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).

• 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

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

  ccds glioblastoma experimental simulated simulated bulk quality

• MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data.

  PMID 29901703 · PMC6025204 · GigaScience · 2018 · 6 claims · 7 setups

  Has reproduction · 95

  A two-step 'omni' RNA-seq pipeline (MetaMap) combining STAR human alignment with CLARK-S metagenomic classification can quantify archaeal, bacterial, and viral reads from the non-human read fraction of human RNA-seq data

  clinical hela tumor rutkowski bulk dual negative

• BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

  PMID 19668202 · PMC3661775 · Nature methods · 2009 · 8 claims · 8 setups

  Full-text index only

  BreakDancer (BreakDancerMax + BreakDancerMini) is a software package that predicts a wide variety of structural variants including deletions, insertions, inversions, and intra/inter-chromosomal translocations from paired-end short-insert sequencing reads.

  reads yoruban cytogenetically predicted simulated paired-end whole-genome

• Patient-Derived Meningioma Organoids: A Reliable Model for Studying Human Tumor Pathophysiology.

  PMID 39941893 · PMC11817449 · Cancers · 2025 · 8 claims · 7 setups

  Has reproduction · 50

  A standardized, reproducible protocol can establish meningioma organoids (MEN-Os) from patient-resected tumor tissue without mechanical/enzymatic dissociation, using serum-free medium lacking growth factors or exogenous ECM.

  patient-resected men-os parent oct-embedded organoid brightfield h&e

• Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.

  PMID 18438408 · PMC2705838 · Nature genetics · 2008 · 8 claims · 8 setups

  Full-text index only

  Massively parallel paired-end sequencing can characterize somatic and germline structural rearrangements to base-pair resolution across a whole cancer genome

  nci-h2171 nci-h1770 massively genomic rt-pcr

• Complex landscapes of somatic rearrangement in human breast cancer genomes.

  PMID 20033038 · PMC3398135 · Nature · 2009 · 8 claims · 6 setups

  Full-text index only

  There are more somatic rearrangements in some breast cancers than previously appreciated by cytogenetic methods.

  breast subset confirmed paired-end fish exon-exon

• An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.

  PMID 19881495 · PMC3086882 · Nature biotechnology · 2009 · 8 claims · 8 setups

  Full-text index only

  A 'concept signature' (ConSig) score algorithm ranks genes by association with molecular concepts characteristic of fusion or mutation cancer genes, nominating biologically important fusions from large candidate sets.

  lung known leukemia tumor paired-end computational snp

• Differential bone morphology and hypoxia activity in skeletal metastases of ER(+) and ER(-) breast cancer.

  PMID 39572705 · PMC11582807 · Communications biology · 2024 · 8 claims · 8 setups

  Has reproduction · 68

  ER− MDA-MB-231 breast cancer forms more osteolytic bone metastases than ER+ MCF-7 breast cancer

  mcf-7 breast bone tumor-free immunofluorescence co-culture rna-seq

• DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.

  PMID 41673887 · PMC13097799 · Genome biology · 2026 · 8 claims · 9 setups

  Has reproduction · 80

  DMN-seq (DMN+) uses DME to nick DNA specifically at 5mC sites, enabling 5mC detection at single-base resolution via selective adaptor ligation

  synthetic partially embryonic mesc glycosylase dmn-seq ultrafast

• miRge 2.0 for comprehensive analysis of microRNA sequencing data.

  PMID 30153801 · PMC6112139 · BMC bioinformatics · 2018 · 8 claims · 6 setups

  Has reproduction · 89

  miRge 2.0 introduces a novel SVM-based miRNA detection method using both hairpin structure and isomiR composition, yielding higher specificity for miRNA identification

  pooled colon datasets small a-to-i novel