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: brain ✕ Assay: intron ✕ Clear

Neurofibrillary tau pathology modulated by genetic variation of alpha-synuclein.

PMID 18661559 · PMC8957216 · Annals of neurology · 2008 · 7 claims · 5 setups

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The SNCA intron 4 marker rs2572324 is associated with the extent of neurofibrillary tangle (Braak stage) pathology.

postmortem whole-genome-amplified vantaa85+ neuropathological immunohistochemistry snp
Finding signals that regulate alternative splicing in the post-genomic era.

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

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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
Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

PMID 18424448 · PMC2465798 · Human molecular genetics · 2008 · 8 claims · 8 setups

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Genotype CC (rs2234693/PvuII) and C-allele-containing haplotypes in ESR1 intron 1 are more frequent in African American schizophrenics than controls

genomic postmortem nimhgi esr1 targeted case-control family-based
Aberrant mRNA splicing and impaired hippocampal neurogenesis in Grin2b mutant mice.

PMID 41675057 · PMC12886552 · iScience · 2026 · 8 claims · 6 setups

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Grin2b+/C456Y mice show large-scale, age-dependent brain transcriptomic changes, peaking at 4 weeks postnatally

brain hippocampus neuronal bulk trade gene
GENCODE: producing a reference annotation for ENCODE.

PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups

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GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions

tissues encode rt-pcr comparative automated
TM4SF10 gene sequencing in XLMR patients identifies common polymorphisms but no disease-associated mutation.

PMID 15345028 · PMC517934 · BMC medical genetics · 2004 · 8 claims · 4 setups

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No disease-associated mutations were found in TM4SF10 in 16 XLMR patients from 14 families with linkage to the TM4SF10 locus.

genomic dog sage pcr northern sage
Spinocerebellar ataxia type 23: a genetic update.

PMID 19089525 · PMC2694919 · Cerebellum (London, England) · 2009 · 8 claims · 6 setups

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The SCA23 disease locus maps to chromosome 20p13-12.3, spanning ~6 Mb and containing 97 known/predicted genes.

members post-mortem candidate coding genome-wide neuropathological southern
Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes.

PMID 23999385 · PMC6505400 · Scientific reports · 2013 · 8 claims · 8 setups

Has reproduction · 95

Four epigenetic modifications (DNA methylation, H3K4me2, H3K4me3, H3K27me3) in mouse CGIs undergo combinatorial variation (co-variation) across ESCs, NPCs and adult brain during neuron differentiation.

embryonic escs dem-cgis demg methylation chip-seq gene
Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.

PMID 16719907 · PMC1513570 · BMC genomics · 2006 · 8 claims · 5 setups

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A 2 Mb BAC contig of 78 clones was assembled covering the entire bovine FHIT locus

bovine pcr-based comparative rt-pcr
MRX87 family with Aristaless X dup24bp mutation and implication for polyAlanine expansions.

PMID 17480217 · PMC1868705 · BMC medical genetics · 2007 · 8 claims · 7 setups

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The MRX87 disease locus maps to the Xp22-p21 interval, a known hot spot region for mental handicap

peripheral genomic pcr leukocytes two-point direct pcr
The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

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

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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
Identification of the first intragenic deletion of the PITX2 gene causing an Axenfeld-Rieger Syndrome: case report.

PMID 17134502 · PMC1684248 · BMC medical genetics · 2006 · 8 claims · 8 setups

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An intragenic deletion of 3,059 bp within the PITX2 gene, spanning the end of exon 5 through the start of exon 6, causes this family's severe ARS phenotype

genomic lymphoblastoid i-2 patients pcr quantitative long-range
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

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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
The molecular landscape of ASPM mutations in primary microcephaly.

PMID 19028728 · PMC2658750 · Journal of medical genetics · 2009 · 8 claims · 7 setups

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ASPM mutations are the most common cause of MCPH

consanguineous genomic parents one polymorphic sanger family
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

Has reproduction · 86

RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

ccds glioblastoma experimental simulated simulated bulk quality
Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

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XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

hct116 macaque cos-7 genomic cdna est molecular
Molecular and clinical analyses of 84 patients with tuberous sclerosis complex.

PMID 16981987 · PMC1592085 · BMC medical genetics · 2006 · 8 claims · 6 setups

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Mutations were identified in 64 of 84 (76%) TSC probands, comprising 9 TSC1 and 55 TSC2 mutations

genomic pcr-amplified tsc healthy dhplc direct pcr
Intragenic deletion in the LARGE gene causes Walker-Warburg syndrome.

PMID 17436019 · PMC1914248 · Human genetics · 2007 · 7 claims · 8 setups

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A homozygous 63.1-kb intragenic deletion in LARGE (exons 9-10) causes Walker-Warburg syndrome in a consanguineous Saudi family

genomic family skeletal blood microsatellite direct multiplex
Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication.

PMID 18811940 · PMC2564943 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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Teleosts, unlike tetrapods, possess two closely linked paralogous AQP1 genes, aqp1a and aqp1b (formerly AQP1o), arising from a teleost-specific duplication of an ancestral AQP1 gene

aqp1-like pufferfish tissues xenopus phylogenetic genomic rt-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

Neurofibrillary tau pathology modulated by genetic variation of alpha-synuclein.

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

Variants in the estrogen receptor alpha gene and its mRNA contribute to risk for schizophrenia.

Aberrant mRNA splicing and impaired hippocampal neurogenesis in Grin2b mutant mice.

GENCODE: producing a reference annotation for ENCODE.

TM4SF10 gene sequencing in XLMR patients identifies common polymorphisms but no disease-associated mutation.

Spinocerebellar ataxia type 23: a genetic update.

Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes.

Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.

MRX87 family with Aristaless X dup24bp mutation and implication for polyAlanine expansions.

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

Identification of the first intragenic deletion of the PITX2 gene causing an Axenfeld-Rieger Syndrome: case report.

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

The molecular landscape of ASPM mutations in primary microcephaly.

RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

Molecular and clinical analyses of 84 patients with tuberous sclerosis complex.

Intragenic deletion in the LARGE gene causes Walker-Warburg syndrome.

Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication.

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