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).

• Enhanced protein isoform characterization through long-read proteogenomics.

  PMID 35241129 · PMC8892804 · Genome biology · 2022 · 6 claims · 4 setups

  Has reproduction · 79

  A long-read proteogenomics pipeline integrating PacBio long-read RNA-seq with MS-based proteomics enhances isoform-resolved protein characterization

  jurkat jurkat-derived long-read transcript orf

• Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.

  PMID 36457147 · PMC9721438 · RNA biology · 2022 · 8 claims · 7 setups

  Has reproduction · 93

  Long-read RNA-seq detected 53,863 transcript isoforms from 10,426 genes in HUVECs, of which 22,195 were novel

  huvecs huvec long-read bottom-up offline

• Biphasic expression of thyroid hormone receptor TRβ1 in mammalian retina and anterior ocular tissues.

  PMID 37033230 · PMC10076699 · Frontiers in endocrinology · 2023 · 7 claims · 8 setups

  Full-text index only

  TRβ1 shows a biphasic, late-peaking expression profile in retina that contrasts with the early embryonic peak of TRβ2

  retina fetal retinal cones rna-seq lacz immunofluorescence

• HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.

  PMID 24475057 · PMC3903476 · PloS one · 2014 · 8 claims · 5 setups

  Has reproduction · 66

  HTSstation is a web application suite coupling simple web forms to modular analysis pipelines for ChIP-seq, RNA-seq, 4C-seq and re-sequencing HTS applications, accessible at http://htsstation.epfl.ch.

  embryonic mycobacterium forebrain rna-seq re-sequencing 4c-seq

• Caloric Restriction Reprograms Adipose Tissues in Rhesus Monkeys.

  PMID 41042069 · PMC12686577 · Aging cell · 2025 · 8 claims · 8 setups

  Has reproduction · 66

  At baseline, SAT and VAT transcriptomes are highly similar, with only ~1% of genes (30 genes, adjusted p<0.05) differentially expressed between depots in Controls

  subcutaneous sat rhesus bulk gsea xcell

• Betacoronavirus-specific alternate splicing.

  PMID 35074468 · PMC8782732 · Genomics · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  Genes showing differential alternative splicing in SARS-CoV-2 have a similar functional profile to those in SARS-CoV and MERS, affecting a diverse set of genes and biological functions related to virus biology.

  mrc5 calu-3 nasopharyngeal sars-cov-2-infected bulk clinical term

• Long-Read RNA Sequencing Identifies Polyadenylation Elongation and Differential Transcript Usage of Host Transcripts During SARS-CoV-2 In Vitro Infection.

  PMID 35464437 · PMC9019466 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 90

  Differential polyadenylation occurs in infected Calu-3 and Vero cells at a late time point (48 hpi)

  vero calu-3 genes direct pcr poly

• A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.

  PMID 36694043 · PMC9873918 · Communications biology · 2023 · 8 claims · 7 setups

  Has reproduction · 83

  The DSS phenotype-by-time interaction defines parsimonious temporal (dynamic) expression and splicing signatures of acute and chronic colitis distinct from time-specific differential expression.

  intestine colon dss distal bulk phenotypic h&e

• SMRT and Illumina RNA sequencing reveal novel insights into the heat stress response and crosstalk with leaf senescence in tall fescue.

  PMID 32746857 · PMC7397585 · BMC plant biology · 2020 · 7 claims · 5 setups

  Has reproduction · 30

  Short-term heat stress strongly and specifically activates Hsps, Hsfs, FKBPs, calcium signaling, glutathione S-transferase, photosynthesis, and phytohormone signaling genes.

  tall tobacco illumina smrt electrolyte

• Comprehensive Transcriptome Analysis Reveals Genome-Wide Changes Associated with Endoplasmic Reticulum (ER) Stress in Potato (Solanum tuberosum L.).

  PMID 36430273 · PMC9696714 · International journal of molecular sciences · 2022 · 8 claims · 3 setups

  Has reproduction · 62

  TM treatment of potato leaves produces widespread, time-dependent differential gene expression associated with ER stress and the UPR

  potato rna-seq gene alternative

• Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.

  PMID 36760235 · PMC9905242 · Frontiers in cellular and infection microbiology · 2022 · 7 claims · 8 setups

  Has reproduction · 71

  CAI is positively correlated with translational efficiency, supporting its use as a proxy for viral mRNA translation in cell types.

  monocyte-macrophage cd4+ kidney metabolic bulk single-cell codon

• annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.

  PMID 36472574 · PMC9724561 · GigaScience · 2022 · 7 claims · 8 setups

  Has reproduction · 78

  annotate_my_genomes is an easy-to-use genome-guided pipeline that uses hybrid (PacBio+Illumina) assembled transcripts to distinguish coding genes from long non-coding RNAs and reconcile them with prior annotations.

  chick real simulated pacbio illumina hybrid

• Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.

  PMID 32536962 · PMC7291481 · Plant methods · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  ONT Pc produces higher raw data quality (higher alignment rate, lower error rate) than ONT Dc, while PacBio generates the longest reads

  arabidopsis pacbio randomly illumina pacbio nanopore

• 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

• Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

  PMID 22064864 · PMC3245177 · Nucleic acids research · 2012 · 8 claims · 5 setups

  Has reproduction · 83

  Gene Expression Atlas is an added-value database providing curated, re-annotated and statistically analysed gene expression data across cell types, organism parts, developmental stages, disease states and other biological/experimental conditions, derived from ArrayExpress Archive and the European Nucleotide Archive.

  species microrna atlas microarray rna-seq microrna

• 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

• auts2 Features and Expression Are Highly Conserved during Evolution Despite Different Evolutionary Fates Following Whole Genome Duplication.

  PMID 36078102 · PMC9454499 · Cells · 2022 · 8 claims · 7 setups

  Has reproduction · 50

  auts2a and auts2b originate from the teleost-specific whole genome duplication (TGD)

  fish genomic auts2 tissues comparative tblastn phylogenetic

• Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain).

  PMID 37137526 · PMC10214862 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  First high-quality chromosome-level genome assembly and annotation of P. lilfordi, generated via a mixed sequencing strategy (10X linked reads, ONT long reads, Hi-C) plus RNAseq/Iso-Seq

  liver-derived muscle heart pooled 10x oxford hi-c

• 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