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 9

System / cell line: predicted ✕ Assay: cnv ✕ Clear

Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

PMID 37216666 · PMC10411599 · G3 (Bethesda, Md.) · 2023 · 7 claims · 8 setups

Has reproduction · 86

CAGE sequencing of 24 tissues from 3 cattle populations (dairy, beef-dairy cross, Kinsella composite) defines TSS and coexpressed short-range enhancers in the ARS-UCD1.2 reference genome

tissues predicted tss-enhancer cattle cage extraction coexpression
Landscape of allele-specific transcription factor binding in the human genome.

PMID 33980847 · PMC8115691 · Nature communications · 2021 · 8 claims · 6 setups

Has reproduction · 82

A novel statistical framework (ADASTRA) calls allele-specific TF binding from existing ChIP-Seq alignments by jointly correcting for background allelic dosage (BAD, from aneuploidy/CNVs) and reference mapping bias.

gtrd k562 mcf7 types chip-seq variant bayesian
Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.

PMID 17565693 · PMC1920519 · BMC genomics · 2007 · 8 claims · 4 setups

Full-text index only

42 different CNVs were detected in 27 phenotypically normal individuals using 1 Mb resolution BAC array-CGH

genomic metaphase computational array-cgh fish real-time
Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 7 claims · 8 setups

Has reproduction · 71

Two distinct RNA modification patterns exist among BCa samples with radically different clinical outcomes and biological characteristics.

bca meta-geo tcga-blca tcga bulk rna-seq somatic
Tandem repeats modify the structure of human genes hosted in segmental duplications.

PMID 19954527 · PMC2812944 · Genome biology · 2009 · 8 claims · 6 setups

Full-text index only

Around 7% of primate-specific genes located within segmental duplications contain variable internal tandem repeats (ITRs).

genome genomic est paired genome-wide comparative cnv
Single-molecule sequencing of an individual human genome.

PMID 19668243 · PMC4117198 · Nature biotechnology · 2009 · 8 claims · 7 setups

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Single-molecule sequencing without cloning, amplification or ligation can sequence an individual human genome on one instrument by a single operator in four runs

genome staphylococcus single-molecule snp sanger
Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.

PMID 38482016 · PMC10933018 · Frontiers in immunology · 2024 · 7 claims · 8 setups

Has reproduction · 80

C3 PLP2+ Tumor Epithelial Progenitor Cells are a key subpopulation that drives differentiation and progression of cervical carcinoma

tumor tcga siha single-cell bulk rt-qpcr
Phenotypic variation meets systems biology.

PMID 19664197 · PMC2745761 · Genome biology · 2009 · 8 claims · 8 setups

Full-text index only

Cellular differentiation states are constrained by complex networks with substantial positive and negative regulation, challenging the concept of single 'master regulators'

thp-1 arabidopsis unspecified mammalian deepcage protein-protein sequencing
Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals.

PMID 20018283 · PMC2845297 · Atherosclerosis · 2010 · 8 claims · 7 setups

Full-text index only

The ADIPOQ locus is the only major gene locus for plasma adiponectin, reaching genome-wide significance in combined and sex-stratified analyses

population-based cohorts gwa plasma genome-wide replication candidate

Experiments

Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

Landscape of allele-specific transcription factor binding in the human genome.

Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.

Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

Tandem repeats modify the structure of human genes hosted in segmental duplications.

Single-molecule sequencing of an individual human genome.

Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.

Phenotypic variation meets systems biology.

Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals.