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: chromosomal ✕ Assay: est ✕ Clear

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
WebGestalt: an integrated system for exploring gene sets in various biological contexts.

PMID 15980575 · PMC1160236 · Nucleic acids research · 2005 · 8 claims · 6 setups

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WebGestalt is an integrated web-based system composed of four modules: gene set management, information retrieval, organization/visualization, and statistics.

genes gene est-based enrichment kegg
Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

PMID 12783626 · PMC161800 · BMC genomics · 2003 · 8 claims · 5 setups

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A comparative genomics approach using hamster testis cDNA sequencing can identify genes not previously annotated in the human, mouse, rat and Fugu genomes

hamster testis predicted cdna northern comparative
MutScreener: primer design tool for PCR-direct sequencing.

PMID 16845093 · PMC1538803 · Nucleic acids research · 2006 · 8 claims · 4 setups

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MutScreener is a web-based application that automates PCR-direct sequencing assay design by annotating gene structure and designing PCR and sequencing primers.

sim4 cdna gene comparative sequence pcr
Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

PMID 15836796 · PMC1090573 · BMC genomics · 2005 · 8 claims · 7 setups

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89 polymorphic microsatellite markers were developed from rainbow trout EST-derived cDNA clones

normalized rainbow salmonids microsatellite sanger pcr
Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

PMID 15790398 · PMC1082905 · BMC genomics · 2005 · 8 claims · 6 setups

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Twenty-three chemokine genes and 14 chemokine receptor genes were identified in the chicken genome, including 12 new chemokines and 7 new receptors beyond prior reports.

chicken comparative amino phylogenetic
The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

PMID 19094205 · PMC2637867 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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AR was duplicated into two paralogs, AR-A and AR-B, during a teleost-specific whole genome duplication (WGD), after the split of Acipenseriformes but before the divergence of Osteoglossiformes.

fish full-length tetraodon rt-pcr database molecular
Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

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Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

liver genomic tissues embryos rt-pcr genomic secondary
Insights into vertebrate evolution from the chicken genome sequence.

PMID 15693954 · PMC551526 · Genome biology · 2005 · 8 claims · 6 setups

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Chicken has expanded gene families involved in egg production (e.g., avidin) and feather/scale/claw formation (avian-specific keratins) not present or lost in mammals

red chicken whole-genome comparative synteny
SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

PMID 19793867 · PMC2808975 · Nucleic acids research · 2010 · 8 claims · 8 setups

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A new 8.5x-coverage silkworm genome assembly with N50 scaffold size of ~3.7 Mb over a 432 Mb genome represents a significant quality improvement over the prior draft.

bombyx whole-genome snp novo
Have microarrays failed to deliver for developmental biology?

PMID 12225576 · PMC139405 · Genome biology · 2002 · 8 claims · 8 setups

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Despite predictions that microarrays would transform biology, very few published developmental biology microarray studies have generated novel insights.

drosophila caenorhabditis developing xenopus cdna genome-wide microarray
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
A cell biological perspective on genome research.

PMID 8522596 · PMC2120688 · The Journal of cell biology · 1995 · 7 claims · 7 setups

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Genome sequencing represents a sixth stage in the historical progression of structural biology (comparative anatomy through crystallography), and will be similarly valuable once related to function.

saccharomyces caenorhabditis selected fruit genomic saturation physical
A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

PMID 11305939 · PMC31480 · Genome biology · 2001 · 8 claims · 8 setups

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SLC4A9 is a novel human NBC-like gene on chromosome 5q31 encoding a 990-amino-acid, 12-transmembrane-domain protein with high similarity to other sodium bicarbonate cotransporters

bac kidney genomic marathon genomic cdna pcr
Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.

PMID 18226259 · PMC2268926 · BMC genomics · 2008 · 8 claims · 7 setups

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GOLGA8E and WHDC1L1 are characterized for the first time as protein-coding transcripts from the PWS proximal breakpoint region.

genomic chromosome lymphoblasts multi-tissue bioinformatic fish rt-pcr

Experiments

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

WebGestalt: an integrated system for exploring gene sets in various biological contexts.

Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs.

MutScreener: primer design tool for PCR-direct sequencing.

Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics.

The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

Insights into vertebrate evolution from the chicken genome sequence.

SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

Have microarrays failed to deliver for developmental biology?

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

A cell biological perspective on genome research.

A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.