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).

• Transcriptional landscape of repetitive elements in normal and cancer human cells.

  PMID 25012247 · PMC4122776 · BMC genomics · 2014 · 8 claims · 8 setups

  Has reproduction · 76

  RepEnrich, a computational method that uses all mapping reads (uniquely mapping plus multi-mapping reads assigned to repetitive element subfamily assemblies/pseudogenomes), quantifies genome-wide repetitive element enrichment

  chromosomes lines imr-90 prostate simulated pol chip-seq

• Immuno-detection by sequencing enables large-scale high-dimensional phenotyping in cells.

  PMID 29921844 · PMC6008431 · Nature communications · 2018 · 8 claims · 8 setups

  Has reproduction · 96

  ID-seq combines DNA-tagged antibodies with high-throughput sequencing to enable large-scale, high-dimensional, multiplexed (phospho-)protein phenotyping in fixed cell populations across many samples in parallel.

  epidermal id-seq immuno-pcr colony

• 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

• Allelic variation at a single locus distinguishes spring and winter faba beans.

  PMID 41807799 · PMC12987728 · Nature genetics · 2026 · 8 claims · 8 setups

  Full-text index only

  GWAS identifies a major winter hardiness locus whose most strongly associated variant explains the vast majority of phenotypic variation and accurately differentiates winter from spring types

  hedin faba leaf accessions bionano pacbio rna-seq

• SEAseq: a portable and cloud-based chromatin occupancy analysis suite.

  PMID 35193506 · PMC8864840 · BMC bioinformatics · 2022 · 7 claims · 2 setups

  Has reproduction · 94

  SEAseq is a comprehensive, infrastructure-independent pipeline that performs the major analyses needed to process ChIP-Seq/CUT&RUN chromatin binding datasets in a single execution

  any chip-seq cut&run

• Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation.

  PMID 37652021 · PMC10588993 · Immunity · 2023 · 7 claims · 8 setups

  Has reproduction · 83

  Vascular macrophages form a spatiotemporal niche in direct contact with mural cells across microvascular and macrovascular beds

  cx3cr1-mφ rfp-rep coronary peritoneal intravital confocal single-cell

• Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

  PMID 22466171 · PMC3371705 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 80

  BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules

  lncap sonicated adaptor-modified native bischip-seq chromatin chip-qpcr

• A pan-cancer single cell landscape reveals heterogeneity and functional diversity of double-negative T cells.

  PMID 41484771 · PMC12882460 · Molecular cancer · 2026 · 7 claims · 5 setups

  Full-text index only

  Integration of pan-cancer scRNA-seq data yields a comprehensive single-cell atlas of 157,025 high-quality DNT cells across 23 cancer types.

  tumor dnt ffpe mc38 scrna-seq tcr multiplex

• Decoding the heterogeneity of human undifferentiated spermatogonia reveals RAS-dependent regulation of stem cell fate.

  PMID 41579373 · PMC13003925 · Cell reports · 2026 · 8 claims · 7 setups

  Full-text index only

  FSD1 is a cell-surface pan-uSPG marker that enables FACS purification of the entire uSPG population

  testis seminiferous testicular fsd1+ single-cell immunofluorescence whole-mount

• ADAR1 regulates dsRNA formation in nuclear and mitochondrial transcripts through editing-dependent and -independent mechanisms.

  PMID 41800619 · PMC13171160 · Cell reports · 2026 · 8 claims · 8 setups

  Full-text index only

  Human ADAR1 downregulates self-dsRNA abundance through both editing-dependent and editing-independent mechanisms

  hek-293t adar1 dermal e912a antibody western nuclease

• Characterization of ALTO-encoding circular RNAs expressed by Merkel cell polyomavirus and trichodysplasia spinulosa polyomavirus.

  PMID 33999949 · PMC8158866 · PLoS pathogens · 2021 · 8 claims · 8 setups

  Has reproduction · 80

  MCPyV generates two circular RNAs (circALTO1, circALTO2) spanning the early region/ALTO ORF, detectable in VP-MCC cell lines and patient tumors

  mcpyv-infected vp-mcc waga mcc rna-seq inverse qrt-pcr

• Microglia maintain structural integrity during fetal brain morphogenesis.

  PMID 38309258 · PMC10869139 · Cell · 2024 · 8 claims · 8 setups

  Has reproduction · 68

  Embryonic ATM-like microglia accumulate at two fetal cortical boundaries, the cortico-striato-amygdalar boundary (CSA) and cortico-septal boundary (CSB), resembling post-natal axon-tract-associated microglia (ATM)

  embryonic cx3cr1 fetal embryos single-cell immunolabeling phrodo

• A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells.

  PMID 34426512 · PMC8415381 · Genome research · 2021 · 8 claims · 8 setups

  Has reproduction · 57

  About 5% of tested PCRP antibodies showed high-confidence cognate-target enrichment in at least one assay and are strong candidates for further validation.

  k562 hct116 subset chip-exo chip-seq western

• Spatial-reprogramming derived GPNMB(+) macrophages interact with COL6A3(+) fibroblasts to enhance vascular fibrosis in glioblastoma.

  PMID 41174767 · PMC12577258 · Genome medicine · 2025 · 8 claims · 8 setups

  Has reproduction · 64

  COL6A3+ TAFs are a distinct matrix-fibroblast subset significantly enriched in non-responders to neoadjuvant antiangiogenic+ICB combination therapy

  gbm ffpe col6a3+ thp-1 scrna-seq spatial multiplex

• The tumour suppressor L(3)mbt inhibits neuroepithelial proliferation and acts on insulator elements.

  PMID 21857667 · PMC3173870 · Nature cell biology · 2011 · 8 claims · 8 setups

  Has reproduction · 90

  Brain tumors in l(3)mbt mutants originate from overproliferation of neuroepithelial cells of the optic lobes, not from defects in asymmetric cell division.

  drosophila chip-seq chip immunostaining

• Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations.

  PMID 24782521 · PMC4066758 · Nucleic acids research · 2014 · 8 claims · 5 setups

  Has reproduction · 79

  EDD is a new algorithm that detects broad (megabase-size) enrichment domains from ChIP-seq data of widely distributed chromatin proteins such as A- and B-type lamins.

  normal dermal analysis set chip-seq chip-qpcr rna-seq

• Acetylation of H3K115 is associated with fragile nucleosomes at CpG island promoters and active regulatory sites.

  PMID 41778583 · PMC12959880 · eLife · 2026 · 8 claims · 8 setups

  Full-text index only

  H3K115ac is enriched at the TSS of active CpG island (CGI) promoters, far more than non-CGI promoters

  embryonic mescs synthetic mesc chip-seq atac-seq dot

• Stage- and cluster-specific regulation of chondrogenic gene programs by Sox9 in mouse embryonic limb buds.

  PMID 41809054 · PMC12969044 · iScience · 2026 · 8 claims · 7 setups

  Full-text index only

  scRNA-seq across five limb bud stages identifies four Sox9-high populations (chondroprogenitors 1, 2, 3, and mature chondrocytes) with distinct temporal dynamics

  forelimb scrna-seq cut&run embryo single-cell cut&run velocity

• MultiPert: An adversarial alignment and dual attention framework for single-cell multi-omics perturbation prediction.

  PMID 41811907 · PMC12998955 · PLoS computational biology · 2026 · 8 claims · 7 setups

  Full-text index only

  MultiPert reliably predicts both perturbed gene expression and protein abundance profiles from single-cell multi-omics data

  thp-1 kidney gse156478 computational zinb-vae autoencoder eccite-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