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: brain ✕ Assay: probe ✕ Clear

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

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

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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
Survey of transcripts in the adult Drosophila brain.

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

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

drosophila randomly brain cdna reverse sequence
Brain progranulin expression in GRN-associated frontotemporal lobar degeneration.

PMID 19649643 · PMC3104467 · Acta neuropathologica · 2010 · 8 claims · 8 setups

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GRN transcript haploinsufficiency, previously shown in blood-derived cells, does not hold in most brain regions of GRN mutation carriers

peripheral postmortem hek293 qrt-pcr microarray rt-pcr
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

maqc hepatocytes japanese illeum microarray dasl sequence
3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

PMID 19917133 · PMC2781828 · BMC genomics · 2009 · 8 claims · 4 setups

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3' tag DGE transcript profiles are highly reproducible between technical and biological replicates, across libraries made at different labs, and across two generations of Illumina Genome Analyzers (GA I and GA II).

brain hbrr topo-cloned tag microarray quantitative
Exploring Gene Expression Patterns in Alzheimer's Disease Using a Human Microarray Data Meta-Analysis.

PMID 41744654 · PMC12938635 · Biology · 2026 · 6 claims · 7 setups

Has reproduction · 100

AD brains show a distinct transcriptomic profile with up-regulation of immune/inflammation genes and down-regulation of synapse/neuronal-signaling genes

brain sub-studies down-regulated affymetrix quality normalization
Human methylome variation across Infinium 450K data on the Gene Expression Omnibus.

PMID 33937763 · PMC8061458 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups

Has reproduction · 88

Approximately two-thirds of compiled HM450K samples are from blood, one-quarter from brain, and roughly one-third from cancer patients.

hm450k seven annotated illumina beadarray model-based
Genetical genomic determinants of alcohol consumption in rats and humans.

PMID 19874574 · PMC2777866 · BMC biology · 2009 · 8 claims · 6 setups

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A genetical genomics approach combining brain gene expression, bQTL, and eQTL analysis in HXB/BXH RI rats identifies candidate genes for alcohol consumption

hxb naive caucasian two-bottle behavioral brain
High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

PMID 19804644 · PMC2768739 · BMC genetics · 2009 · 8 claims · 6 setups

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The human GWSA uses exon body and exon-exon junction probes to directly measure over 280,000 known and predicted splicing events genome-wide.

universal same lim erythrocyte genome-wide cross-platform rt-pcr
Premature centromere division of the X chromosome in neurons in Alzheimer's disease.

PMID 18624923 · PMC2746937 · Journal of neurochemistry · 2008 · 8 claims · 2 setups

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PCD,X frequency is significantly elevated (~3-fold) in frontal cortex neurons of sporadic AD patients compared to age-matched controls

frontal adjacent fluorescent hematoxylin
Managing incidental findings in human subjects research: analysis and recommendations.

PMID 18547191 · PMC2575242 · The Journal of law, medicine & ethics : a journal of the American Society of Law, Medicine & Ethics · 2008 · 8 claims · 5 setups

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Little guidance currently exists on managing research IFs, and no consensus exists on the best approach across genetic/genomic and imaging research domains.

affected large research consent linkage genomic structural
Loss of heterozygosity at 2q37 in sporadic Wilms' tumor: putative role for miR-562.

PMID 19789318 · PMC2756455 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 8 setups

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2q37 harbors a tumor suppressor gene important in Wilms tumor pathogenesis

sporadic wilms fetal 293t loh multiplex genome-wide
CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.

PMID 12556968 · PMC2376780 · British journal of cancer · 2003 · 8 claims · 4 setups

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RB1 CpG island hypermethylation is a common epigenetic event associated with development of malignant nervous system tumours

nervous bisulphite-modified same pcr-sscp methylation-specific bisulphite
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
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

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

Survey of transcripts in the adult Drosophila brain.

Brain progranulin expression in GRN-associated frontotemporal lobar degeneration.

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

Exploring Gene Expression Patterns in Alzheimer's Disease Using a Human Microarray Data Meta-Analysis.

Human methylome variation across Infinium 450K data on the Gene Expression Omnibus.

Genetical genomic determinants of alcohol consumption in rats and humans.

High resolution analysis of the human transcriptome: detection of extensive alternative splicing independent of transcriptional activity.

Premature centromere division of the X chromosome in neurons in Alzheimer's disease.

Managing incidental findings in human subjects research: analysis and recommendations.

Loss of heterozygosity at 2q37 in sporadic Wilms' tumor: putative role for miR-562.

CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.

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

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