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 56

System / cell line: clones ✕ Assay: cdna ✕ Clear

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
A catalog of human cDNA expression clones and its application to structural genomics.

PMID 15345055 · PMC522878 · Genome biology · 2004 · 8 claims · 7 setups

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A high-throughput screening approach can identify human cDNA clones from the hEx1 library that express soluble protein in E. coli

hex1 ensembl coli recombinant small-scale tag-sequencing blastp
Characterization of 954 bovine full-CDS cDNA sequences.

PMID 16305752 · PMC1314900 · BMC genomics · 2005 · 7 claims · 8 setups

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954 bovine full-length insert cDNA (bFLIC) clones representing 762 distinct loci were sequenced and characterized

bovine translated bflic sequence est primer-walking blastp
IgVH genes from different anatomical regions, with different histopathological patterns, of a rheumatoid arthritis patient suggest cyclic re-entry of mature synovial B-cells in the hypermutation process.

PMID 11056671 · PMC17813 · Arthritis research · 2000 · 8 claims · 5 setups

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Somatically mutated IgVH genes with amino acid deletions and mixed IgV molecules were found in all three anatomical regions, suggesting a novel pathway for generating (auto)antibody specificities

synovial same cryosections formalin-fixed cdna seminested double
hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

PMID 17207965 · PMC4647941 · Genomics · 2007 · 8 claims · 7 setups

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hORFeome v3.1 is a resource of 12,212 cloned human ORFs representing 10,214 genes, a 51% expansion over hORFeome v1.1

mgc cloned orfs genome gateway orf blat
The effect of IL-13 and IL-13R130Q, a naturally occurring IL-13 polymorphism, on the gene expression of human airway smooth muscle cells.

PMID 15661077 · PMC548512 · Respiratory research · 2005 · 6 claims · 3 setups

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IL-13 and IL-13R130Q modulate the same set of genes in human airway smooth muscle cells (HASMC)

airway hasmc cdna taqman flow
Survey of transcripts in the adult Drosophila brain.

PMID 11276425 · PMC30707 · Genome biology · 2001 · 8 claims · 4 setups

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The adult Drosophila brain cDNA library contains approximately 6.75 million independent clones

drosophila randomly brain cdna reverse sequence
Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

PMID 15860772 · PMC1087780 · Nucleic acids research · 2005 · 8 claims · 8 setups

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Constructed a large-scale dataset of 6876 human alternative protein isoforms from 2624 genes by combining H-Invitational full-length cDNA data and SwissProt VARSPLIC entries

full-length alternative refseq genome pairwise mitochondrial signal
Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

PMID 18294402 · PMC2287170 · BMC genomics · 2008 · 8 claims · 6 setups

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Constructed full-length-enriched cDNA libraries and determined 85,721 EST sequences and 9407 full-insert sequences from cynomolgus macaque brain (7 regions), testis, and liver

cynomolgus 3-year-old macaque est full-insert oligonucleotide
Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

PMID 12908878 · PMC194569 · BMC genomics · 2003 · 8 claims · 7 setups

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XRRA1 is a novel gene down-regulated ~2-fold in XR-resistant HCT116 Clone2_XRR relative to HCT116 Clone10, identified via cDNA microarray

hct116 macaque cos-7 genomic cdna est molecular
A genome annotation-driven approach to cloning the human ORFeome.

PMID 15461802 · PMC545604 · Genome biology · 2004 · 8 claims · 8 setups

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Existing human cDNA clone collections together provide only 60% coverage of full-length chromosome 22 ORFs, with the best single collection (MGC) providing 48%

chromosome pooled t-tailed naga comparative rt-pcr sanger
Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons.

PMID 15018647 · PMC365025 · BMC genomics · 2004 · 8 claims · 8 setups

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Combined SSH subtractive cloning and array CGH is an efficient strategy to identify overexpressed genes located within DNA amplicons.

imr-32 subtracted mycn-amplified suppression differential array
Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

PMID 15836796 · PMC1090573 · BMC genomics · 2005 · 8 claims · 7 setups

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89 polymorphic microsatellite markers were developed from rainbow trout EST-derived cDNA clones

normalized rainbow salmonids microsatellite sanger pcr
Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system.

PMID 15115540 · PMC420239 · BMC genomics · 2004 · 6 claims · 3 setups

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Bioinformatic sequence comparison of 60,770 RIKEN FANTOM2 mouse cDNA clones identified 2,578 sequences with 70-85% identity to known human disease genes/proteins

riken medline sequence manual semi-automated
Distinct mutations in two patients with leukocyte adhesion deficiency and their functional correlates.

PMID 1694220 · PMC2188166 · The Journal of experimental medicine · 1990 · 8 claims · 8 setups

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Patient 14 (moderate phenotype) carries a C-to-T substitution at nucleotide 517 of the beta subunit cDNA, changing amino acid 149 from leucine to proline

ebv-transformed cos 51cr-labeled rnase cdna pcr
Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.

PMID 10449521 · PMC2195597 · The Journal of experimental medicine · 1999 · 7 claims · 8 setups

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A novel C→A point mutation at nucleotide 850 of GCSFR cDNA causes a Pro→His substitution at position 206 (P206H) in the proline-rich hinge of the CRH domain of the G-CSF receptor extracellular domain in an SCN patient hyporesponsive to G-CSF.

bone fibroblast 32d.cl8.6 32d rt-pcr genomic flow
Interspecies diversity of the occludin sequence: cDNA cloning of human, mouse, dog, and rat-kangaroo homologues.

PMID 8601611 · PMC2120780 · The Journal of cell biology · 1996 · 8 claims · 7 setups

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Full-length cDNAs encoding occludin were cloned and sequenced from rat-kangaroo (potoroo), human, mouse, and dog

ptk2 t84 escherichia computational expression immunofluorescence immunoblotting
Evolutionarily conserved human targets of adenosine to inosine RNA editing.

PMID 15731336 · PMC549564 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Identified four novel human ADAR editing substrates causing amino acid changes: FLNA, BLCAP, CYFIP2 and IGFBP7

panel brain chicken flna comparative rt-pcr homology
Genome-wide estimation of transcript concentrations from spotted cDNA microarray data.

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

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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
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

Experiments

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

A catalog of human cDNA expression clones and its application to structural genomics.

Characterization of 954 bovine full-CDS cDNA sequences.

IgVH genes from different anatomical regions, with different histopathological patterns, of a rheumatoid arthritis patient suggest cyclic re-entry of mature synovial B-cells in the hypermutation process.

hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

The effect of IL-13 and IL-13R130Q, a naturally occurring IL-13 polymorphism, on the gene expression of human airway smooth muscle cells.

Survey of transcripts in the adult Drosophila brain.

Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals.

Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta.

Molecular cloning, genomic characterization and over-expression of a novel gene, XRRA1, identified from human colorectal cancer cell HCT116Clone2_XRR and macaque testis.

A genome annotation-driven approach to cloning the human ORFeome.

Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons.

Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss).

Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system.

Distinct mutations in two patients with leukocyte adhesion deficiency and their functional correlates.

Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.

Interspecies diversity of the occludin sequence: cDNA cloning of human, mouse, dog, and rat-kangaroo homologues.

Evolutionarily conserved human targets of adenosine to inosine RNA editing.

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

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.