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).

Publications 1.3k Datasets 392.5k Experiments 60

System / cell line: seq ✕ Assay: targeted ✕ Clear

CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization.

PMID 41723172 · PMC13036076 · Nature communications · 2026 · 8 claims · 7 setups

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CRAGE-RB-PI-seq, combining CRAGE genome engineering with randomly-barcoded promoter-library insertion sequencing, enables targeted amplification of barcoded bacterial transcripts that bypasses plant RNA interference.

pseudomonas arabidopsis targeted pi-seq conventional
A multi-omics features-based approach integrating immunogenicity and inflammation enhances immunotherapy benefit in clear cell renal cell carcinoma.

PMID 41640425 · PMC12864441 · Frontiers in cell and developmental biology · 2025 · 7 claims · 8 setups

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The TIs-ML multi-omics model predicts ICB response/survival in ccRCC with superior accuracy (AUC > 0.997) compared to single biomarkers like PD-L1 and TMB

autoimmune igan scrna-seq bulk bulk scrna-seq scissor-based
A Scalable Framework for Comprehensive Typing of Polymorphic Immune Genes from Long-Read Data.

PMID 41669879 · PMC13088316 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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SpecImmune is the first unified computational framework to simultaneously genotype HLA, KIR, IG, TCR, and CYP genes from long-read data.

1kgp hprc hgsvc long-read targeted germline
DNA methylation profiles at hospital admission are associated with subsequent severe COVID-19 outcomes.

PMID 42021404 · PMC13251264 · Clinical epigenetics · 2026 · 7 claims · 5 setups

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DNA methylation profiles at hospital admission differ among disease trajectory groups (TGs) and are associated with subsequent disease progression.

pbmcs blood immune end-stage targeted rna-seq mass
Detecting unannotated splicing events in short-read RNA-seq with SAMI, a UMI-aware Nextflow pipeline.

PMID 42166739 · PMC13242923 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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SAMI is a UMI-aware, Singularity-contained Nextflow pipeline that detects splicing events diverging from transcript annotations directly from raw FASTQ files.

seraseq simulated small processed targeted simulated computation
Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.

PMID 19835606 · PMC2784330 · Genome biology · 2009 · 7 claims · 2 setups

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Hybrid selection of cDNA dramatically increases the specificity of sequencing reads mapping to targeted cancer-related transcripts.

k-562 targeted sanger
PeakPrime: a peak-guided primer design pipeline for target enrichment in 3'-end RNA-seq.

PMID 41919010 · PMC13034549 · Bioinformatics advances · 2026 · 8 claims · 7 setups

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PeakPrime is a reproducible Nextflow pipeline that calls 3′ RNA-seq coverage peaks (MACS2), selects exonic windows, designs strand-appropriate primers (Primer3), and screens specificity (Bowtie2)

imr-32 universal candidate 10m-read rna-seq targeted quantitative
RSK1 is an exploitable dependency in myeloproliferative neoplasms and secondary acute myeloid leukemia.

PMID 39820365 · PMC11739599 · Nature communications · 2025 · 8 claims · 8 setups

Has reproduction · 73

RSK1 is a conserved, exploitable therapeutic dependency across MPN and secondary AML

sorted mpn cd34+ aml bulk targeted mass
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
Dioxin-elicited decrease in cobalamin redirects propionyl-CoA metabolism to the β-oxidation-like pathway resulting in acrylyl-CoA conjugate buildup.

PMID 35931118 · PMC9418907 · The Journal of biological chemistry · 2022 · 8 claims · 8 setups

Has reproduction · 73

TCDD dose-dependently decreases cobalamin (Cbl) levels, compromising MUT activity and redirecting propionyl-CoA metabolism from the canonical Cbl-dependent carboxylation pathway to the alternate Cbl-independent β-oxidation-like pathway.

liver hepatic intestinal serum targeted untargeted chip-seq
Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 5 setups

Has reproduction

Expression stability in CHO cell lines is controlled at three levels: choice of integration site, transgene integrity/concatemerization pattern, and stress-related cellular processes.

horizon same cho genome rna-seq targeted
FOXA1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity.

PMID 41621066 · PMC13050545 · Cell reports · 2026 · 8 claims · 8 setups

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FOXA1 mutations in a 874-tumor cohort cluster into missense, in-frame indel, and truncation subgroups, with indels concentrated at residues M253/E255

prostate targeted single-nucleus scatac-seq
An NSP2-MYB module orchestrates flavonoid biosynthesis and nodule symbiosis.

