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 22

System / cell line: beta ✕ Assay: transcript ✕ Clear

GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats.

PMID 16698959 · PMC3303178 · Nucleic acids research · 2006 · 7 claims · 5 setups

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GREM enables genome-wide isolation and quantitative analysis of transcriptionally active (promoter-active) repetitive elements while excluding read-through transcript background

testicular genomic coli grem rt-pcr race
Chromosome-level genome assembly of Siberian kale (Brassica napus subsp. pabularia).

PMID 41760683 · PMC13066399 · Scientific data · 2026 · 8 claims · 8 setups

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A chromosome-level genome assembly of Siberian kale variety Beta was generated using PacBio HiFi long reads, Illumina short reads, and Hi-C data

beta illumina pacbio hi-c
High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis.

PMID 23222129 · PMC3553938 · Nucleic acids research · 2013 · 8 claims · 7 setups

Has reproduction · 69

NusA interacts with RNAP ubiquitously throughout the M. tuberculosis chromosome and its ChIP-seq profile mirrors RNAP distribution in both exponential and stationary phase, despite NusA not binding DNA directly.

mycobacterium tuberculosis chip-seq input strand-specific
Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

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Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

c57bl orthologous alpha-defensin defensin manual comparative sequence
FracFixR: a compositional statistical framework for absolute proportion estimation between fractions in RNA sequencing data.

PMID 41264734 · PMC12866640 · Bioinformatics (Oxford, England) · 2026 · 7 claims · 5 setups

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FracFixR reconstructs original fraction proportions by modeling the compositional relationship between whole and fractionated RNA samples using non-negative least squares (NNLS) regression on selected transcripts

gm12878 mixtures reh long-read polysome synthetic
Dysregulation of alternative splicing patterns in the ovaries of reproductively aged mice.

PMID 41630016 · PMC13046076 · Reproduction (Cambridge, England) · 2026 · 8 claims · 5 setups

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Reproductive aging in mouse ovaries is associated with widespread alternative splicing changes, including shifts in exon usage, splice site selection, and transcript boundaries.

ovary computational direct cryosectioning translation
Identification of a novel spliced variant of the SYT gene expressed in normal tissues and in synovial sarcoma.

PMID 11308259 · PMC2363857 · British journal of cancer · 2001 · 8 claims · 8 setups

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Two forms of SYT mRNA, N-SYT and a novel form I-SYT, are co-expressed in normal human tissues and in synovial sarcomas

synovial ss-derived normal liver rt-pcr cloning densitometric
Identification and characterization of a novel mammalian Mg2+ transporter with channel-like properties.

PMID 15804357 · PMC1129089 · BMC genomics · 2005 · 8 claims · 6 setups

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MagT1 is a novel mammalian Mg2+ transporter with channel-like properties, showing no amino acid sequence identity to other known transporters

kidney mdct tissues xenopus oligonucleotide northern real-time
Epigenomic, transcriptomic, and proteomic characterization of breast cancer cell line reference samples.

PMID 41539304 · PMC12853167 · Cell reports methods · 2026 · 8 claims · 5 setups

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Comprehensive multi-omics reference materials (ATAC-seq, Methyl-seq, RNA-seq, MS-proteomics) were generated for paired HCC1395/HCC1395BL cell lines as a community benchmarking resource

hcc1395 atac-seq methyl-seq bulk
Detection of the DCC gene product in normal and malignant colorectal tissues and its relation to a codon 201 mutation.

PMID 9484816 · PMC2149930 · British journal of cancer · 1998 · 6 claims · 5 setups

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DCC protein expression is lost in the majority of colorectal tumours while retained in all normal colonic tissue

matched cryosections genomic pcr-rflp rt-pcr northern
Genetic and epigenetic analyses of MBD3 in colon and lung cancer.

PMID 15138480 · PMC2410281 · British journal of cancer · 2004 · 7 claims · 5 setups

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MBD3 is not a major target of genetic or epigenetic alteration in colon and lung cancer

colon normal pcr-sscp rt-pcr northern
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

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

pax6 brain yeast sequence yeast semi-quantitative
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
The genomic analysis of lactic acidosis and acidosis response in human cancers.

PMID 19057672 · PMC2585811 · PLoS genetics · 2008 · 8 claims · 8 setups

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Lactic acidosis and hypoxia induce largely distinct gene expression programs in HMECs, with lactic acidosis producing a much larger and more dramatic response

mammary hmec gene breast gene real-time bayesian
Nutrigenetic association of the 5-lipoxygenase gene with myocardial infarction.

PMID 18842779 · PMC3014055 · The American journal of clinical nutrition · 2008 · 8 claims · 4 setups

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A significant gene x diet interaction exists between 5-LO promoter short alleles (3,4 repeats) and dietary AA intake in determining MI risk

costa buffy genetic real-time allele-specific
Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.

PMID 19765279 · PMC2760583 · BMC genomics · 2009 · 8 claims · 5 setups

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Global microarray profiling reveals 421 genes differentially expressed in DBA patient fibroblasts compared to healthy controls

dermal same fibroblasts analysis microarray quantitative rt-pcr
Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.

PMID 19763266 · PMC2740864 · PloS one · 2009 · 8 claims · 8 setups

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Androgen treatment alters the whole-cell proteome of LNCaP prostate cancer cells

lncap androgen prostate itraq mudpit immunoblot
Estrogen Production in Pancreatic Cancer Shapes a Tumor-Suppressive Stromal Microenvironment.

PMID 41258799 · PMC12862343 · Cancer research · 2026 · 8 claims · 6 setups

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Serum levels of stromal biomarkers associated with favorable outcomes were significantly higher in female patients with PDAC than in male patients

pdac pdx magnetic bioinformatic single-nucleus
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
Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

PMID 17705821 · PMC2045109 · BMC molecular biology · 2007 · 8 claims · 8 setups

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Multiple alternatively spliced 5'-UTR isoforms of human PPARdelta mRNA differ in translation efficiency

placenta five lines huh7 5'-race rt-pcr real-time

Experiments

GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats.

Chromosome-level genome assembly of Siberian kale (Brassica napus subsp. pabularia).

High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis.

Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

FracFixR: a compositional statistical framework for absolute proportion estimation between fractions in RNA sequencing data.

Dysregulation of alternative splicing patterns in the ovaries of reproductively aged mice.

Identification of a novel spliced variant of the SYT gene expressed in normal tissues and in synovial sarcoma.

Identification and characterization of a novel mammalian Mg2+ transporter with channel-like properties.

Epigenomic, transcriptomic, and proteomic characterization of breast cancer cell line reference samples.

Detection of the DCC gene product in normal and malignant colorectal tissues and its relation to a codon 201 mutation.

Genetic and epigenetic analyses of MBD3 in colon and lung cancer.

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

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

The genomic analysis of lactic acidosis and acidosis response in human cancers.

Nutrigenetic association of the 5-lipoxygenase gene with myocardial infarction.

Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.

Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.

Estrogen Production in Pancreatic Cancer Shapes a Tumor-Suppressive Stromal Microenvironment.

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

Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.