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).

• Genomic structure and alterations of homeobox gene CDX2 in colorectal carcinomas.

  PMID 10027310 · PMC2362430 · British journal of cancer · 1999 · 8 claims · 6 setups

  Full-text index only

  CDX2 expression is decreased in colorectal carcinomas in prior studies

  genomic sporadic hnpcc carcinoma standard pcr-sscp cloning

• Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae.

  PMID 38918881 · PMC11373658 · G3 (Bethesda, Md.) · 2024 · 8 claims · 8 setups

  Has reproduction · 81

  Improved E. guineensis genome assembly achieved with substantially increased continuity and completeness compared to prior assemblies

  guineensis oleifera root pacbio proximity optical

• A near complete genome for goat genetic and genomic research.

  PMID 34507524 · PMC8434745 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

  Has reproduction · 89

  Saanen_v1 is a high-quality de novo goat genome assembly from a male Saanen buck, including the first goat Y chromosome scaffold.

  saanen goat testicular saanen_v1 pacbio illumina hi-c

• Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy.

  PMID 36596305 · PMC9839361 · Cell host & microbe · 2023 · 8 claims · 7 setups

  Has reproduction · 80

  After long-term ART, intact HIV-1 proviruses are predominantly integrated in heterochromatin locations, most prominently centromeric satellite/micro-satellite DNA.

  pbmc single cd4 flip-seq mip-seq prip-seq

• The SARS-CoV-2 subgenome landscape and its novel regulatory features.

  PMID 33713597 · PMC7927579 · Molecular cell · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  Template switching in SARS-CoV-2 can occur bidirectionally, generating diverse subgenomes through successive template-switching events

  vero caco-2 sars-cov-2 ngs nanopore northern

• Bayesian transcriptome assembly.

  PMID 25367074 · PMC4397945 · Genome biology · 2014 · 8 claims · 8 setups

  Has reproduction · 68

  Bayesembler, a probabilistic transcriptome assembler built on a Bayesian model of the RNA sequencing process with Gibbs sampling over expressed candidates, abundances and read assignments, is introduced.

  k562 embryonic dendritic rna-seq simulated paired-end long-read

• A crowdsourced set of curated structural variants for the human genome.

  PMID 32559231 · PMC7329145 · PLoS computational biology · 2020 · 7 claims · 6 setups

  Has reproduction · 71

  A crowdsourcing web application (SVCurator) enables curators to manually review and label large indels and SVs by displaying short, long, and linked read sequencing evidence from GIAB HG002.

  giab illumina haplotype-partitioned manual

• Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia.

  PMID 18248679 · PMC2277413 · BMC genomics · 2008 · 8 claims · 4 setups

  Full-text index only

  Chromatin remodelling-associated genes SMARCC1, NCOR1, MRFAP1 and MORF4L2 are upregulated during progression of cervical intraepithelial neoplasia

  cervical independent computational long real-time gene

• Free circular introns with an unusual branchpoint in neuronal projections.

  PMID 31697236 · PMC6879206 · eLife · 2019 · 8 claims · 7 setups

  Has reproduction · 99

  A set of free circular introns with a non-canonical (C) branchpoint is enriched in distal neuronal projections; these appear to be tailless lariats that escape debranching.

  hippocampal cytoplasmic rrna-depleted polya-site ribosome

• Chromosome-level genome of the long-tailed marine-living ornate spiny lobster, Panulirus ornatus.

  PMID 38909031 · PMC11193758 · Scientific data · 2024 · 6 claims · 5 setups

  Has reproduction · 80

  A chromosome-level genome of P. ornatus spanning 2.65 Gb was assembled with a contig N50 of 51.05 Mb, anchoring 99.11% of sequences to 73 chromosomes.

  ornatus wgs hi-c rna-seq

• Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.

  PMID 36295018 · PMC9605557 · Life (Basel, Switzerland) · 2022 · 8 claims · 7 setups

  Has reproduction

  Transposable elements make up nearly 45% of the human genome, vastly exceeding the ~1.5% that is protein-coding.

  genome normal drosophila long short-read whole-genome synthetic

• Analysis of TSG101 tumour susceptibility gene transcripts in cervical and endometrial cancers.