PMID 41643674 · PMC7619063 · Current biology : CB · 2026 · 8 claims · 8 setups

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NSP1 and NSP2 promote expression of flavonoid biosynthesis genes during nutrient starvation and rhizobial symbiosis in Medicago truncatula

medicago nicotiana recombinant yeast rna-seq qpcr targeted
Microbiota-derived IPA protects against colitis by regulating intestinal HMGCS2-mediated ketogenesis to facilitate mucosal healing.

PMID 41651833 · PMC12988232 · Nature communications · 2026 · 8 claims · 8 setups

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IPA is consistently depleted in IBD/colitis patients and in murine colitis models relative to healthy controls

fecal c57bl germ-free mice quasi-targeted dss-induced tnbs-induced
Dopamine enhances surface glial glycolysis via acetylcholine and insulin/insulin-like growth factor signaling in the honeybee.

PMID 41797926 · PMC12964235 · iScience · 2026 · 8 claims · 5 setups

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Bromocriptine (dopamine receptor agonist) increases glycolytic flux in forager bee brains

forager targeted qpcr single-cell
Current status of use of high throughput nucleotide sequencing in rheumatology.

PMID 33408124 · PMC7789458 · RMD open · 2021 · 8 claims · 8 setups

Has reproduction · 83

RNA-Seq is the most represented HTS assay used in rheumatology research, primarily for biomarker identification in blood or synovial tissue.

pubmed sequence blood patients systematic sra rna-seq
Integrated multiomic analysis reveals disulfidptosis subtypes in glioblastoma: implications for immunotherapy, targeted therapy, and chemotherapy.

PMID 38504986 · PMC10950096 · Frontiers in immunology · 2024 · 8 claims · 8 setups

Has reproduction · 73

Consensus clustering on 32 disulfidptosis-associated genes stratifies GBM patients into two subtypes, DRGcluster A and B, with distinct survival outcomes.

fresh tcga gbm bulk rna-seq consensus
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
Mutational Signatures and Clonal Hematopoiesis in Intestinal Metaplasia across Countries with Varying Stomach Cancer Incidence.

PMID 41532847 · PMC13056296 · Cancer discovery · 2026 · 8 claims · 8 setups

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High-depth targeted sequencing of >1,500 IM samples from six countries identified 47 significantly mutated driver genes, including ARID1A, KRAS/MAPK pathway genes, and PIGR

subset matched saliva hek293t high-depth whole-genome genome-wide
Single-nucleus RNA sequencing identifies a novel tenogenic heterologous differentiation in endometrial carcinosarcomas: implications for diagnosis and tumor classification.

PMID 41537454 · PMC12805614 · The Journal of pathology · 2026 · 6 claims · 7 setups

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snRNA-seq identifies a novel tenogenic heterologous differentiation program (SCX, MKX, TNMD) in an endometrial carcinosarcoma

ffpe sections tumor cs4 single-nucleus immunohistochemistry fluorescence

Experiments

CRAGE-RB-PI-seq reveals transcriptional dynamics of plant-associated bacteria during root colonization.

A multi-omics features-based approach integrating immunogenicity and inflammation enhances immunotherapy benefit in clear cell renal cell carcinoma.

A Scalable Framework for Comprehensive Typing of Polymorphic Immune Genes from Long-Read Data.

DNA methylation profiles at hospital admission are associated with subsequent severe COVID-19 outcomes.

Detecting unannotated splicing events in short-read RNA-seq with SAMI, a UMI-aware Nextflow pipeline.

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.

PeakPrime: a peak-guided primer design pipeline for target enrichment in 3'-end RNA-seq.

RSK1 is an exploitable dependency in myeloproliferative neoplasms and secondary acute myeloid leukemia.

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

Dioxin-elicited decrease in cobalamin redirects propionyl-CoA metabolism to the β-oxidation-like pathway resulting in acrylyl-CoA conjugate buildup.

Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

FOXA1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity.

An NSP2-MYB module orchestrates flavonoid biosynthesis and nodule symbiosis.

Microbiota-derived IPA protects against colitis by regulating intestinal HMGCS2-mediated ketogenesis to facilitate mucosal healing.

Dopamine enhances surface glial glycolysis via acetylcholine and insulin/insulin-like growth factor signaling in the honeybee.

Current status of use of high throughput nucleotide sequencing in rheumatology.

Integrated multiomic analysis reveals disulfidptosis subtypes in glioblastoma: implications for immunotherapy, targeted therapy, and chemotherapy.

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

Mutational Signatures and Clonal Hematopoiesis in Intestinal Metaplasia across Countries with Varying Stomach Cancer Incidence.

Single-nucleus RNA sequencing identifies a novel tenogenic heterologous differentiation in endometrial carcinosarcomas: implications for diagnosis and tumor classification.