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).

• 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

• A data-driven estimation of the ribosome drop-off rate in S. cerevisiae reveals a correlation with the genes length.

  PMID 38638702 · PMC11025885 · NAR genomics and bioinformatics · 2024 · 8 claims · 7 setups

  Has reproduction · 98

  Ribosome drop-off events occur at a significant rate in S. cerevisiae cultured in standard conditions

  cerevisiae ribo-seq ribosome rna-seq read

• De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis.

  PMID 34072576 · PMC8227486 · Genes · 2021 · 6 claims · 8 setups

  Has reproduction · 87

  A consensus transcriptome assembled by combining reads from five independent studies is the most complete E. gracilis transcriptome released to date, outperforming the two previously available transcriptomes (GEFR01 and GDJR01).

  euglena gracilis five transcriptomes bulk novo transcriptome

• MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets.

  PMID 32256520 · PMC7089958 · Frontiers in genetics · 2020 · 7 claims · 8 setups

  Has reproduction · 50

  MasterOfPores is a NextFlow-based, containerized workflow that processes raw FAST5 direct RNA sequencing data through base-calling, demultiplexing, filtering, QC, mapping, and quantification, plus downstream RNA modification and polyA tail length analyses.

  saccharomyces cerevisiae barcoded direct base-calling read

• RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

  PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 38

  A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

  gossypium uppermost root reads bulk leaf rt-qpcr

• 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

• Transcriptome annotation using tandem SAGE tags.

  PMID 17709346 · PMC2034470 · Nucleic acids research · 2007 · 8 claims · 7 setups

  Full-text index only

  A novel algorithm pairs tandem SAGE tags anchored on two different restriction sites (CATG and GATC) to define tag-delimited genomic sequences (TDGS)

  monocyte-derived unigene genome macrophage sage modified virtual

• A global change in RNA polymerase II pausing during the Drosophila midblastula transition.

  PMID 23951546 · PMC3743134 · eLife · 2013 · 8 claims · 8 setups

  Has reproduction · 71

  Massive de novo recruitment of Pol II (and TBP) with widespread pausing occurs during the Drosophila midblastula transition, at 4007 promoters (~one third of all genes).

  hand-sorted drosophila chip-seq immunostaining dapi

• The 10 sea urchin receptor for egg jelly proteins (SpREJ) are members of the polycystic kidney disease-1 (PKD1) family.

  PMID 17629917 · PMC1934368 · BMC genomics · 2007 · 8 claims · 5 setups

  Full-text index only

  Sea urchins possess 10 SpREJ (PKD1 family) genes, compared to five in humans, all defined by possession of a ~600 residue REJ domain

  strongylocentrotus sprej purpuratus full-length cdna secondary real-time

• Identification of common genetic variation that modulates alternative splicing.

  PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

  Full-text index only

  Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

  ceph lcls skipped additional rt-pcr snp resequencing

• 93rd Annual Meeting of the American Association for Cancer Research, San Francisco, CA, USA, 6-10 April 2002.

  PMID 12100742 · PMC138737 · Breast cancer research : BCR · 2002 · 8 claims · 8 setups

  Full-text index only

  Serial analysis of gene expression identifies genes preferentially expressed in ductal carcinoma in situ

  breast laser serum bladder cdna western seldi-tof

• Optimal scaling of digital transcriptomes.

  PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.

  tissues bodymap mapped 16-sample bulk read transcript

• In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.

  PMID 15871745 · PMC1156887 · BMC genomics · 2005 · 7 claims · 6 setups

  Full-text index only

  Only 14±2% of canine transcripts were detected by U133A probe sets versus 49±6% of human transcripts when hybridized to the same chip

  canine tissues hg-u133a probes microarray sequence ortholog

• Genome-wide estimation of transcript concentrations from spotted cDNA microarray data.

  PMID 16204447 · PMC1243803 · Nucleic acids research · 2005 · 8 claims · 3 setups

  Full-text index only

  A Bayesian model incorporating experimental covariates (array, pen, probe, dye, scanning) can estimate absolute transcript concentrations from spotted microarray intensities without needing calibration of each sample or gene individually

  cervix same spotted quantitative

• Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo.

  PMID 35784648 · PMC9243631 · Cell reports methods · 2022 · 8 claims · 7 setups

  Has reproduction · 66

  A purification-free hyperTRIBE adaptation using FMR1-ADARcd-V5 identifies stress granule RNAs via condition-specific A-to-G editing read out by VASA-seq.

  drosophila predicted vasa-seq single-cell single-molecule

• Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

  PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.

  single methanol-fixed reads slice mrna-seq light-microscopy read

• Interpretation of genomic data: questions and answers.

  PMID 18582627 · PMC2528831 · Seminars in hematology · 2008 · 8 claims · 6 setups

  Full-text index only

  The main challenge in using genomic technology in cancer research is not managing the volume of data but the proper design, analysis, and reporting of studies.

  genetically wound tumor breast gene expression comparative

• Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

  PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

  Full-text index only

  1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

  genome rhesus vega-annotated tpas transcript-to-genome same synteny

• Fluent genomics with  plyranges and  tximeta.

  PMID 32528659 · PMC7243206 · F1000Research · 2020 · 6 claims · 2 setups

  Has reproduction · 69

  A simple three-step workflow (import, model, integrate) using R/Bioconductor enables fluent, reproducible genomics data analysis integrating RNA-seq and ATAC-seq.

  ipsc-derived bulk atac-seq

• Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming.

  PMID 31515287 · PMC6771397 · Genome research · 2019 · 8 claims · 5 setups

  Has reproduction · 75

  XCR during iPSC reprogramming is hierarchical, with subsets of X-linked genes reactivating early, intermediate, late, and very late.

  mus embryonic reprogramming ipsc allele-specific fluorescence-activated live