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).

• EpiToolKit--a web server for computational immunomics.

  PMID 18440979 · PMC2447732 · Nucleic acids research · 2008 · 7 claims · 3 setups

  Full-text index only

  EpiToolKit is a web server integrating five MHC class I and two MHC class II epitope prediction methods in a unified, user-friendly interface.

  randomly novel minor mhc polymorphic

• RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data.

  PMID 36339261 · PMC9626663 · iScience · 2022 · 8 claims · 4 setups

  Has reproduction · 79

  RetroSnake is an end-to-end, modular, computationally efficient Snakemake pipeline for detecting HERV-K insertions in short-read NGS data, from raw alignment files to an annotated interactive HTML report

  wgs single whole-genome nested capillary

• Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina.

  PMID 14519200 · PMC328454 · Genome biology · 2003 · 8 claims · 5 setups

  Full-text index only

  Annotation of 8,633 high-quality non-mitochondrial/non-ribosomal ESTs shows 57% represent known genes and 43% are unknown or novel, with M15E having the highest proportion of novel ESTs

  embryonic high-quality unique m15e est sequence comparative

• Genome informatics: taming the avalanche of genomic data.

  PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

  Full-text index only

  Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

  genes arabidopsis genome vertebrate comparative conservation whole-genome

• 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

  Full-text index only

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

  k-562 targeted sanger

• 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

• Lack of involvement of known DNA methyltransferases in familial hydatidiform mole implies the involvement of other factors in establishment of imprinting in the human female germline.

  PMID 12546714 · PMC149328 · BMC genetics · 2003 · 8 claims · 5 setups

  Full-text index only

  A human oocyte-specific DNMT1 isoform (DNMT1o), driven by a novel upstream exon 1o, is expressed in mature oocytes and early embryos but not in somatic tissues

  oocytes genomic fbhm population rt-pcr est direct

• Evolutionarily conserved and diverged alternative splicing events show different expression and functional profiles.

  PMID 16195578 · PMC1240112 · Nucleic acids research · 2005 · 8 claims · 5 setups

  Full-text index only

  Alternative splices in 10,818 human-mouse gene pairs can be classified as conserved, novel, or diverged based on genomic and transcript-level cross-species comparison.

  orthologous diverse tissues gene comparative est microarray

• GENCODE: producing a reference annotation for ENCODE.

  PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups

  Full-text index only

  GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions

  tissues encode rt-pcr comparative automated

• Genetic and biochemical studies in Argentinean patients with variegate porphyria.

  PMID 18570668 · PMC2467414 · BMC medical genetics · 2008 · 8 claims · 6 setups

  Full-text index only

  All 18 studied VP patients harbored PPOX gene mutations in heterozygous state

  peripheral blood relative urine pcr rt-pcr enzyme

• New mutations in the PKD1 gene in Czech population with autosomal dominant polycystic kidney disease.

  PMID 19686598 · PMC2736583 · BMC medical genetics · 2009 · 8 claims · 7 setups

  Full-text index only

  DGGE screening of the non-duplicated PKD1 region detects likely pathogenic mutations in Czech ADPKD patients

  genomic pcr polycystin-1 czech denaturing sanger family

• Integration of a neuronal RNAseq dataset with the draft Gryllus bimaculatus transcriptome refines gene predictions and highlights potential systematic response to injury.

  PMID 42054377 · PMC13127959 · PloS one · 2026 · 8 claims · 7 setups

  Full-text index only

  Integrating prothoracic ganglion RNAseq data with the draft genome refines gene predictions, adding 3,868 novel genes and 9,172 new transcript isoforms (including non-coding transcripts)

  bimaculatus prothoracic differentially gbig rna-seq genome differential

• Exome sequencing in 38 patients with intracranial aneurysms and subarachnoid hemorrhage.

  PMID 32367296 · PMC7419486 · Journal of neurology · 2020 · 8 claims · 6 setups

  Has reproduction · 78

  Sequence variants in PCNT, RNF213 and THSD1 support a role as susceptibility factors for cerebrovascular disease (UIA/aSAH)

  unrelated affected additional 75-patient exome sanger gene

• Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice.

  PMID 27655631 · PMC5175363 · Nucleic acids research · 2016 · 8 claims · 8 setups

  Has reproduction · 10

  Embryonic ATZ exposure affects meiosis, spermiogenesis and reduces spermatozoa number in F3 generation male mice

  testis dissociated epididymis chip-seq strand-specific h&e

• Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs.

  PMID 38594607 · PMC11003151 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  H3K27ac ChIP-seq and RNA-seq were used to construct eRNA expression profiles across multiple tissues in Enshi Black (ES) and Duroc pigs, revealing tissue-level eRNA regulatory landscapes

  longissimus muscle snps pig h3k27ac strand-specific starr-seq

• Protocol for the generation of single-nuclei RNA-seq libraries and quantification of heterogeneous cell types activated during social interaction.

  PMID 39423127 · PMC11532268 · STAR protocols · 2024 · 7 claims · 5 setups

  Has reproduction · 78

  A protocol for dissecting mouse PFC, hippocampus, and cerebellum and generating snRNA-seq libraries can identify neuronal populations activated during social interaction.

  medial hippocampus cerebellum brain single-nuclei nuclei bulk

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

  PMID 34308351 · PMC8294687 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups

  Has reproduction

  miRge3.0 is a Python 3-based small RNA-seq and tRF analysis pipeline that improves on miRge2.0 (which was Python 2.7-based)

  sra synthetic qiagen-processed same small umi mirna

• 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

• Association of replication error positive phenotype with lymphocyte infiltration in endometrial cancers.

  PMID 9818024 · PMC5921952 · Japanese journal of cancer research : Gann · 1998 · 7 claims · 4 setups

  Full-text index only

  RER+ phenotype (microsatellite instability at ≥2 of 7 loci) occurs in a subset (21-23%) of sporadic endometrioid endometrial adenocarcinomas but not in other histological types or endometrial hyperplasia

  paired tumor hematoxylin-eosin-stained pcr sequencing histopathological

• 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