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).

• Optimizing Single-Cell Long-Read Sequencing for Enhanced Isoform Detection in Pancreatic Islets.

  PMID 41563441 · PMC13007207 · Diabetes · 2026 · 8 claims · 7 setups

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  5′ single-cell library preparation protocols outperform 3′ protocols for transcript identification and read length

  lines pancreatic spleen dtc single-cell bulk ngs

• Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data.

  PMID 34927097 · PMC8649395 · STAR protocols · 2021 · 6 claims · 7 setups

  Has reproduction · 50

  A combined mechanical and enzymatic dissociation protocol using the gentleMACS Dissociator yields a single-cell suspension from mouse pancreatic tumor tissue suitable for scRNA-seq while preserving cell characteristics

  pancreatic dissociated single-cell scrna-seq tumor dead red

• Massively parallel reporter assay for mapping gene-specific regulatory regions at single-nucleotide resolution.

  PMID 41738738 · PMC12935429 · eLife · 2026 · 8 claims · 8 setups

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  LS-MPRA (BAC-based) and d-MPRA (systematic mutagenesis) are complementary methods for unbiased, high-resolution mapping of cis-regulatory modules.

  mus e14 retina candidate ls-mpra single-cell individual

• Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

  PMID 32596448 · PMC7299619 · Science advances · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  Transcriptional bursting kinetics is regulated by a combination of promoter- and gene body-binding proteins, including the polycomb repressive complex 2 (PRC2) and transcription elongation factors

  cast knock-in mesc mescs single-cell single-molecule flow

• Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.

  PMID 37994351 · PMC10663991 · F1000Research · 2023 · 8 claims · 6 setups

  Has reproduction · 67

  A comprehensive open-source R workflow combining trajectory inference (monocle3) and pseudo-bulk time course analysis (edgeR) can be applied to multi-sample scRNA-seq data of the mouse mammary gland.

  mammary aggregated single-cell quality doublet

• Single-cell sequencing reveals unexpected genetic diversity among Bodo spp. flagellates and their bacterial endosymbionts.

  PMID 41848149 · PMC12999062 · Microbial genomics · 2026 · 8 claims · 8 setups

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  Seven single-cell genomes assembled from uncultured environmental Bodo cells represent three potentially novel Bodo species

  uncultured environmental single-cell bodo single-cell fluorescence-activated whole-genome

• Single-Cell Lineage Tracing Uncovers Resistance Signatures and Sensitizing Strategies to FLT3 Inhibitors in Acute Myeloid Leukemia.

  PMID 41270153 · PMC7618455 · Cancer research · 2026 · 8 claims · 8 setups

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  ReSisTrace single-cell lineage tracing identifies pre-resistant and pre-sensitive cell states to FLT3 inhibitors midostaurin and quizartinib in FLT3-ITD-positive MOLM-13 AML cells before treatment

  molm-13 aml-pdx1 single-cell lineage gene

• Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.

  PMID 41528844 · PMC12971065 · Cell reports · 2026 · 8 claims · 8 setups

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  Generated a single-cell gene expression and chromatin accessibility (multiome) atlas of human RPE and choroid from control and AMD eyes

  rpe-choroid rpe arpe-19 scatac-seq joint h3k27ac activity-by-contact

• Single-cell exon deletion profiling reveals splicing events that shape gene expression and cell state dynamics.

  PMID 41633991 · PMC12868714 · Nature communications · 2026 · 8 claims · 5 setups

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  scCHyMErA-Seq enables simultaneous single-cell capture of Cas9 and Cas12a guide RNAs together with polyadenylated transcripts, integrating exon-deletion CRISPR screening with 10x Genomics scRNA-seq

  hap1 nrf1 flow northern droplet-based

• A high throughput method for genome-wide analysis of retroviral integration.

  PMID 17028098 · PMC1636494 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  VITA uses MmeI to cleave DNA at a fixed distance from its recognition site, generating 21-22 bp genomic tags that serve as signatures of lentiviral integration sites.

  hela ht3 genome chromosomes isf vita sanger

• Whole genome amplification and de novo assembly of single bacterial cells.

