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 74

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

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
Proteomic analysis of differential proteins in pancreatic carcinomas: Effects of MBD1 knock-down by stable RNA interference.

PMID 18445260 · PMC2386481 · BMC cancer · 2008 · 8 claims · 5 setups

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Stable RNAi-mediated MBD1 knock-down was successfully established in the BxPC-3 pancreatic cancer cell line using a recombinant siRNA plasmid

bxpc-3 2-d maldi-tof-ms western
A distinct epigenetic signature at targets of a leukemia protein.

PMID 17266773 · PMC1796549 · BMC genomics · 2007 · 7 claims · 7 setups

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Combining gene expression microarray analysis with bioinformatic search for AML1-consensus sequences identifies direct AML1 targets that expression analysis alone cannot resolve

32d sequence gene bioinformatic real-time
Manipulation of Alternative Splicing of IKZF1 Elicits Distinct Gene Regulatory Responses in T Cells.

PMID 41677588 · PMC12896614 · Cells · 2026 · 8 claims · 6 setups

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Alternative splicing of IKZF1 in human T cells strongly influences gene expression, chromatin accessibility, and protein production.

jurkat genomic cd4+ rna-seq atac-seq immunoblotting
Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes.

PMID 7606775 · PMC3730239 · Cell · 1995 · 6 claims · 8 setups

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Expression of a specific var gene (A4var) correlates with A4 antigenic type and with binding to ICAM-1

falciparum cdna c18 genomic rt-pcr southern genomic
SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans.

PMID 16381914 · PMC1347399 · Nucleic acids research · 2006 · 8 claims · 8 setups

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SGCEdb is a flexible, reusable database and web interface for reporting and analyzing structural genomics experiment results, focused on C. elegans

elegans expressed soluble crystallized recombinant solubility purification
Molecular cloning and characterisation of the RESA gene, a marker of genetic diversity of Plasmodium falciparum.

PMID 19816792 · PMC2900597 · Molecular biology reports · 2010 · 8 claims · 8 setups

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RESA was cloned from a P. falciparum Dd2 expression library screened with human immune sera, yielding a 1,336 bp insert with a 936 bp ORF encoding a 317-aa protein.

falciparum falciparum-infected coli sera cdna sequencing pcr
Identification of new ETV6 modulators through a high-throughput functional screening.

PMID 35198911 · PMC8851229 · iScience · 2022 · 7 claims · 8 setups

Has reproduction · 68

A genome-wide shRNA screen in an engineered ETV6-dependent Blasticidin-sensitive pre-B ALL cell line can identify modulators of ETV6 repressive transcriptional activity

reh genome-wide qrt-pcr chip-seq
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
Relative impact of nucleotide and copy number variation on gene expression phenotypes.

PMID 17289997 · PMC2665772 · Science (New York, N.Y.) · 2007 · 8 claims · 5 setups

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SNPs and CNVs capture largely non-overlapping signals of genetic variation affecting gene expression

lymphoblastoid same computational subset gene snp array
Alkyltransferase-mediated toxicity of 1,3-butadiene diepoxide.

PMID 18712882 · PMC2614079 · Chemical research in toxicology · 2008 · 8 claims · 6 setups

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hAGT expression increases mutations and cytotoxicity following BDO exposure, and hAGT-DNA cross-links form in the presence of BDO

recombinant wt-hagt [35s]-labelled trg8 sds-page time-course forward
Mutation detection using ENDO1: application to disease diagnostics in humans and TILLING and Eco-TILLING in plants.

PMID 18433472 · PMC2386800 · BMC molecular biology · 2008 · 7 claims · 6 setups

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Co-agroinfiltration of ENDO1 and p19 constructs into N. benthamiana leaves gives high-level transient expression of active, mismatch-specific ENDO1 via a simple purification protocol

benthamiana test genomic hiv-1 transient heteroduplex mutation
CRISPR/Cas9 Screens Reveal Multiple Layers of B cell CD40 Regulation.

PMID 31365872 · PMC6684324 · Cell reports · 2019 · 8 claims · 8 setups

Has reproduction

Genome-wide CRISPR/Cas9 screening in Daudi B cells using CD40L-induced Fas upregulation as a readout identifies both positive and negative regulators of CD40

daudi splenic genome-wide immunoblot qpcr
Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo.

PMID 35784648 · PMC9243631 · Cell reports methods · 2022 · 8 claims · 7 setups

Has reproduction · 66

A purification-free hyperTRIBE method (FMR1-ADARcd-V5) can identify stress granule RNAs in bulk and single Drosophila S2 cells and in Drosophila neurons

fmr1-adarcd-v5 single bioinformatic drosophila immunofluorescence western bulk
Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 5 setups

Has reproduction

Expression stability in CHO cell lines is controlled at three levels: choice of integration site, transgene integrity/concatemerization pattern, and stress-related cellular processes.

horizon same cho genome rna-seq targeted
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
A gene encoding antigenic peptides of human squamous cell carcinoma recognized by cytotoxic T lymphocytes.

PMID 9449708 · PMC2212124 · The Journal of experimental medicine · 1998 · 8 claims · 8 setups

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A gene, SART-1, encoding antigenic peptides recognized by HLA-A2601-restricted CTLs was identified from human squamous cell carcinoma cells.

ke4 normal pbmcs va13 expression northern western
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
Are gene expression microarray analyses reliable? A review of studies of retinoic acid responsive genes.

PMID 15626329 · PMC5171945 · Genomics, proteomics & bioinformatics · 2003 · 6 claims · 8 setups

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Published microarray studies aiming to identify RA-responsive genes show substantial, often contradictory, differences in results across research groups.

nb4 tf1 tracheobronchial moser affymetrix cdna microarray
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

Experiments

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

Proteomic analysis of differential proteins in pancreatic carcinomas: Effects of MBD1 knock-down by stable RNA interference.

A distinct epigenetic signature at targets of a leukemia protein.

Manipulation of Alternative Splicing of IKZF1 Elicits Distinct Gene Regulatory Responses in T Cells.

Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes.

SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans.

Molecular cloning and characterisation of the RESA gene, a marker of genetic diversity of Plasmodium falciparum.

Identification of new ETV6 modulators through a high-throughput functional screening.

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

Relative impact of nucleotide and copy number variation on gene expression phenotypes.

Alkyltransferase-mediated toxicity of 1,3-butadiene diepoxide.

Mutation detection using ENDO1: application to disease diagnostics in humans and TILLING and Eco-TILLING in plants.

CRISPR/Cas9 Screens Reveal Multiple Layers of B cell CD40 Regulation.

Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo.

Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

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

A gene encoding antigenic peptides of human squamous cell carcinoma recognized by cytotoxic T lymphocytes.

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.

Are gene expression microarray analyses reliable? A review of studies of retinoic acid responsive genes.

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