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).

• The genomic diversity of SARS-CoV-2 Omicron lineages collected during routine sentinel surveillance in Tanzania between November 2022 and July 2023.

  PMID 41688918 · PMC13011721 · BMC genomics · 2026 · 8 claims · 5 setups

  Full-text index only

  Seven Omicron Nextstrain clades were identified among Tanzanian sequences, with clades 22F (XBB*) and 22E (BQ.1) predominant, comprising 56.3% and 21.35% of samples respectively

  nasal sars-cov-2-positive multiplexed tanzanian rt-qpcr whole-genome bioinformatic

• Characterization of genome-wide p53-binding sites upon stress response.

  PMID 18474530 · PMC2441782 · Nucleic acids research · 2008 · 7 claims · 7 setups

  Full-text index only

  Genome-wide ChIP-on-chip identified 1546 high-confidence p53-binding sites upon Actinomycin D treatment in U2OS cells

  u2os saos-2 chip-on-chip chip-qpcr western

• Specific Marker Gene Analysis for Primary Central Nervous System Lymphoma Based on Methylation Difference and Development of Detection Primers.

  PMID 41097902 · PMC12528802 · Brain and behavior · 2025 · 7 claims · 5 setups

  Has reproduction · 62

  450K microarray analysis identified 26 overlapping differential methylation sites distinguishing PCNSL from CNS and non-CNS groups

  tcga ccle clinical pcnsl 450k rrbs roc

• ZAP targets aberrant mRNA transcripts encoding proteins with defective signal peptides for degradation.

  PMID 41820617 · PMC13084044 · The EMBO journal · 2026 · 8 claims · 7 setups

  Has reproduction · 50

  ZAP (ZC3HAV1/PARP13) is a key component of the RAPP quality control pathway

  k562 zap-s rt-qpcr western immunofluorescence

• Comprehensive analysis of m(6)A methylome alterations after azacytidine plus venetoclax treatment for acute myeloid leukemia by nanopore sequencing.

  PMID 38510975 · PMC10950754 · Computational and structural biotechnology journal · 2024 · 8 claims · 6 setups

  Has reproduction

  m6A site number and m6A levels are significantly lower in post-treatment complete remission (CR) bone marrow than in pre-treatment AML bone marrow

  paired hl-60 gene aml nanopore functional kaplan-meier

• Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

  PMID 16899447 · PMC1557810 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The RE1 PSSM identifies functional RE1 binding sites with greater sensitivity and selectivity than the previously used RE1 consensus sequence

  fibroblast hela hek293 set genome-wide electrophoretic rt-pcr

• β-Catenin activity induces an RNA biosynthesis program promoting therapy resistance in T-cell acute lymphoblastic leukemia.

  PMID 36597789 · PMC9906382 · EMBO molecular medicine · 2023 · 8 claims · 8 setups

  Has reproduction · 65

  β-catenin binds directly to promoters of RNA processing, splicing, and ribosomal biogenesis genes in T-ALL cells

  rpmi8402 chipseq chip-qpcr sequencing

• GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring.

  PMID 35087491 · PMC8787282 · Frontiers in microbiology · 2021 · 8 claims · 8 setups

  Has reproduction · 50

  GAL08 is a dominant bacterial clade in Dewar Creek hot spring sediment, comprising up to 29.2% of the microbial community by relative read abundance

  hot 16s gal08 16s qpcr single-cell

• Analysis of the Hypoxic Response in a Mouse Cortical Collecting Duct-Derived Cell Line Suggests That Esrra Is Partially Involved in Hif1α-Mediated Hypoxia-Inducible Gene Expression in mCCD(cl1) Cells.

  PMID 35806266 · PMC9267015 · International journal of molecular sciences · 2022 · 8 claims · 7 setups

  Has reproduction · 76

  mCCD cl1 cells mount a broad transcriptional response to 24 h hypoxia (0.2% O2), with 3086 genes differentially expressed

  mccd lines bulk rt-qpcr western

• 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

• RNA structure maps across mammalian cellular compartments.

  PMID 30886404 · PMC6640855 · Nature structural & molecular biology · 2019 · 8 claims · 6 setups

  Has reproduction · 45

  icSHAPE can map RNA secondary structure in vivo across three subcellular compartments (chromatin, nucleoplasm, cytoplasm) in both human and mouse cells

  v6.5 naked fractionated icshape rt-qpcr western

• Integrated bioinformatics analysis screened the key genes and pathways of idiopathic pulmonary fibrosis.

  PMID 40280949 · PMC12032202 · Scientific reports · 2025 · 8 claims · 8 setups

  Has reproduction · 93

  5328 differentially expressed transcripts (4083 genes) were identified in GSE173355 by limma, with 4012 transcripts (3206 genes) confirmed by both limma and edgeR (logFC>1, FDR<0.05)

  ipf degs differentially bleomycin-induced bulk methylation kegg

• Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

  PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups

  Has reproduction · 74

  Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.

  intestinalis same rna-seq strand-specific technical reverse

• RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.

  PMID 41755635 · PMC12956339 · Nucleic acids research · 2026 · 7 claims · 8 setups

  Full-text index only

  RAPseq is a novel in vitro, antibody-free and cross-linking-free method that profiles RBP binding to native cellular RNA transcriptome-wide using recombinant Halo-tagged RBPs and affinity purification followed by sequencing.

  hepg2 hur igf2bp1 ythdf1 rapseq cross-species co-rapseq

• Endogenous retroviral elements LTR8B and MER65 rewire PSG9 regulation to control trophoblast syncytialization and pre-eclampsia risk.

  PMID 41796334 · PMC12969887 · Genome biology · 2026 · 8 claims · 8 setups

  Has reproduction · 68

  LTR8B is a placentally-relevant cis-regulatory element (CRE), notably within the PSG array

  sghpl-4 bewo recombinant serum chip-exonuclease transient quantitative

• N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.

  PMID 36422864 · PMC9731578 · eLife · 2022 · 8 claims · 8 setups

  Has reproduction · 55

  Pho92 specifically binds m6A-modified RNA via its YTH domain, both in vitro and in vivo

  cerevisiae diploid yeast recombinant affinity rt-qpcr chip-seq

• Nucleosome regulatory dynamics in response to TGFβ.

  PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups

  Has reproduction · 59

  SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.

  hepatocellular hepg2 130-bp mnase strand-specific taqman

• Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection.

  PMID 19109909 · PMC2630178 · Neuron · 2008 · 8 claims · 8 setups

  Full-text index only

  MEF2 directly regulates a genome-wide program of 182 activity-dependent target genes in hippocampal neurons

  e18 hippocampal forebrain profiling rt-qpcr chip-chip

• 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

  Full-text index only

  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

• A cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a.

  PMID 28642491 · PMC5481429 · Scientific reports · 2017 · 8 claims · 8 setups

  Has reproduction · 76

  Hnf4a is a major transcriptional regulator of Dnajc22

  atlas roadmap liver-specific kidney co-expression transcription reanalysis