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).

• miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline.

  PMID 34308351 · PMC8294687 · NAR genomics and bioinformatics · 2021 · 6 claims · 5 setups

  Has reproduction

  miRge3.0 with 12 CPUs consistently has the best execution speed compared to miRge2.0, Chimira and sRNAbench

  sra synthetic qiagen small small umi differential

• IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner.

  PMID 33522913 · PMC7852101 · BMC bioinformatics · 2021 · 8 claims · 2 setups

  Has reproduction · 78

  IsomiR Window is an integrated, user-friendly platform that systematically identifies, quantifies, and functionally explores isomiR expression in small-RNA-seq datasets without requiring computational skills

  simulated basal small-rna-seq

• Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.

  PMID 19724645 · PMC2731166 · PloS one · 2009 · 7 claims · 5 setups

  Full-text index only

  159 novel miRNAs and 116 novel miRNA*s were identified from ALL patient and normal donor small RNA libraries

  pooled sequenced analysis predicted small bioinformatic qrt-pcr

• 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

• A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer.

  PMID 35047825 · PMC8759566 · NAR cancer · 2022 · 7 claims · 7 setups

  Has reproduction · 100

  Five miRNAs (Mir-210_3p, Mir-191_5p, Mir-8-P1b_3p [miR-141-3p], Mir-1307_5p, Mir-155_5p) are up-regulated at multiple metastatic sites in colorectal cancer.

  pcrc mli mirna-seq mirna mirna qpcr differential

• SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

  PMID 20008100 · PMC2836562 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  SeqBuster is a versatile web-based and stand-alone bioinformatic toolkit for processing and analyzing large-scale small RNA deep sequencing datasets.

  embryonic hesc small sequence adapter

• miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems.

  PMID 32374865 · PMC7319446 · Nucleic acids research · 2020 · 8 claims · 3 setups

  Has reproduction · 61

  miEAA 2.0 supports miRNA/precursor enrichment input from ten frequently investigated organisms, expanding beyond the human-only first release.

  kidney breast blood mirna-seq mirna small

• Global and precise identification of functional miRNA targets in mESCs by integrative analysis.

  PMID 35899551 · PMC9442311 · EMBO reports · 2022 · 8 claims · 8 setups

  Has reproduction · 93

  Fewer than 10% of expressed genes are directly and functionally regulated by miRNAs in mESCs

  mirna_ko mescs drosha_ko escs bulk western ago2

• sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression.

  PMID 31114926 · PMC6602500 · Nucleic acids research · 2019 · 8 claims · 3 setups

  Has reproduction

  sRNAtoolbox 2019 adds all major small RNA library preparation protocols (including UMI-based) to sRNAbench with automatic protocol-specific preprocessing.

  biological srp046046 ensembl small consensus genome

• Widespread nitrous oxide undersaturation in farm waterbodies creates an unexpected greenhouse gas sink.

  PMID 31036633 · PMC6525509 · Proceedings of the National Academy of Sciences of the United States of America · 2019 · 7 claims · 5 setups

  Has reproduction · 87

  The majority (67%) of small agricultural farm reservoirs are undersaturated and act as atmospheric N2O sinks despite being highly eutrophic and N-rich.

  small agricultural reservoir dissolved water physical

• Comprehensive data for studying serum exosome microRNA transcriptome in Parkinson's disease patients.

  PMID 39406833 · PMC11480472 · Scientific data · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  The study presents comprehensive serum exosome miRNA transcriptome data from four independent Japanese cohorts of PD patients and controls.

  serum patients small mirna 123i-mibg

• Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure.

  PMID 33690630 · PMC7978347 · PLoS genetics · 2021 · 8 claims · 4 setups

  Has reproduction · 97

  Active (R) and silent (S) epialleles are associated with distinct sRNA size classes: mainly 21 nt sRNAs at R and mostly 24 nt sRNAs at S, regardless of ploidy.

  day-old seedlings tetraploid arabidopsis small hygromycin crispr-cas9

• Starvation-induced transgenerational inheritance of small RNAs in C. elegans.

  PMID 25018105 · PMC4377509 · Cell · 2014 · 8 claims · 7 setups

  Has reproduction · 64

  L1 starvation induces changes in endogenous 22G small RNAs (STGs) that are inherited for at least three generations in fed descendants.

  elegans small small sequencing lifespan

• The fragile breakage versus random breakage models of chromosome evolution.

  PMID 16501665 · PMC1378107 · PLoS computational biology · 2006 · 8 claims · 6 setups

  Full-text index only

  Sankoff and Trinh's synteny block identification algorithm (ST-Synteny) is flawed, producing erroneous block identifications even in small toy examples.

  small synthetic synteny random whole-genome

• Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

  PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.

  erwinia intergenic candidate wounded small northern race

• Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

  PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 7 claims · 8 setups

  Has reproduction · 91

  175 conserved and 83 novel miRNAs were identified mainly in one bud and two tender leaves of tea plant via small RNA sequencing combined with genome survey data

  camellia sinensis small genome mirna

• Expression analysis of candidate breast tumour suppressor genes on chromosome 16q.

  PMID 16280054 · PMC1410740 · Breast cancer research : BCR · 2005 · 8 claims · 7 setups

  Full-text index only

  None of the six candidate genes (CBFA2T3, TERF2, TERF2IP, FBXL8, LRRC29, FANCA) showed inactivating mutations or expression differences clearly associated with 16q LOH status

  breast quantitative fragment gene-expression

• Comparative proteomic analysis of cell lines and scrapings of the human intestinal epithelium.

  PMID 17407598 · PMC1852558 · BMC genomics · 2007 · 8 claims · 7 setups

  Full-text index only

  Global protein expression profiles of cultured intestinal epithelial cell lines differ from those of intestinal epithelial scrapings in vivo

  caco-2 ht-29 hep muscle 2-d 2-de principal

• Empirical Bayes analysis of quantitative proteomics experiments.

  PMID 19829701 · PMC2759080 · PloS one · 2009 · 8 claims · 4 setups

  Full-text index only

  Developed a new empirical Bayes framework that models log2 SILAC protein ratios and is robust to non-Gaussian tails and data sparsity, unlike Gaussian mixture models or Efron's original spline-based approach

  hela predicted computational silac utr gaussian

• Profiling Selective Packaging of Host RNA and Viral RNA Modification in SARS-CoV-2 Viral Preparations.

  PMID 35186917 · PMC8851031 · Frontiers in cell and developmental biology · 2022 · 8 claims · 3 setups

  Has reproduction · 56

  SARS-CoV-2 viral preparations show selective enrichment of specific host tRNAs, tRNA fragments, and SRP RNA compared to uninfected VeroE6 cells

  veroe6 cell-free small large trna