicken neuropeptide and prohormone convertase genes.

PMID 20006904 · PMC2814002 · Neuropeptides · 2010 · 8 claims · 5 setups

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Bioinformatic survey of chicken genome/EST/HTGS databases identifies previously unreported chicken neuropeptide genes

chicken blast microarray est
Next-generation sequencing in aging research: emerging applications, problems, pitfalls and possible solutions.

PMID 19900591 · PMC2878865 · Ageing research reviews · 2010 · 8 claims · 8 setups

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NGS platforms offer superior performance, specificity, and cost-effectiveness compared to traditional Sanger sequencing

genome alzheimer's embryonic tissues genome genotyping rna-seq
Congenital bovine spinal dysmyelination is caused by a missense mutation in the SPAST gene.

PMID 19714378 · PMC2854348 · Neurogenetics · 2010 · 8 claims · 5 setups

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A missense mutation (R560Q) in the SPAST gene's ATPase domain causes bovine spinal dysmyelination

cattle bovine coli affinity-purified snp reverse cdna
Proteomic-based identification of maternal proteins in mature mouse oocytes.

PMID 19646285 · PMC2730056 · BMC genomics · 2009 · 8 claims · 6 setups

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625 different proteins were identified from 2700 zona pellucida-free mature mouse MII oocytes, the largest oocyte proteome catalog to date

mature mii identified tissues sds-page acid gene
Overview of microarray analysis of gene expression and its applications to cervical cancer investigation.

PMID 18182341 · PMC7129792 · Taiwanese journal of obstetrics & gynecology · 2007 · 6 claims · 5 setups

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Oligonucleotide microarray and cDNA microarray are the two main microarray platforms used to study gene expression genome-wide.

cervical cdna microarray combinatorial
T1DBase, a community web-based resource for type 1 diabetes research.

PMID 15608258 · PMC540049 · Nucleic acids research · 2005 · 8 claims · 6 setups

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T1DBase is an integrated, open-access web resource that unifies genetic, genomic, and biological data to support type 1 diabetes (T1D) research

pancreatic t1d tissues nod microarray genetic est-based
DDBJ in collaboration with mass-sequencing teams on annotation.

PMID 15608189 · PMC539974 · Nucleic acids research · 2005 · 7 claims · 5 setups

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DDBJ collected and released 1,066,084 entries (718,072,425 bases) in the past year, including the complete chimpanzee chromosome 22 sequence and silkworm whole-genome shotgun data

chimpanzee silkworm mus homo whole-chromosome whole-genome cage
Phenotypic variation meets systems biology.

PMID 19664197 · PMC2745761 · Genome biology · 2009 · 8 claims · 8 setups

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Cellular differentiation states are constrained by complex networks with substantial positive and negative regulation, challenging the concept of single 'master regulators'

thp-1 arabidopsis unspecified mammalian deepcage protein-protein sequencing
The ENCODE Project at UC Santa Cruz.

PMID 17166863 · PMC1781110 · Nucleic acids research · 2007 · 8 claims · 4 setups

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The UCSC ENCODE portal serves as the primary repository and access point for sequence-based ENCODE pilot phase data

genome mammals lines tissues radical sequence chromatin
The cold-induced lipokine 12,13-diHOME promotes fatty acid transport into brown adipose tissue.

PMID 28346411 · PMC5699924 · Nature medicine · 2017 · 8 claims · 8 setups

Has reproduction · 78

12,13-diHOME is a cold-induced lipokine that stimulates BAT activity

plasma bat serum mice lc-ms correlation 18f-fdg
Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 7 claims · 8 setups

Has reproduction · 91

175 conserved and 83 novel miRNAs were identified mainly in one bud and two tender leaves of tea plant via small RNA sequencing combined with genome survey data

camellia sinensis small genome mirna

Experiments

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

GeneSpeed Beta Cell: an online genomics data repository and analysis resource tailored for the islet cell biologist.

Gene structure and mutant alleles of PCDH15: nonsyndromic deafness DFNB23 and type 1 Usher syndrome.

Genotypic analysis of two hypervariable human cytomegalovirus genes.

Identifying alternative hyper-splicing signatures in MG-thymoma by exon arrays.

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

Characterization of novel isoforms and evaluation of SNF2L/SMARCA1 as a candidate gene for X-linked mental retardation in 12 families linked to Xq25-26.

Genome-wide census and expression profiling of chicken neuropeptide and prohormone convertase genes.

Next-generation sequencing in aging research: emerging applications, problems, pitfalls and possible solutions.

Congenital bovine spinal dysmyelination is caused by a missense mutation in the SPAST gene.

Proteomic-based identification of maternal proteins in mature mouse oocytes.

Overview of microarray analysis of gene expression and its applications to cervical cancer investigation.

T1DBase, a community web-based resource for type 1 diabetes research.

DDBJ in collaboration with mass-sequencing teams on annotation.

Phenotypic variation meets systems biology.

The ENCODE Project at UC Santa Cruz.

The cold-induced lipokine 12,13-diHOME promotes fatty acid transport into brown adipose tissue.

Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.