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).

Publications 1.3k Datasets 392.5k Experiments 15

System / cell line: clone ✕ Assay: clustering ✕ Clear

Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

genome poly est cdna est blast cdna
A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

PMID 11305939 · PMC31480 · Genome biology · 2001 · 8 claims · 8 setups

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SLC4A9 is a novel human NBC-like gene on chromosome 5q31 encoding a 990-amino-acid, 12-transmembrane-domain protein with high similarity to other sodium bicarbonate cotransporters

bac kidney genomic marathon genomic cdna pcr
DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

PMID 16625196 · PMC2610434 · Nature · 2006 · 8 claims · 7 setups

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A finished sequence of human chromosome 17 (78,839,971 bases, ~2.8% of the euchromatic genome) was generated.

chromosome dog macaque genomic comparative segmental
Molecular analysis of Plasmodium ovale variants.

PMID 15324543 · PMC3323326 · Emerging infectious diseases · 2004 · 8 claims · 5 setups

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P. ovale isolates separate into two genetically distinct types, classic (Nigerian I/CDC) and variant (LS), consistent across four independent gene loci.

ovale plasmodium pcr first comparative
EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics.

PMID 34805989 · PMC8598301 · NAR genomics and bioinformatics · 2021 · 8 claims · 5 setups

Has reproduction · 54

EpiDiverse Toolkit provides Nextflow-based pipelines for WGBS mapping, methylation calling, variant calling, differential methylation, and EWAS tailored to non-model plant ecology

populus nigra genome variant clustering
The vaginal bacterial communities of Japanese women resemble those of women in other racial groups.

PMID 19912342 · PMC2868947 · FEMS immunology and medical microbiology · 2010 · 7 claims · 5 setups

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The types of vaginal bacterial communities found in Japanese women closely resemble those previously found in White and Black North American women.

vaginal japanese t-rflp clone cluster
Shotgun haplotyping: a novel method for surveying allelic sequence variation.

PMID 16221968 · PMC1253838 · Nucleic acids research · 2005 · 8 claims · 7 setups

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A novel shotgun haplotyping method generates haplotypic sequences from long PCR products by shotgun sequencing both alleles concurrently and using read-pair information to separate alleles during assembly

genomic long pcr ampicillin-resistant long cloning short
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

PMID 19796657 · PMC3568755 · Journal of microbiological methods · 2009 · 8 claims · 6 setups

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The 16S rRNA V5 hypervariable region, amplified as a short ~82-base segment, provides reliable taxonomic identification of oral bacteria against public databases like HOMD.

pooled 16s sequenced topo 16s primer taxonomic
Bases and spaces: resources on the web for accessing the draft human genome.

PMID 11178254 · PMC138875 · Genome biology · 2000 · 8 claims · 8 setups

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By combining currently available genomic databases and mapping resources (GenBank/Entrez, UniGene, RH maps, BAC fingerprint maps, Ensembl, NIX), it is possible to devise strategies that fully exploit the fragmentary draft human genome sequence.

bac whole-genome draft submitted bac radiation initio
Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

PMID 15103394 · PMC393292 · PLoS biology · 2004 · 8 claims · 5 setups

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41,118 full-length human cDNAs from six high-throughput sequencing projects were exhaustively integratively characterized

genome transcriptome gene genes full-length genome cdna
A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.

PMID 18682527 · PMC2532719 · Nucleic acids research · 2008 · 8 claims · 7 setups

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Biodiversity observed by RSR analysis is consistent with that obtained by 16S rDNA analysis

faecal rsr 16s sargasso shotgun blastn-based 16s
Correlation between pre-treatment quasispecies complexity and treatment outcome in chronic HCV genotype 3a.

PMID 18613968 · PMC2483966 · Virology journal · 2008 · 7 claims · 7 setups

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Quasispecies complexity and diversity within HVR1 are lower in the SVR group than in the TF group

serum hvr1 svr rt-pcr shannon hamming
Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes.

PMID 30503143 · PMC6327112 · Cell stem cell · 2019 · 8 claims · 6 setups

Has reproduction · 30

A core set of 60 genes captures a continuous pseudotemporal disease axis from control to PD GBA-N370S iPSC-derived dopamine neurons (52 downregulated, 8 upregulated).

facs-purified facs-sorted ipsc ipsc-derived bulk single-cell facs
Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

PMID 18366763 · PMC2292204 · BMC molecular biology · 2008 · 8 claims · 8 setups

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Transcription start sites of human DYRK1A are distributed over an 800 bp region within an unmethylated CpG island

pc3 saos2 resting phoenix 5'-race-pcr rt-pcr chip-seq
The N-terminus and alpha-5, alpha-6 helices of the pro-apoptotic protein Bax, modulate functional interactions with the anti-apoptotic protein Bcl-xL.

PMID 17519046 · PMC1890283 · BMC cell biology · 2007 · 8 claims · 8 setups

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Deletion of the first 29 N-terminal amino acids (Bax 30-192) causes constitutive mitochondrial accumulation and high cytotoxicity that is poorly inhibited by Bcl-xL or Bcl-2.

jurkat drosophila hek apoptotic uas-gal4 western

Experiments

Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

Molecular analysis of Plasmodium ovale variants.

EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics.

The vaginal bacterial communities of Japanese women resemble those of women in other racial groups.

Shotgun haplotyping: a novel method for surveying allelic sequence variation.

Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

Bases and spaces: resources on the web for accessing the draft human genome.

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library.

Correlation between pre-treatment quasispecies complexity and treatment outcome in chronic HCV genotype 3a.

Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes.

Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

The N-terminus and alpha-5, alpha-6 helices of the pro-apoptotic protein Bax, modulate functional interactions with the anti-apoptotic protein Bcl-xL.