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: antisense ✕ Assay: expression ✕ Clear

Genome Network and FANTOM3: assessing the complexity of the transcriptome.

PMID 16683037 · PMC1449904 · PLoS genetics · 2006 · 8 claims · 7 setups

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63% of the genome is transcribed from at least one strand, versus the earlier belief that only 2% is transcribed into protein-coding mRNA

fantom3 genome large-scale mammalian cage full-length genome
Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription.

PMID 17386095 · PMC1868932 · Genome biology · 2007 · 8 claims · 4 setups

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More than 55,000 totally intronic noncoding (TIN) RNAs are transcribed from the introns of 74% of unique RefSeq genes.

dbest liver cultures refseq est oligoarray polymerase
Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.

PMID 17598913 · PMC1929078 · BMC genomics · 2007 · 8 claims · 4 setups

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Standard Affymetrix expression GeneChips (MOE430, HG-U133) contain probe sets that detect natural antisense transcripts (NATs)

moe430 pooled organs probe strand-specific microarray
Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

PMID 17601345 · PMC1929076 · BMC genomics · 2007 · 8 claims · 8 setups

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MPSS detected 10,279 UniGene clusters, representing 7,475 known genes, in human hepatocytes

hepatocytes promoters genes hepatocyte mpss rt-pcr hierarchical
Genome-wide analysis of antisense transcription with Affymetrix exon array.

PMID 18211689 · PMC2257944 · BMC genomics · 2008 · 8 claims · 4 setups

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A modified cDNA synthesis protocol (ATE: Antisense Transcriptome analysis using Exon array), which skips the first-cycle cDNA synthesis and IVT amplification step, labels cDNA in reverse orientation, enabling Exon arrays to detect antisense transcripts

jurkat exon orientation-specific
Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

PMID 16089502 · PMC1166352 · PLoS biology · 2005 · 8 claims · 8 setups

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277 unique transcripts are differentially expressed between Rho lo and Rho hi HSC-enriched/depleted populations, conserved across both umbilical cord blood and bone marrow

umbilical ucb zebrafish microarray fluorescence-activated quantitative
Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts.

PMID 16204454 · PMC1243798 · Nucleic acids research · 2005 · 8 claims · 4 setups

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Cis-encoded natural antisense RNAs show striking preferential complementarity to 3′-UTRs of their target genes in human and mouse genomes

human-mouse model genome-wide comparative computational
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
Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

PMID 18676839 · PMC2597340 · Cancer research · 2008 · 8 claims · 7 setups

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MicroRNA processing components (Dicer, DGCR8) and microRNA host genes (MCM7, C9orf5) are significantly up-regulated in prostate tumors versus non-tumor tissue

prostate subset lncap 22rv1 microrna quantitative western
Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.

PMID 19906709 · PMC2811022 · Nucleic acids research · 2010 · 8 claims · 5 setups

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A genome-wide catalog of up to ~9000 overlapping antisense loci (23,782 non-redundant SAT pairs, clustered into 8894) was compiled and stored in the USAGP database

genome affymetrix antisense mirna computational microarray sage
Genomic and proteomic techniques applied to reproductive biology.

PMID 11574051 · PMC138959 · Genome biology · 2001 · 8 claims · 8 setups

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Knockout of the E6-AP (UBE3A) gene reduces testis and prostate size in male mice and compromises estradiol action in females

e6-ap fgf9-deficient jsd one-cell gene germ-cell interference
Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.

PMID 17428321 · PMC1853088 · BMC genomics · 2007 · 8 claims · 7 setups

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Cis-regulatory elements responsible for liver-specific HL expression are conserved among mammalian HL genes

5'-flanking upstream transiently genomic comparative tfbs promoter-reporter
Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.

PMID 16849434 · PMC1524920 · Nucleic acids research · 2006 · 8 claims · 7 setups

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A fast integrative in silico pipeline combining UniGene mRNA/EST mapping to GoldenPath genomes with CDS, poly(A) signal, poly(A) tail and splicing site evidence can reliably identify cis-NATs genome-wide across multiple species

est gene worm fly blat-based transcription comparative
Proteomics in animal models of Alzheimer's and Parkinson's diseases.

PMID 18703168 · PMC2630427 · Ageing research reviews · 2009 · 8 claims · 6 setups

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Proteomics studies in APPSw transgenic mice reveal differential expression of proteins involved in metabolism, ubiquitin/proteasome system, cellular transport, synaptic/axonal integrity, and inflammation

app swedish p301l gskβ page proteomics redox
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
CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

PMID 18577749 · PMC2483574 · Journal of the National Cancer Institute · 2008 · 7 claims · 8 setups

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CHD5 promoter is highly methylated in neuroblastoma cell lines with 1p deletion and absent CHD5 expression (NLF, IMR5)

neuroblastoma nlf athymic methylation-specific quantitative soft
Sox8 remodels the cranial ectoderm to generate the ear.

PMID 35867760 · PMC9282420 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 8 claims · 8 setups

Has reproduction · 100

Sox8 sits at the top of a core transcriptional circuit (Sox8, Pax2, Lmx1a, Zbtb16) that determines otic identity

chick bulk single-cell chipseq
Starvation-induced transgenerational inheritance of small RNAs in C. elegans.

PMID 25018105 · PMC4377509 · Cell · 2014 · 8 claims · 7 setups

Has reproduction · 64

L1 starvation induces changes in endogenous 22G small RNAs (STGs) that are inherited for at least three generations in fed descendants.

elegans small small sequencing lifespan
Integrative microRNA and proteomic approaches identify novel osteoarthritis genes and their collaborative metabolic and inflammatory networks.

PMID 19011694 · PMC2582945 · PloS one · 2008 · 8 claims · 8 setups

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A 16-microRNA signature (9 up, 7 down) distinguishes osteoarthritic from normal cartilage.

patient-derived normal integrated taqman qrt-pcr northern
Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.

PMID 18806875 · PMC2532751 · PloS one · 2008 · 8 claims · 8 setups

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PCMT overexpression protects porcine aortic endothelial cells (PAEC) from H2O2-induced apoptosis, raising the threshold H2O2 concentration required to trigger cell death.

porcine paec umbilical huvec methyltransferase sds-page fragmentation

Experiments

Genome Network and FANTOM3: assessing the complexity of the transcriptome.

Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription.

Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.

Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

Genome-wide analysis of antisense transcription with Affymetrix exon array.

Functional analysis of human hematopoietic stem cell gene expression using zebrafish.

Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts.

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

Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer.

Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.

Genomic and proteomic techniques applied to reproductive biology.

Comparative genomics and experimental promoter analysis reveal functional liver-specific elements in mammalian hepatic lipase genes.

Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species.

Proteomics in animal models of Alzheimer's and Parkinson's diseases.

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

CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

Sox8 remodels the cranial ectoderm to generate the ear.

Starvation-induced transgenerational inheritance of small RNAs in C. elegans.

Integrative microRNA and proteomic approaches identify novel osteoarthritis genes and their collaborative metabolic and inflammatory networks.

Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.