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).

• Biotin tagging coupled with amino acid-coded mass tagging for efficient and precise screening of interaction proteome in mammalian cells.

  PMID 19834888 · PMC4302342 · Proteomics · 2009 · 7 claims · 7 setups

  Full-text index only

  BioCAT (biotin tagging + AACT) enables highly sensitive and accurate single-step screening of mammalian protein-protein interactions without establishing a stable cell line

  293t standard nk92mi list western sds-page nanolc-ms

• COMP mutation screening as an aid for the clinical diagnosis and counselling of patients with a suspected diagnosis of pseudoachondroplasia or multiple epiphyseal dysplasia.

  PMID 15756302 · PMC2673054 · European journal of human genetics : EJHG · 2005 · 8 claims · 4 setups

  Full-text index only

  COMP mutations were identified in 78% of families referred with PSACH

  genomic sequence subset pcr bidirectional sequence

• Proteomics identifies multipotent and low oncogenic risk stem cells of the spleen.

  PMID 20005973 · PMC2891339 · The international journal of biochemistry & cell biology · 2010 · 8 claims · 5 setups

  Full-text index only

  CD45- splenic stem cell-specific proteins are identical to core iPS/ES markers OCT3/4, SOX2, KLF4, c-MYC and NANOG.

  spleen cd45 hox11+ lc-ms rt-pcr immunofluorescence

• PigGIS: Pig Genomic Informatics System.

  PMID 17090590 · PMC1669765 · Nucleic acids research · 2007 · 7 claims · 7 setups

  Full-text index only

  PigGIS identified 15,700 pig consensus sequences covering 18.5 Mb of homologous human exons

  million pig matched wgs blastx repeat sequence

• 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

• Global variation in copy number in the human genome.

  PMID 17122850 · PMC2669898 · Nature · 2006 · 8 claims · 6 setups

  Full-text index only

  A first-generation CNV map of the human genome was constructed from 270 HapMap individuals across four populations, identifying 1,447 CNV regions covering ~360 Mb (12%) of the genome.

  hapmap subset blood snp array karyotyping

• Detecting tipping points of complex diseases by network information entropy.

  PMID 38960408 · PMC11221888 · Briefings in bioinformatics · 2024 · 8 claims · 4 setups

  Has reproduction · 78

  NIEE can detect critical states or tipping points in diverse data types, including bulk and single-sample expression data

  real stringdb individual genes network background sample-specific

• Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

  PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups

  Has reproduction · 54

  Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes

  breast epcam+cd45-cd8a-cd4-cd19-cd3e cancer identified single-cell differential crispr-cas9

• 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

• A novel mutation and phenotypes in phosphodiesterase 6 deficiency.

  PMID 18723146 · PMC2593460 · American journal of ophthalmology · 2008 · 8 claims · 8 setups

  Full-text index only

  A high-throughput arRP genotyping microarray (APEX technology) combined with sequencing can efficiently identify disease-associated alleles across 17 arRP genes in RP patients

  blood-extracted family 8-member pde6-deficient arrp direct pedigree

• Phosphoproteomic analysis of human embryonic stem cells.

  PMID 19664994 · PMC2726933 · Cell stem cell · 2009 · 8 claims · 6 setups

  Full-text index only

  MDLC-MS/MS phosphoproteomics identified 2546 phosphorylation sites on 1602 phosphoproteins in undifferentiated hESCs and their differentiated derivatives

  esc hescs hesc-derived undifferentiated mdlc-ms immunocytochemistry western

• Proteomic-based identification of maternal proteins in mature mouse oocytes.

  PMID 19646285 · PMC2730056 · BMC genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  625 different proteins were identified from 2700 zona pellucida-free mature mouse MII oocytes, the largest oocyte proteome catalog to date

  mature mii identified tissues sds-page acid gene

• Determination of glycosylation sites and site-specific heterogeneity in glycoproteins.

  PMID 19700364 · PMC2749913 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

  Full-text index only

  Mass spectrometry has emerged as the premier tool for structural determination of oligosaccharides/glycans and glycopeptides

  glycoproteins n-linked serum complex maldi tryptic nonspecific

• The manganese transporter SLC39A8 links alkaline ceramidase 1 to inflammatory bowel disease.

  PMID 38839750 · PMC11153611 · Nature communications · 2024 · 8 claims · 8 setups

  Has reproduction · 70

  Intestinal epithelial cell-specific deletion of Slc39a8 causes systemic manganese (Mn) deficiency in blood and multiple organs.

  c57bl frozen tissues slc39a8-iec qpcr immunofluorescence icp-ms

• NETISCE: a network-based tool for cell fate reprogramming.

  PMID 35725577 · PMC9209484 · NPJ systems biology and applications · 2022 · 8 claims · 4 setups

  Has reproduction · 85

  NETISCE predicts cell fate reprogramming targets in static (GRN/signaling) networks without needing full kinetic parameterization of a dynamical model.

  ascidian pluripotent drosophila signal fvs-finding sfa

• A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

  PMID 17186946 · PMC1860054 · Molecular & cellular proteomics : MCP · 2007 · 8 claims · 8 setups

  Full-text index only

  Three complementary membrane-enrichment proteomic methods (lectin affinity, biotin/NeutrAvidin affinity, free flow electrophoresis) combined with LC-MS/MS identify 136 transmembrane proteins in human platelets, including many novel ones.

  washed platelets tryptic hek293t lc-ms free longsage

• Unraveling the histone's potential: a proteomics perspective.

  PMID 18849650 · PMC2662511 · Epigenetics · 2008 · 8 claims · 8 setups

  Full-text index only

  Mass spectrometry can determine the full repertoire of histone PTMs, their residue-specific location, and combinatorial patterns without requiring prior knowledge of the modification, unlike antibody-based methods

  histone overexpressed lysate top-down middle-down quantitative

• Proteomics studies reveal important information on small molecule therapeutics: a case study on plasma proteins.

  PMID 18973825 · PMC7185545 · Drug discovery today · 2008 · 8 claims · 8 setups

  Full-text index only

  Abundant plasma proteins (albumin, IgG, transferrin) act as 'molecular sponges' that bind and transport low molecular weight proteins/peptides and drugs, extending their half-life by preventing rapid renal clearance.

  blood schizophrenia sjl serum proteomic differential comparative

• Prevalence and penetrance of BRCA1 and BRCA2 mutations in a population-based series of breast cancer cases. Anglian Breast Cancer Study Group.

  PMID 11044354 · PMC2408797 · British journal of cancer · 2000 · 6 claims · 4 setups

  Full-text index only

  BRCA1 and BRCA2 mutations are rare in the general population and account for only a small fraction of all breast cancer in the UK

  genomic pedigrees first-degree study pcr pedigree-based age

• Modeling chromosomes in mouse to explore the function of genes, genomic disorders, and chromosomal organization.

  PMID 16839184 · PMC1500809 · PLoS genetics · 2006 · 8 claims · 8 setups

  Full-text index only

  Cre/loxP recombination in ES cells can generate megabase-scale deletions, duplications, and inversions depending on loxP orientation, cis/trans configuration, and cell cycle stage

  hybrid recombinant mice homologous cre clone