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).

• ChIP-seq Data Processing and Relative and Quantitative Signal Normalization for Saccharomyces cerevisiae.

  PMID 40364978 · PMC12067309 · Bio-protocol · 2025 · 8 claims · 6 setups

  Has reproduction · 100

  siQ-ChIP measures absolute protein–DNA interaction (IP efficiency) genome-wide without relying on exogenous spike-in chromatin, overcoming limitations of spike-in normalization.

  cerevisiae pombe concatenated chip-seq chip-seq high-throughput fastq

• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

  PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 74

  ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

  small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot

• A global change in RNA polymerase II pausing during the Drosophila midblastula transition.

  PMID 23951546 · PMC3743134 · eLife · 2013 · 8 claims · 8 setups

  Has reproduction · 71

  Massive de novo recruitment of Pol II (and TBP) with widespread pausing occurs during the Drosophila midblastula transition, at 4007 promoters (~one third of all genes).

  hand-sorted drosophila chip-seq immunostaining dapi

• Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments.

  PMID 18765474 · PMC2577354 · Nucleic acids research · 2008 · 6 claims · 6 setups

  Full-text index only

  Extensive sonication reduces crosslinked chromatin to an average fragment size of ~200 bp (range 75–300 bp) and fragmentation is largely random with respect to genomic region and nucleosome position.

  cerevisiae hela chip-qpcr nucleosome gel

• Vespucci: a system for building annotated databases of nascent transcripts.

  PMID 24304890 · PMC3936758 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 73

  Existing ChIP-seq and RNA-seq analysis platforms (e.g. Cufflinks, peak callers) are unsuited to GRO-seq because they assume spliced/exonic reads, uniform density and paired-end data, and cannot identify transcriptional units de novo across the whole genome.

  thioglycollate-elicited mcf-7 macrophages mm9 gro-seq chip-seq short-read

• Power analysis for genome-wide association studies.

  PMID 17725844 · PMC2042984 · BMC genetics · 2007 · 8 claims · 6 setups

  Full-text index only

  Developed a method to compute genome-wide association study power using tag SNPs and representative population genotype data (HapMap), equivalent to the cumulative r2-adjusted power of Jorgenson and Witte.

  hapmap power pairwise tag

• Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae.

  PMID 35605195 · PMC9284283 · Plant communications · 2022 · 8 claims · 4 setups

  Has reproduction · 95

  Triti-Map is a computational package suite plus web interface specifically optimized for bulk-segregated gene mapping in Triticeae, accepting DNA-seq, RNA-seq/ChIP-seq, and traditional QTL data as input

  wheat hordeum bulk-segregated interval novo

• Detection of YMDD motif mutants by oligonucleotide chips in lamivudine-untreated patients with chronic hepatitis B virus infection.

  PMID 15308845 · PMC2816888 · Journal of Korean medical science · 2004 · 6 claims · 5 setups

  Full-text index only

  An oligonucleotide chip was developed using probes for wild-type YMDD, M552V, and three M552I probe variants to detect HBV polymerase YMDD motif mutations

  serum hbv nested pcr oligonucleotide pcr restriction

• CancerGenes: a gene selection resource for cancer genome projects.

  PMID 17088289 · PMC1781153 · Nucleic acids research · 2007 · 6 claims · 4 setups

  Full-text index only

  CancerGenes is a gene list-centric web resource that combines expert-annotated gene lists with data from public databases (Entrez Gene, Ensembl BioMart, Kim et al. promoter data, Sanger COSMIC) to support gene selection for cancer re-sequencing projects.

  genes chip-on-chip literature entrez

• maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks.

  PMID 36719906 · PMC9917285 · PLoS computational biology · 2023 · 8 claims · 6 setups

  Has reproduction · 98

  maxATAC is a suite of deep neural network models enabling state-of-the-art, genome-scale TFBS prediction from ATAC-seq, with models for 127 human transcription factors

  lines hepg2 types single chip-seq omni-atac-seq atac-seq

• High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites.

  PMID 18988630 · PMC2662491 · Nucleic acids research · 2009 · 8 claims · 8 setups

  Full-text index only

  Incorporating H3K4me3 chromatin modification estimates greatly improves the accuracy of in silico prediction of in vivo TF binding for a wide range of TFs in human and mouse

  embryonic neural t-cells mm8 chip-seq chip-chip pwm

• PReMod: a database of genome-wide mammalian cis-regulatory module predictions.

  PMID 17148480 · PMC1761432 · Nucleic acids research · 2007 · 8 claims · 3 setups

  Full-text index only

  PReMod is a database of genome-wide predicted cis-regulatory modules (pCRMs) for the human and mouse genomes.

  genome chip-chip comparative

• The impact of haplotypes derived from Chinese pigs on genetic variation and economic traits in the Duroc breed.

  PMID 41131451 · PMC12551222 · Genetics, selection, evolution : GSE · 2025 · 7 claims · 8 setups

  Has reproduction

  Significant genetic introgression from Chinese pigs into commercial European lines was confirmed, with introgressed segments predominantly deriving from Southern Chinese domestic pigs (CSDP) with additional contributions from Eastern Chinese domestic pigs (CEDP).

  pigs duroc muscle snp whole-genome low-coverage

• Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma.

  PMID 31784732 · PMC6886578 · Nature genetics · 2019 · 8 claims · 8 setups

  Has reproduction · 58

  SOX8 is a previously unrecognized core regulatory TF in FP-RMS, co-localizing with other CR TFs at SEs and essential for tumor cell growth

  rms rh4 h3k27ac pooled chip-seq

• 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

• TFBScluster web server for the identification of mammalian composite regulatory elements.

  PMID 16845063 · PMC1538905 · Nucleic acids research · 2006 · 7 claims · 5 setups

  Full-text index only

  TFBScluster is a web server that identifies genome-wide clusters of TFBSs conserved in multiple mammalian species using human or mouse as the reference genome.

  imr90 tissues dog transgenic microarray-based gene

• Detection of mutations in EGFR in circulating lung-cancer cells.

  PMID 18596266 · PMC3551471 · The New England journal of medicine · 2008 · 8 claims · 7 setups

  Full-text index only

  The CTC-chip microfluidic device isolates CTCs from NSCLC patients in sufficient quantity and purity to permit EGFR mutational analysis

  blood archived nsclc plasma microfluidic allele-specific standard

• miRGen 2.0: a database of microRNA genomic information and regulation.

  PMID 19850714 · PMC2808909 · Nucleic acids research · 2010 · 7 claims · 6 setups

  Full-text index only

  miRGen 2.0 is a database providing comprehensive information about the genomic position of human and mouse microRNA coding transcripts and their regulation by transcription factors

  lung organ malme embryonic polii small nucleosome

• Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes.

  PMID 16840528 · PMC1524903 · Nucleic acids research · 2006 · 7 claims · 5 setups

  Full-text index only

  MS-PET, which dimerizes PETs prior to 454 multiplex sequencing, achieves an approximate 100-fold efficiency increase over standard Sanger-based PET analysis

  mcf7 hct116 flcdna gis-pet chip-pet quantitative

• Differential analysis for high density tiling microarray data.

  PMID 17892592 · PMC2231405 · BMC bioinformatics · 2007 · 8 claims · 6 setups

  Full-text index only

  gSAM, a generalized extension of Significance Analysis of Microarrays (SAM), uses a piece-wise function to segment genome-wide differential response by protein-coding vs non-coding regions and by 5' vs 3' vs intra-genic bias within genes, rather than treating a gene as an atomic unit.

  hl60 profiling chip-on-chip