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 63

System / cell line: sequence ✕ Assay: brain ✕ Clear

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

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

Full-text index only

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

normalized rainbow salmonids microsatellite sanger pcr
Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

PMID 18294402 · PMC2287170 · BMC genomics · 2008 · 8 claims · 6 setups

Full-text index only

Constructed full-length-enriched cDNA libraries and determined 85,721 EST sequences and 9407 full-insert sequences from cynomolgus macaque brain (7 regions), testis, and liver

cynomolgus 3-year-old macaque est full-insert oligonucleotide
Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome.

PMID 15534692 · PMC526178 · PLoS biology · 2004 · 8 claims · 6 setups

Full-text index only

Intramolecular pairs of oppositely oriented Alu elements within the same pre-mRNA form dsRNA foldback structures that are major substrates for A-to-I RNA editing

huge brain pre-mrna greater genomic rt-pcr quantitative
A screen for proteins that interact with PAX6: C-terminal mutations disrupt interaction with HOMER3, DNCL1 and TRIM11.

PMID 16098226 · PMC1208879 · BMC genetics · 2005 · 8 claims · 7 setups

Full-text index only

PAX6 interacts with three novel proteins: HOMER3, DNCL1 and TRIM11

pax6 brain yeast sequence yeast semi-quantitative
Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

PMID 15921519 · PMC1166541 · BMC bioinformatics · 2005 · 6 claims · 4 setups

Full-text index only

A minimum evolution algorithm (implemented in software 'phyrex') can reconstruct ancestral states of continuous characters like gene expression or splicing levels along a phylogeny

gene upstream chimpanzee reconstructed minimum sequence ancestral
Sequence, "subtle" alternative splicing and expression of the CYYR1 (cysteine/tyrosine-rich 1) mRNA in human neuroendocrine tumors.

PMID 17442112 · PMC1863428 · BMC cancer · 2007 · 7 claims · 5 setups

Full-text index only

CYYR1 mRNA undergoes a 'subtle' alternative splicing event generating two isoforms (CAG- and CAG+) differing by a single alanine codon at the exon3/exon4 junction

neuroendocrine tumors normal cyyr1 rt-pcr quantitative psti
Multiple polymorphisms, but no mutations, in the WAF1/CIP1 gene in human brain tumours.

PMID 7577473 · PMC2033923 · British journal of cancer · 1995 · 8 claims · 5 setups

Full-text index only

No somatic mutations of WAF1/CIP1 were found in 158 primary human brain tumours

reamplified same brain healthy sscp direct microsatellite
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

Full-text index only

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
snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome.

PMID 16990247 · PMC1636440 · Nucleic acids research · 2006 · 8 claims · 5 setups

Full-text index only

snoSeeker (comprising CDseeker and ACAseeker) is a computational package that can screen for both guide and orphan snoRNA genes, unlike prior programs limited to guide snoRNAs

whole-genome genome computational gene northern
G2Cdb: the Genes to Cognition database.

PMID 18984621 · PMC2686544 · Nucleic acids research · 2009 · 7 claims · 7 setups

Full-text index only

G2Cdb integrates experimentally validated synapse proteome datasets with mouse/human genomic annotation, phenotype, and human disease data in a gene-centric database.

brain nervous genome synaptic proteomic large-scale sequence
Tubulin proteomics: towards breaking the code.

PMID 18840397 · PMC4039029 · Analytical biochemistry · 2009 · 8 claims · 8 setups

Full-text index only

Tubulin isotype and posttranslational-modification diversity constitutes a 'tubulin code' that is read by microtubule-associated proteins and translates into specific in vivo functions

bovine mda-mb-231 cancer a549 maldi-tof tandem sds-page
Genome-wide census and expression profiling of chicken neuropeptide and prohormone convertase genes.

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

Full-text index only

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

chicken blast microarray est
Survey of transcripts in the adult Drosophila brain.

PMID 11276425 · PMC30707 · Genome biology · 2001 · 8 claims · 4 setups

Full-text index only

The adult Drosophila brain cDNA library contains approximately 6.75 million independent clones

drosophila randomly brain cdna reverse sequence
Finding signals that regulate alternative splicing in the post-genomic era.

PMID 12429065 · PMC244920 · Genome biology · 2002 · 8 claims · 8 setups

Full-text index only

Alternative splicing generates protein and regulatory diversity from a limited number of genes and modulates isoform levels in a cell-context-specific manner

intron-containing genome brain-specific cell-free computational comparative selex
The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups

Full-text index only

The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.

genomic predicted cdna tissues genomic sequence pcr
A genomics-based approach to biodefence preparedness.

PMID 14708013 · PMC7097618 · Nature reviews. Genetics · 2004 · 7 claims · 8 setups

Full-text index only

Genome sequence data are now available for essentially all 25-30 principal human bacterial pathogens, including most CDC category A-C bioterror agents

bacillus brucella neisseria gastric comparative transcriptome two-dimensional
Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies.

PMID 16855283 · PMC1524921 · Nucleic acids research · 2006 · 8 claims · 5 setups

Full-text index only

Four novel brain-specific paternally expressed transcripts (BB077283, BM117114, AK080843, AV328498) were identified and validated on proximal Chr 7.

tissues inter-subspecies placenta genomic microarray rt-pcr sequencing
Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

PMID 18710585 · PMC2533671 · BMC microbiology · 2008 · 7 claims · 6 setups

Full-text index only

A four-SNP set (glnA36, glnA429, glcK180, adhP111) identified via the Not-N algorithm plus empirical testing divides GBS into 10 groups concordant with eBURST-defined population structure.

gbs clinical bioinformatic eburst kinetic
A distinct clinical, neuropsychological and radiological phenotype is associated with progranulin gene mutations in a large UK series.

PMID 18234697 · PMC2577762 · Brain : a journal of neurology · 2008 · 8 claims · 7 setups

Full-text index only

Five different pathogenic GRN mutations (frameshift/premature termination) were identified in 25 affected members of a large UK FTLD cohort, with no whole-gene deletions detected

ftld grn genomic post-mortem clinical volumetric direct
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

Full-text index only

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

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

Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome.

A screen for proteins that interact with PAX6: C-terminal mutations disrupt interaction with HOMER3, DNCL1 and TRIM11.

Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

Sequence, "subtle" alternative splicing and expression of the CYYR1 (cysteine/tyrosine-rich 1) mRNA in human neuroendocrine tumors.

Multiple polymorphisms, but no mutations, in the WAF1/CIP1 gene in human brain tumours.

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

snoSeeker: an advanced computational package for screening of guide and orphan snoRNA genes in the human genome.

G2Cdb: the Genes to Cognition database.

Tubulin proteomics: towards breaking the code.

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

Survey of transcripts in the adult Drosophila brain.

Finding signals that regulate alternative splicing in the post-genomic era.

The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

A genomics-based approach to biodefence preparedness.

Chromosome-wide identification of novel imprinted genes using microarrays and uniparental disomies.

Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

A distinct clinical, neuropsychological and radiological phenotype is associated with progranulin gene mutations in a large UK series.

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