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).

• Epigenetic loss of heterogeneity from low to high grade localized prostate tumours.

  PMID 34911933 · PMC8674326 · Nature communications · 2021 · 7 claims · 4 setups

  Has reproduction · 79

  Shared chromatin accessibility features among low-grade (Gleason pattern 3) prostate cancer cells are lost in high-grade (Gleason pattern 4) tumours.

  flash-frozen prostate ffpe single-cell bulk cyclic

• Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics.

  PMID 37012480 · PMC10172113 · Nature methods · 2023 · 8 claims · 5 setups

  Has reproduction · 90

  pSCoPE (prioritized precursor selection via MaxQuant.Live) increases sensitivity, data completeness, and proteome coverage more than twofold over shotgun single-cell proteomics

  bulk hek293 single-cell bone prioritized single-cell spike-in

• DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight.

  PMID 18628296 · PMC2504308 · Nucleic acids research · 2008 · 8 claims · 6 setups

  Full-text index only

  Digital PCR compartmentalizes individual bisulfite-converted DNA template molecules into separate wells, enabling single-molecule DNA methylation analysis

  fresh-frozen same sssi-methylated mixture digital conventional classic

• Analyses and comparison of accuracy of different genotype imputation methods.

  PMID 18958166 · PMC2569208 · PloS one · 2008 · 8 claims · 3 setups

  Full-text index only

  Stronger LD produces higher imputation accuracy rates for all five methods

  simulated real linux genotype computational

• In vivo structural characterization of the SARS-CoV-2 RNA genome identifies host proteins vulnerable to repurposed drugs.

  PMID 33636127 · PMC7871767 · Cell · 2021 · 8 claims · 8 setups

  Has reproduction · 95

  icSHAPE was used to determine the in vivo and in vitro structural landscape of the SARS-CoV-2 RNA genome in infected Huh7.5.1 cells, plus UTR structures of six other coronaviruses

  huh7.5.1 sars-cov-2 utrs 18s icshape structure deep-learning

• Decision tree-driven tandem mass spectrometry for shotgun proteomics.

  PMID 18931669 · PMC2597439 · Nature methods · 2008 · 8 claims · 5 setups

  Full-text index only

  A decision tree (DT) algorithm that selects CAD or ETD per precursor based on z and m/z yields more peptide identifications than either CAD or ETD alone

  saccharomyces proteome embryonic nlc-ms phosphoproteomics sequential

• Antigenic diversity, transmission mechanisms, and the evolution of pathogens.

  PMID 19847288 · PMC2759524 · PLoS computational biology · 2009 · 8 claims · 3 setups

  Full-text index only

  Three distinct infection types (A, B, C) emerge as maxima in the pathogen fitness landscape, each with characteristic within-host dynamics, contact network structure, and transmission mode

  generic simulated hiv-1 stochastic dynamic regression

• Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

  PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.

  single methanol-fixed reads slice mrna-seq light-microscopy read

• A single-cell survey of Drosophila blood.

  PMID 32396065 · PMC7237219 · eLife · 2020 · 8 claims · 6 setups

  Has reproduction · 94

  scRNA-seq of Drosophila larval hemocytes across unwounded, wounded, and wasp-infested conditions resolves 17 clusters spanning plasmatocytes, crystal cells, lamellocytes, and a non-hemocyte population.

  drosophila single-cell quantitative bulk

• Single-cell transcriptional dynamics of flavivirus infection.

  PMID 29451494 · PMC5826272 · eLife · 2018 · 8 claims · 6 setups

  Has reproduction · 90

  viscRNA-Seq simultaneously quantifies whole single-cell host transcriptome and intracellular viral RNA from the same cell, including non-polyadenylated viruses via a virus-specific oligo

  hepatoma single huh7 denv-infected single-cell qpcr loss-of-function

• Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data.

