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 20

System / cell line: term ✕ Assay: pcr ✕ Clear

Widely variable endogenous retroviral methylation levels in human placenta.

PMID 17617638 · PMC1950553 · Nucleic acids research · 2007 · 6 claims · 6 setups

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Three HERV-E LTRs that function as alternative gene promoters (LTR-PTN, LTR-EBR, LTR-MID1) are unmethylated in placenta but heavily methylated in blood cells, where they are not active promoters

term placenta genome bisulfite rt-pcr genome-wide
Apolipoprotein e, alcohol consumption, and risk of ischemic stroke: the Framingham Heart Study revisited.

PMID 19717024 · PMC2743951 · Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association · 2009 · 8 claims · 6 setups

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ApoE E4 allele does not significantly modify the association between alcohol consumption and risk of ischemic stroke in subjects <65 years

framingham plasma genotyping structured clinical
Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

PMID 17452356 · PMC1904267 · Nucleic acids research · 2007 · 8 claims · 7 setups

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PASE (Prediction of Alternative Signaling Exons) is a computational algorithm combining Markov splice-site models, a Bayesian classifier, species conservation, and Scansite motif scoring to identify novel alternative cassette exons involved in cell signaling.

elegans pooled pcr known semi-nested cloning initio
N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

PMID 18402670 · PMC2330028 · BMC medical genetics · 2008 · 7 claims · 6 setups

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NAT8 is a novel positional candidate gene for blood pressure and renal function based on its chromosomal location within a BP linkage region and its expression in embryonic/adult kidney and liver

random reference healthy long-term resequencing quantitative sequence
Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing.

PMID 19822575 · PMC2794179 · Nucleic acids research · 2009 · 8 claims · 6 setups

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ChIP-seq identified 3064 GABP peaks, 7266 FOXA2 peaks and 18783 HNF4a peaks in HepG2 cells

hepg2 liver chip-seq quantitative co-immunoprecipitation
Insights into the physiology of childbirth using transcriptomics.

PMID 16752954 · PMC1475648 · PLoS medicine · 2006 · 7 claims · 4 setups

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Labor results in a change in the transcriptome in each component of the uterus studied

uterine lower microarray quantitative re-analysis
Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation.

PMID 17608949 · PMC1934372 · BMC genomics · 2007 · 7 claims · 5 setups

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Developed a statistical model-fitting method to infer generalized (multi-allelic, copy-number-aware) genotypes from raw SNP microarray data

individuals mother-father-child transcribed snp quantitative multiplex
CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.

PMID 36262316 · PMC9574418 · iScience · 2022 · 7 claims · 8 setups

Has reproduction · 62

CASK LOF increases neuronal complexity (neurite overgrowth) in developing/immature human excitatory neurons

cask ko1 day mature bulk qrt-pcr western
Vascular adhesion protein-1 defines a unique subpopulation of human hematopoietic stem cells and regulates their proliferation.

PMID 34719737 · PMC8629906 · Cellular and molecular life sciences : CMLS · 2021 · 7 claims · 8 setups

Has reproduction · 50

VAP-1 is expressed on a subset of human HSC and on bone marrow vasculature, forming a hematogenic niche.

facs-sorted sorted cd34+ bulk single-cell flow
Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing.

PMID 30208848 · PMC6134632 · BMC genomics · 2018 · 8 claims · 7 setups

Has reproduction · 50

2867 circRNAs were identified in soybean flower buds via high-throughput sequencing with RNase R enrichment, of which 1009 were differentially expressed between NJCMS1A and NJCMS1B

flower roots analysis parental high-throughput quantitative pcr
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
Proteomic analysis of differential proteins in pancreatic carcinomas: Effects of MBD1 knock-down by stable RNA interference.

PMID 18445260 · PMC2386481 · BMC cancer · 2008 · 8 claims · 5 setups

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Stable RNAi-mediated MBD1 knock-down was successfully established in the BxPC-3 pancreatic cancer cell line using a recombinant siRNA plasmid

bxpc-3 2-d maldi-tof-ms western
Reusable building blocks in biological systems.

PMID 30958230 · PMC6303794 · Journal of the Royal Society, Interface · 2018 · 8 claims · 4 setups

Has reproduction · 82

Biological systems can be decomposed into phenotypic building blocks (PBBs) via k-maximally reusable decompositions (k-MRD) that maximize average reusability across conditions.

tissues conditions randomized est-based mirna randomization
Cohesin regulates alternative splicing.

PMID 36857449 · PMC9977177 · Science advances · 2023 · 7 claims · 8 setups

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Cohesin regulates alternative splicing independently of its effects on transcription.

hct116rmac hct116 recombinant hek293 bulk rt-pcr proximity
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
Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

PMID 18003658 · PMC2248751 · Nucleic acids research · 2008 · 8 claims · 8 setups

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p110 CUX1 is recruited to promoters of cell cycle-related target genes preferentially during S phase

hela hs578t nih3t3 genomic chap-chip conventional scanning
A biomedically enriched collection of 7000 human ORF clones.

PMID 18231609 · PMC2211400 · PloS one · 2008 · 8 claims · 4 setups

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Produced and made available over 7000 fully sequence-verified plasmid ORF clones representing over 3400 unique human genes, in both closed (stop codon) and fusion (no stop codon) formats.

genes mgc plasmid literature pcr sequence
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
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.

PMID 35773379 · PMC9247108 · Scientific reports · 2022 · 6 claims · 7 setups

Has reproduction · 46

De novo transcriptome assembly of S. latifolia produced 48,549 unigenes, 71.53% (34,728) of which were annotated against KEGG, GO, and/or KOG databases

sparassis latifolia bulk transcriptome sequence
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.

PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups

Has reproduction · 27

A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.

radish assembled rna-seq novo functional

Experiments

Widely variable endogenous retroviral methylation levels in human placenta.

Apolipoprotein e, alcohol consumption, and risk of ischemic stroke: the Framingham Heart Study revisited.

Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human.

N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing.

Insights into the physiology of childbirth using transcriptomics.

Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation.

CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.

Vascular adhesion protein-1 defines a unique subpopulation of human hematopoietic stem cells and regulates their proliferation.

Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing.

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

Proteomic analysis of differential proteins in pancreatic carcinomas: Effects of MBD1 knock-down by stable RNA interference.

Reusable building blocks in biological systems.

Cohesin regulates alternative splicing.

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

Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

A biomedically enriched collection of 7000 human ORF clones.

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

De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.

Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.