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).

• RNA structure maps across mammalian cellular compartments.

  PMID 30886404 · PMC6640855 · Nature structural & molecular biology · 2019 · 8 claims · 6 setups

  Has reproduction · 45

  icSHAPE can map RNA secondary structure in vivo across three subcellular compartments (chromatin, nucleoplasm, cytoplasm) in both human and mouse cells

  v6.5 naked fractionated icshape rt-qpcr western

• Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

  PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups

  Has reproduction · 70

  AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella

  head-kidney idella assembled il-12p40α rna-seq rt-qpcr pcr

• Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.

  PMID 38482016 · PMC10933018 · Frontiers in immunology · 2024 · 8 claims · 8 setups

  Has reproduction · 80

  C3 PLP2+ Tumor Epithelial Progenitor Cells are a noteworthy subpopulation exerting a pivotal influence on CC differentiation and progression

  cervical tcga siha scrna-seq bulk rt-qpcr

• Perturbation of placental protein glycosylation by endoplasmic reticulum stress promotes maladaptation of maternal hepatic glucose metabolism.

  PMID 36660474 · PMC9843443 · iScience · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  ER stress reduces the complexity and sialylation of trophoblast protein N-glycosylation

  bewo eif2s1 umbilical placenta maldi-tof western rt-pcr

• Unveiling the immunometabolic landscape of colorectal cancer through PANoptosis-related gene expression.

  PMID 41601652 · PMC12832467 · Frontiers in immunology · 2025 · 8 claims · 8 setups

  Has reproduction · 41

  PANoptosis-related genes show significant expression heterogeneity across CRC samples, with apoptosis-related genes comprising the largest proportion (87.4%)

  crc hct116 bulk bulk single-cell rt-qpcr

• A transcriptomic atlas of Aedes aegypti reveals detailed functional organization of major body parts and gut regional specializations in sugar-fed and blood-fed adult females.

  PMID 35471187 · PMC9113746 · eLife · 2022 · 8 claims · 5 setups

  Has reproduction · 73

  Created Aegypti-Atlas, an online RNAseq resource covering Ae. aegypti body parts, gut regions, and a blood meal digestion time course

  dissected five anterior midguts rnaseq rt-qpcr

• Transcriptional regulation and chromatin architecture maintenance are decoupled functions at the Sox2 locus.

  PMID 35710138 · PMC9296009 · Genes & development · 2022 · 8 claims · 7 setups

  Has reproduction · 81

  Sox2 transcriptional activation is traced almost entirely to two key transcription factor-bound regions (SRR107 and SRR111) within the SCR

  escs esc sequence compiled allele-specific chip-seq motif

• Identification of novel gene amplifications in breast cancer and coexistence of gene amplification with an activating mutation of PIK3CA.

  PMID 19706770 · PMC2745517 · Cancer research · 2009 · 8 claims · 8 setups

  Full-text index only

  Genome-wide DNA copy number analysis of 161 primary breast tumors identified six novel focally amplified genes: POLD3, IRAK4, IRX2, TBL1XR1, ASPH, and BRD4

  breast mcf10a mcf10ca1h snp quantitative rt-qpcr

• Directing stem cell differentiation by chromatin state approximation.

  PMID 41734818 · PMC12956330 · Nucleic acids research · 2026 · 8 claims · 8 setups

  Full-text index only

  Greedy selection of culture conditions by chromatin (ATAC-seq) distance to target is a viable optimisation strategy for differentiation protocols

  cd34+ cd34+-derived erythroid bone atac-seq flow rt-qpcr

• YAP/TAZ-VGLL3 governs adipocyte fate via epigenetic reprogramming of PPARγ and its target enhancers.

  PMID 41533786 · PMC12802833 · Science advances · 2026 · 8 claims · 8 setups

  Full-text index only

  TAZ represses PPARγ-bound target enhancers, evidenced by markedly reduced H3K27ac occupancy, leading to transcriptional repression of adipogenic genes including Pparg2

  c3h10t1 inguinal iwat adipose atac-seq rna-seq immunoblot

• 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

• Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer.

  PMID 33890574 · PMC8104967 · eLife · 2021 · 8 claims · 8 setups

  Has reproduction · 76

  FOXM1 and RHNO1 are head-to-head bidirectional genes regulated by a shared bidirectional promoter (F/R-BDP)

  tcga ft282 gistic expression rt-qpcr

• CRISPR/Cas9 Screens Reveal Multiple Layers of B cell CD40 Regulation.

  PMID 31365872 · PMC6684324 · Cell reports · 2019 · 8 claims · 8 setups

  Has reproduction

  Genome-wide CRISPR/Cas9 screening in Daudi B cells using CD40L-induced Fas upregulation as a readout identifies both positive and negative regulators of CD40

  daudi splenic genome-wide immunoblot qpcr

• PDGFRA defines the mesenchymal stem cell Kaposi's sarcoma progenitors by enabling KSHV oncogenesis in an angiogenic environment.

  PMID 31881074 · PMC6980685 · PLoS pathogens · 2019 · 8 claims · 8 setups

  Has reproduction · 85

  Pα(+)S (PDGFRA-positive/SCA-1-positive) bone marrow-derived MSCs are KS spindle-cell progenitors

  bone k-pα nude flow viral immunofluorescence

• Downregulation of Splicing Factor PTBP1 Curtails FBXO5 Expression to Promote Cellular Senescence in Lung Adenocarcinoma.

  PMID 39057099 · PMC11276454 · Current issues in molecular biology · 2024 · 8 claims · 8 setups

  Has reproduction · 59

  PTBP1 is significantly upregulated across multiple cancer types including LUAD, and higher PTBP1 levels are associated with worse LUAD patient survival

  cancer luad fibroblast a549 pan-cancer differential replicative

• 7SL RNA and signal recognition particle orchestrate a global cellular response to acute thermal stress.

  PMID 39952919 · PMC11828898 · Nature communications · 2025 · 8 claims · 8 setups

  Has reproduction · 93

  Heat shock induces de novo transcription and nuclear accumulation of 7SL RNA together with SRP proteins, which then bind chromatin at promoters

  embryonic nih3t3 pro-seq fractionation fluorescence

• 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

• Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

  PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  Two distinct RNA modification patterns exist among BCa samples with radically varying clinical outcomes and biological characteristics

  meta-geo tcga-blca bca genomics unsupervised lasso weighted

• CD14(lo)CD301b(+) macrophages gathering as a proangiogenic marker in adipose tissues.

  PMID 39645040 · PMC11745947 · Journal of lipid research · 2025 · 8 claims · 8 setups

  Has reproduction · 59

  Cd14−/− mice exhibit a leaner body shape and are protected from HFD-induced obesity compared to WT mice

  epididymal adipose cd14low macrophage bulk scrna-seq pseudotime

• Expression of neurofibromin 1 in colorectal cancer and cetuximab resistance.

  PMID 34779495 · PMC8611403 · Oncology reports · 2022 · 7 claims · 8 setups

  Has reproduction · 73

  NF1 is highly expressed in cetuximab-sensitive colorectal cancer cell lines (NCI-H508, Caco2) but weakly expressed in cetuximab-resistant lines (KM12C, SW480)

  crc cetuximab-sensitive nf1 cetuximab-resistant western sirna dapi