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 28

System / cell line: pcr ✕ Assay: race ✕ Clear

B lymphocytes of xeroderma pigmentosum or Cockayne syndrome patients with inherited defects in nucleotide excision repair are fully capable of somatic hypermutation of immunoglobulin genes.

PMID 9236193 · PMC2198998 · The Journal of experimental medicine · 1997 · 6 claims · 3 setups

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EBV-transformed B cells from NER-defective patients (XP-B, XP-D, XP-V, CS-A) show a high frequency of point mutations in Ig heavy and light chain V regions but not in C regions

ebv-transformed cloned rt-pcr southern sequence
EGASP: the human ENCODE Genome Annotation Assessment Project.

PMID 16925836 · PMC1810551 · Genome biology · 2006 · 8 claims · 6 setups

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Best-performing computational gene prediction methods correctly predict at least one transcript for close to 70% of annotated genes in the ENCODE regions.

encode computational manual rt-pcr
Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

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Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

liver genomic tissues embryos rt-pcr genomic secondary
BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification.

PMID 35704392 · PMC9546494 · The Plant journal : for cell and molecular biology · 2022 · 8 claims · 6 setups

Has reproduction · 94

BaRTv2.18 is the most comprehensive and resolved reference transcriptome in barley to date, containing 39,434 genes and 148,260 transcripts

barley pacbio illumina read
Identification of transcription start sites and preferential expression of select CB2 transcripts in mouse and human B lymphocytes.

PMID 19757078 · PMC2843092 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2009 · 7 claims · 8 setups

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Human B cells express one CB2 transcript while mouse B cells express three CB2 transcripts

splenocytes pbmc-derived splenic genbank race pcr quantitative
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
Characterization of rabbit myocilin: Implications for human myocilin glycosylation and signal peptide usage.

PMID 12697062 · PMC156599 · BMC genetics · 2003 · 8 claims · 6 setups

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Rabbit MYOC encodes a 490 amino acid, 54,882-Da protein that is 84% identical overall to human myocilin

rabbit gtm66 myoc myocilin cdna sds-page transfection
Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

PMID 17705821 · PMC2045109 · BMC molecular biology · 2007 · 8 claims · 8 setups

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Multiple alternatively spliced 5'-UTR isoforms of human PPARdelta mRNA differ in translation efficiency

placenta five lines huh7 5'-race rt-pcr real-time
Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

PMID 18588709 · PMC2464599 · BMC genetics · 2008 · 8 claims · 7 setups

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Porcine PNAS-4 encodes a 194-amino-acid protein that localizes to the Golgi complex

chinese tissues skeletal pk15 full-length real-time gfp
GENCODE: producing a reference annotation for ENCODE.

PMID 16925838 · PMC1810553 · Genome biology · 2006 · 8 claims · 8 setups

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GENCODE annotation combines initial manual annotation by HAVANA, experimental validation, and refinement based on results to identify protein-coding genes in ENCODE regions

tissues encode rt-pcr comparative automated
Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

PMID 15169551 · PMC441375 · BMC genomics · 2004 · 8 claims · 8 setups

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A very large, previously uncharacterized gene, AHI1, containing WD40 and SH3 domains was discovered in the candidate interval

cdna image hbs1l ahi1 rt-pcr est northern
Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution.

PMID 17480121 · PMC1865561 · PLoS genetics · 2007 · 7 claims · 8 setups

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KLF14 is a novel imprinted gene showing monoallelic maternal expression in embryonic and extra-embryonic tissues of both human and mouse

embryonic fetal monochromosomal fibroblasts allele-specific rt-pcr chromatin
GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats.

PMID 16698959 · PMC3303178 · Nucleic acids research · 2006 · 7 claims · 5 setups

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GREM enables genome-wide isolation and quantitative analysis of transcriptionally active (promoter-active) repetitive elements while excluding read-through transcript background

testicular genomic coli grem rt-pcr race
Novel SCN1A frameshift mutation with absence of truncated Nav1.1 protein in severe myoclonic epilepsy of infancy.

PMID 18680191 · PMC3708306 · American journal of medical genetics. Part A · 2008 · 8 claims · 3 setups

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A novel heterozygous SCN1A frameshift mutation, c.3608delA (p.Gln1203HisfsX4), was identified in a postmortem SMEI patient, located in the D2-D3 intracellular linker of NaV1.1.

postmortem cdna western quantitative
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

Has reproduction · 91

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

camellia sinensis small genome mirna
Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups

Has reproduction · 70

AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella

head-kidney idella assembled il-12p40α rna-seq rt-qpcr pcr
Genome-wide screening of potential RNase Y-processed mRNAs in the M49 serotype Streptococcus pyogenes NZ131.

PMID 29900693 · PMC6460267 · MicrobiologyOpen · 2019 · 8 claims · 7 setups

Has reproduction · 57

RNase Y selectively processes GAS mRNA, but its overall impact is confined to a limited set of virulence factor transcripts.

streptococcus rna-seq tiling northern
52-kD SS-A/Ro: genomic structure and identification of an alternatively spliced transcript encoding a novel leucine zipper-minus autoantigen expressed in fetal and adult heart.

PMID 7561701 · PMC2192297 · The Journal of experimental medicine · 1995 · 7 claims · 7 setups

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The 52-kD SS-A/Ro gene spans 10 kb of DNA and is composed of seven exons, with the translation initiation codon in exon 2 and the leucine zipper encoded by exon 4.

molt-4 placental placenta fetal cdna genomic race
Characterization of a new full length TMPRSS3 isoform and identification of mutant alleles responsible for nonsyndromic recessive deafness in Newfoundland and Pakistan.

PMID 15447792 · PMC523852 · BMC medical genetics · 2004 · 8 claims · 8 setups

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TMPRSS3 mutations were identified in four additional Pakistani families with recessive, nonsyndromic congenital deafness co-segregating with DFNB8/B10 haplotypes

pakistani affected retina tissues linkage sanger race
Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups

Has reproduction · 74

Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.

intestinalis same rna-seq strand-specific technical reverse

Experiments

B lymphocytes of xeroderma pigmentosum or Cockayne syndrome patients with inherited defects in nucleotide excision repair are fully capable of somatic hypermutation of immunoglobulin genes.

EGASP: the human ENCODE Genome Annotation Assessment Project.

Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification.

Identification of transcription start sites and preferential expression of select CB2 transcripts in mouse and human B lymphocytes.

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

Characterization of rabbit myocilin: Implications for human myocilin glycosylation and signal peptide usage.

Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

GENCODE: producing a reference annotation for ENCODE.

Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution.

GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats.

Novel SCN1A frameshift mutation with absence of truncated Nav1.1 protein in severe myoclonic epilepsy of infancy.

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.

Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

Genome-wide screening of potential RNase Y-processed mRNAs in the M49 serotype Streptococcus pyogenes NZ131.

52-kD SS-A/Ro: genomic structure and identification of an alternatively spliced transcript encoding a novel leucine zipper-minus autoantigen expressed in fetal and adult heart.

Characterization of a new full length TMPRSS3 isoform and identification of mutant alleles responsible for nonsyndromic recessive deafness in Newfoundland and Pakistan.

Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.