  PMID 19724646 · PMC2731171 · PloS one · 2009 · 8 claims · 6 setups

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  FACS-based single-cell isolation combined with strict handling procedures virtually eliminates contaminating DNA from single-cell MDA reactions

  prochlorococcus single-cell seven sag genome spike-in amplification

• High-throughput mapping of spontaneous mitotic crossover and genome instability events with sci-L3-Strand-seq.

  PMID 41674384 · PMC12895072 · Nucleic acids research · 2026 · 8 claims · 6 setups

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  sci-L3-Strand-seq is a combinatorial indexing method with linear amplification for DNA template strand sequencing that cost-effectively scales to millions of single cells

  hap1 bj-5ta patski sci-l3-strand-seq sci-l3-strand-seq library read

• Spatial perturb-seq: single-cell functional genomics within intact tissue architecture.

  PMID 41723140 · PMC13035813 · Nature communications · 2026 · 8 claims · 8 setups

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  Spatial Perturb-Seq simultaneously measures whole transcriptome (cell type), CRISPR barcodes (perturbation), spatial coordinates, and cell-cell interactions through a single Stereo-seq and/or Xenium run.

  hippocampus bone brain aav-transduced scrna-seq snrna-seq spatial

• Decoding the Mechanisms of Hepatocellular Carcinoma Cancer Stem Cells and Identifying Potential Therapeutic Strategies Based on Single-cell Omics.

  PMID 41771574 · PMC12951371 · Cancer genomics & proteomics · 2026 · 7 claims · 8 setups

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  Malignant cells from HCC tumors resolve into six transcriptionally distinct subpopulations, including a progenitor-like CSC subset expressing EPCAM, SOX9, and SOX4

  malignant tumor csc six single-cell spatial copy

• De novo identification of CD4(+) T cell epitopes.

  PMID 38658646 · PMC11093748 · Nature methods · 2024 · 7 claims · 8 setups

  Has reproduction · 83

  SABR-IIs (chimeric receptors linking a covalently attached peptide-MHC-II to CD28-CD3ζ signaling domains) present epitopes to CD4+ T cells and induce a readable NFAT-GFP/CD69 signal upon cognate TCR recognition

  nfat-gfp hla-dq8 5kc daudi nfat-gfp co-incubation species

• Stress Responsive bZIP Transcription Factors ATF4 and BACH1 Cooperate With MAF-Family bZIP Protein NRL to Fine-Tune Rod Photoreceptor Gene Expression.

  PMID 42246540 · PMC13249099 · Investigative ophthalmology & visual science · 2026 · 8 claims · 7 setups

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  ATF4 and BACH1 are identified as bZIP protein interactors of NRL

  y2hgold hek293 p28 flow-sorted yeast co-immunoprecipitation immunofluorescence

• nf-core/crisprseq: a versatile pipeline for comprehensive analysis of CRISPR gene editing and screening assays.

  PMID 41551929 · PMC12805889 · NAR genomics and bioinformatics · 2026 · 8 claims · 5 setups

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  nf-core/crisprseq is the first generic pipeline enabling analysis of the broad spectrum of CRISPR designs, from targeted gene edits (KO, KI, BE, PE) to large-scale functional screens

  spike-in prjeb53901 a375 prjna326019 targeted crispr computing

• Resolving clonal evolution and selection of extrachromosomal DNA at single-cell resolution.

  PMID 41606654 · PMC12853921 · Genome biology · 2026 · 7 claims · 8 setups

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  ecSingle, a computational method integrating allelic imbalance (BAF deviation) and outlier expression from scRNA-seq, can identify oncogene-carrying ecDNA at single-cell resolution.

  colo320dm glioblastoma medulloblastoma ce26 scrna-seq whole-genome long-read

• pmid-41776501

  PMID 41776501 · PMC13162433 · 8 claims · 6 setups

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  MeRLin, a single-vector high-complexity lineage tracing platform integrating cellular barcoding, scRNA-seq, RNA-FISH, and computational analysis, was developed to track clonal and transcriptional dynamics in a melanoma PDX model

  wm4237-1 nsg bulk scrna-seq clonal

• FRMD8 inhibits tumor metastasis in BRCA1-associated TNBC by negatively regulating tmTNF-α.

  PMID 40619383 · PMC12229025 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

  Has reproduction · 73

  Low FRMD8 expression in BRCA1-mutant breast cancer cells significantly enhances metastatic potential to various organs

  tnbc geo breast frmd8 bulk meta-analysis single-cell