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 · 27
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.
PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups
A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.
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Has reproduction · 61
Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.
PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups
Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.
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Has reproduction · 73
Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance.
PMID 25943316 · PMC4422317 · BMC genomics · 2015 · 7 claims · 6 setups
De novo assembly of the S. fruticosa transcriptome (Velvet/Oases k-45, CDHIT-EST) produced 54,526 high-quality unigenes with N50 of 957 bp
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Has reproduction · 72
Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.
PMID 29041914 · PMC5644144 · BMC genomics · 2017 · 8 claims · 8 setups
A high-quality ~375 Mbp draft genome and transcriptome of Holacanthella duospinosa was assembled and annotated, providing a genomic resource for hexapod evolution.
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Has reproduction · 95
transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation.
PMID 37016291 · PMC10074830 · BMC bioinformatics · 2023 · 6 claims · 7 setups
transXpress is a Snakemake pipeline that streamlines de novo transcriptome assembly, quantification, and annotation for non-model organisms
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Has reproduction · 80
Structure of the intergenic spacers in chicken ribosomal DNA.
PMID 31655542 · PMC6815422 · Genetics, selection, evolution : GSE · 2019 · 7 claims · 6 setups
Long-read PacBio sequencing of a chicken NOR-containing BAC clone resolved three complete IGS sequences plus rRNA gene clusters that are otherwise missing from genome assemblies.
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Has reproduction · 90
Gap-free telomere-to-telomere haplotype assembly of the tomato hind (Cephalopholis sonnerati).
PMID 39578472 · PMC11584678 · Scientific data · 2024 · 8 claims · 8 setups
Two T2T gap-free haplotype assemblies of C. sonnerati (YSFRI_Csonn_HA_1.0 and YSFRI_Csonn_HB_1.0) were successfully generated, each spanning 24 chromosomes with no gaps.
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Has reproduction · 100
Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice.
PMID 29123534 · PMC5662881 · Frontiers in plant science · 2017 · 8 claims · 8 setups
NGS/RNA-seq enables unbiased, hypothesis-free detection of multiple known and emergent plant viruses, unlike RT-PCR which only detects one or a few known viruses per test.
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Has reproduction · 91
Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.
PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 7 claims · 8 setups
175 conserved and 83 novel miRNAs were identified mainly in one bud and two tender leaves of tea plant via small RNA sequencing combined with genome survey data