  PMID 10027311 · PMC2362423 · British journal of cancer · 1999 · 6 claims · 5 setups

  Full-text index only

  Abnormal (aberrant) TSG101 transcripts are common in both cancerous and non-cancerous cervical/endometrial tissue as well as in normal peripheral mononuclear cells

  cervical peripheral rt-pcr southern long

• Molecular variants of the ATM gene in Hodgkin's disease in children.

  PMID 14735203 · PMC2409549 · British journal of cancer · 2004 · 8 claims · 4 setups

  Full-text index only

  Missense variants of the ATM gene occur in childhood Hodgkin lymphoma but at low frequency (9%), and thus do not play a major role in oncogenesis of the disease

  frozen matched paired rt-pcr germ-line sscp

• Accurate whole human genome sequencing using reversible terminator chemistry.

  PMID 18987734 · PMC2581791 · Nature · 2008 · 8 claims · 7 setups

  Full-text index only

  A novel sequencing platform using fluorescent reversible terminator nucleotides on clonally amplified single-molecule DNA clusters generates several billion bases of accurate sequence per experiment at low cost.

  bac flow-sorted same yoruba reversible snp targeted

• Whole genome sequences of Yersinia pestis strains of ancient phylogenetic branch 0.ANT5 isolated in the 21st century in the Tien-Shan in Kyrgyzstan.

  PMID 39206953 · PMC11478111 · Microbiology resource announcements · 2024 · 6 claims · 5 setups

  Full-text index only

  Eleven Yersinia pestis strains of the ancient phylogenetic branch 0.ANT5, isolated in the Tien Shan focus (Kyrgyzstan) in 1952, 1971, and 2013–2023, were hybrid-sequenced (MGI short reads + ONT long reads)

  yersinia whole-genome hybrid plasmid

• Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.

  PMID 30010758 · PMC6065499 · GigaScience · 2018 · 6 claims · 7 setups

  Has reproduction · 91

  A hybrid de novo assembly combining high-depth Illumina short reads (376.6X) and low-depth PacBio long reads (9.7X) produced the YO draft genome Ogye_1.1 with contig and scaffold NG50 of 362.3 Kbp and 16.8 Mbp.

  yeonsan tissues ogye_1.1 locus whole-genome sequencing reduced

• Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis.

  PMID 26333840 · PMC4632049 · G3 (Bethesda, Md.) · 2015 · 8 claims · 8 setups

  Has reproduction · 58

  Virulence attenuation in the longer-passaged Bd isolate (JEL427-P39) is associated with loss of chromosome copy number relative to the shorter-passaged, more virulent isolate (JEL427-P9)

  strain jel427-p9 genes whole-genome snp indel

• Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) enriettii, Isolate CUR178, Strain LV763.

  PMID 34498918 · PMC8428246 · Microbiology resource announcements · 2021 · 7 claims · 7 setups

  Has reproduction · 80

  Complete chromosome-scale genome sequence of Leishmania (Mundinia) enriettii isolate CUR178, strain LV763 was assembled using combined short-read and long-read sequencing

  leishmania whole-genome long-read genome

• Chromosome-Scale Assembly of the Complete Genome Sequence of Porcisia hertigi, Isolate C119, Strain LV43.

  PMID 34647802 · PMC8515887 · Microbiology resource announcements · 2021 · 6 claims · 8 setups

  Has reproduction · 88

  The complete, chromosome-scale genome sequence of Porcisia hertigi (isolate C119, strain LV43) was assembled using combined short- and long-read sequencing technologies.

  porcisia hertigi parasite extraction short-read

• Chromosome-Scale Assembly of the Complete Genome Sequence of Leishmania (Mundinia) orientalis, Isolate LSCM4, Strain LV768.

  PMID 34498920 · PMC8428255 · Microbiology resource announcements · 2021 · 6 claims · 8 setups

  Has reproduction · 78

  The complete genome sequence of Leishmania (Mundinia) orientalis, isolate LSCM4, strain LV768, was determined using combined short-read and long-read sequencing.

  leishmania orientalis culture extraction short-read