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).
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Has reproduction · 75
Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics.
PMID 35983322 · PMC9378778 · Frontiers in microbiology · 2022 · 6 claims · 7 setups
RPL29 (60S ribosomal protein L29) is highly/consistently expressed across all COVID-19 infected groups regardless of severity, suggesting it as a novel host therapeutic target for mRNA-based nanomedicines.
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Has reproduction · 67
Optimal scaling of digital transcriptomes.
PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups
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.
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Has reproduction · 63
Extensive tissue-specific expression variation and novel regulators underlying circadian behavior.
PMID 33514540 · PMC7846174 · Science advances · 2021 · 8 claims · 8 setups
More than 1700 mostly tissue-specific cycling genes are detected across four Drosophila tissues, substantially expanding the catalog of clock-controlled genes
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Has reproduction · 50
Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.
PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups
330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.
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Has reproduction · 38
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
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).
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Has reproduction · 89
MirDIP 5.2: tissue context annotation and novel microRNA curation.
PMID 36453996 · PMC9825511 · Nucleic acids research · 2023 · 7 claims · 6 setups
mirDIP 5.2 removed eight outdated resources, added miRNATIP, and ran five prediction algorithms against miRBase and mirGeneDB miRNAs to expand and improve interaction coverage
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Has reproduction · 78
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
A protocol for dissecting mouse PFC, hippocampus, and cerebellum and generating snRNA-seq libraries can identify neuronal populations activated during social interaction.
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Has reproduction · 86
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.
PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups
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.
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Full-text index only
Searching for SNPs with cloud computing.
PMID 19930550 · PMC3091327 · Genome biology · 2009 · 8 claims · 4 setups
Crossbow combines the Bowtie short-read aligner and SOAPsnp SNP caller into a seamless, automatic Hadoop/MapReduce pipeline for whole-genome resequencing analysis