  PMID 33746712 · PMC7966716 · Frontiers in molecular neuroscience · 2021 · 6 claims · 7 setups

  Has reproduction · 50

  A computational method using high-quality scRNA-seq reference data can estimate per-sample, per-cell-type off-target contamination coefficients in sctRNA-seq datasets.

  brain cortex allen lcm-seq lcm-seq scrna-seq marker

• An SVM-based system for predicting protein subnuclear localizations.

  PMID 16336650 · PMC1325059 · BMC bioinformatics · 2005 · 7 claims · 3 setups

  Full-text index only

  New kernels defined on k-peptide vectors mapped by BLOSUM62-based high-scored pair matrices (D1, D2, D3) improve SVM discrimination of protein subnuclear localization compared to conventional k-peptide encodings.

  single-localization multi-localization same svm sequence

• PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.

  PMID 30951143 · PMC6450036 · Database : the journal of biological databases and curation · 2019 · 7 claims · 7 setups

  Has reproduction · 80

  PanglaoDB is a web server providing pre-processed and pre-computed analyses of >1054 single-cell experiments (>4 million cells) from mouse and human across many tissues and platforms.

  grch38 homogeneous per single single-cell clustering cell-type

• Single-cell analysis of testicular bacterial microbiome changes during aging and effect on reproductive capacity in mice.

  PMID 41438041 · PMC12719757 · iScience · 2025 · 8 claims · 7 setups

  Has reproduction · 78

  INVADE-seq simultaneously captures host and bacterial transcripts to map bacteria-host interactions across diverse testicular cell types at single-cell resolution

  testes testis young testicular invade-seq histology sperm

• Single-cell transcriptome maps of myeloid blood cell lineages in Drosophila.

  PMID 32900993 · PMC7479620 · Nature communications · 2020 · 8 claims · 8 setups

  Has reproduction · 86

  Single-cell RNA-seq of developing Drosophila lymph glands resolves heterogeneity of hemocytes and identifies major and sub cell types.

  drosophila lymph single single-cell bulk gene

• Systems spatiotemporal dynamics of traumatic brain injury at single-cell resolution reveals humanin as a therapeutic target.

  PMID 35951114 · PMC9372016 · Cellular and molecular life sciences : CMLS · 2022 · 8 claims · 8 setups

  Has reproduction · 98

  Coordinated gene expression patterns across cell types are disrupted and re-organized by mTBI with distinct regional, cellular, and temporal (24-h vs 7-day) specificity.

  hippocampus frontal peripheral cell-type single-cell svm-based ligand-receptor

• Promoting human promoters.

  PMID 16760901 · PMC1681504 · Molecular systems biology · 2006 · 8 claims · 5 setups

  Full-text index only

  A computational protocol using MARS on known sequence motifs can quantify transcription factor effects on human gene expression despite noise and data size challenges

  gene liver cycle genes computational expression time-course

• Dark matter in a deep-sea vent and in human mouth.

  PMID 17803764 · PMC2040194 · Environmental microbiology · 2007 · 7 claims · 8 setups

  Full-text index only

  The first genome sequence from the uncultured TM7 phylum was obtained by capturing and sequencing DNA from a single cell using a microfluidic device, yielding a 2.86 Mb assembly with 3245 predicted genes.

  uncultured mycoplasma cyanidioschyzon kineococcus single-cell genome whole-genome

• The liver as an immunological barrier redefined by single-cell analysis.

  PMID 32176810 · PMC7218664 · Immunology · 2020 · 8 claims · 8 setups

  Has reproduction · 100

  Single-cell RNA-seq enables unbiased characterization of liver cell states, developmental trajectories and rare immune populations that bulk averaging obscures, redefining liver cell-type mapping.

  c57bl liver whole-liver hepatocytes scrna-seq facs-based plate-based

• Lineage commitment of dermal fibroblast progenitors is controlled by Kdm6b-mediated chromatin demethylation.

  PMID 37602956 · PMC10548174 · The EMBO journal · 2023 · 6 claims · 5 setups

  Has reproduction · 91

  E14.5 DFPs have a repressed transcriptional profile marked by high H3K27me3 and inaccessible chromatin at lineage-specific genes

  skin dermal single-cell chamber chip-seq