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 15

System / cell line: unigene ✕ Assay: mapping ✕ Clear

ARED 3.0: the large and diverse AU-rich transcriptome.

PMID 16381826 · PMC1347415 · Nucleic acids research · 2006 · 7 claims · 6 setups

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ARED 3.0 computationally mapped more than 4000 ARE-mRNAs to the human genome, representing 5-8% of human genes.

records est est-derived combined computational est sequence
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
A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

PMID 18344523 · PMC2377433 · Nucleic acids research · 2008 · 7 claims · 6 setups

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Spaln maps and aligns large cDNA sequence sets onto whole mammalian genomes using substantially less memory than comparable existing tools

unigene shuffled real genomes genome-wide alignment gene
Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

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1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

genome rhesus vega-annotated tpas transcript-to-genome same synteny
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
Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

PMID 15949044 · PMC1181805 · BMC bioinformatics · 2005 · 7 claims · 6 setups

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Satellog is a database cataloging all pure 1-16 unit satellite repeats in the human genome with supplementary polymorphism, gene-location, and expression data for prioritizing repeats in disease-association studies.

reference unigene ensembl normal tandem polymorphism gene
Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats.

PMID 17038195 · PMC1618849 · BMC genomics · 2006 · 8 claims · 6 setups

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EXPOLDB is a novel database integrating human gene expression variability data (including monozygotic twin comparisons) with (TG/CA)n repeat polymorphism information

blood genomic genes housekeeping microarray repeat est-based
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
Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance.

PMID 25943316 · PMC4422317 · BMC genomics · 2015 · 7 claims · 6 setups

Has reproduction · 73

De novo assembly of the S. fruticosa transcriptome (Velvet/Oases k-45, CDHIT-EST) produced 54,526 high-quality unigenes with N50 of 957 bp

suaeda rna-seq novo blastx
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
Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

PMID 14519200 · PMC328454 · Genome biology · 2003 · 8 claims · 5 setups

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Annotation of 8,633 high-quality non-mitochondrial/non-ribosomal ESTs shows 57% represent known genes and 43% are unknown or novel, with M15E having the highest proportion of novel ESTs

embryonic high-quality unique m15e est sequence comparative
PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays.

PMID 19906711 · PMC2808952 · Nucleic acids research · 2010 · 6 claims · 4 setups

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PLANdbAffy is a database of Affymetrix probe alignments to the human genome for five widely used arrays (HG-U133A, HG-U133B, HG-U133 Plus 2.0, Human Exon 1.0, Human Gene 1.0)

hg-u133a ucsc dbsnp probe blat est snp
Recent additions and improvements to the Onto-Tools.

PMID 15980579 · PMC1160233 · Nucleic acids research · 2005 · 7 claims · 3 setups

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The Onto-Tools back-end database was redesigned around the Entrez Gene data model after NCBI phased out LocusLink in February 2005.

homo example mus functional pathway cross-database
Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

PMID 15169551 · PMC441375 · BMC genomics · 2004 · 8 claims · 8 setups

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A very large, previously uncharacterized gene, AHI1, containing WD40 and SH3 domains was discovered in the candidate interval

cdna image hbs1l ahi1 rt-pcr est northern
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

ARED 3.0: the large and diverse AU-rich transcriptome.

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

A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence.

Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

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

Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats.

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

Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance.

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

Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

PLANdbAffy: probe-level annotation database for Affymetrix expression microarrays.

Recent additions and improvements to the Onto-Tools.

Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

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