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 226

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

NovelFam3000--uncharacterized human protein domains conserved across model organisms.

PMID 16533400 · PMC1440326 · BMC genomics · 2006 · 8 claims · 7 setups

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NovelFam3000 is an online data centre unifying bioinformatics resource links, news, comments, and user-submitted experimental data (including a Gene Characterization Index) for ~3000 uncharacterized Pfam-B/DUF domain families conserved across worm, fly, and human

lines mammalian hek drosophila rt-pcr immunofluorescence counterstaining
Molecular genetic analysis of an endotoxin nonresponder mutant cell line: a point mutation in a conserved region of MD-2 abolishes endotoxin-induced signaling.

PMID 11435474 · PMC2193443 · The Journal of experimental medicine · 2001 · 8 claims · 7 setups

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MD-2 is a required component of the LPS signaling complex; a point mutation in MD-2 abolishes LPS-induced signaling

cho hek western nf-kb il-6
Decreased expression of the Id3 gene at 1p36.1 in ovarian adenocarcinomas.

PMID 11161400 · PMC2363740 · British journal of cancer · 2001 · 7 claims · 7 setups

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Id3 mRNA and protein expression are decreased in ovarian cancer cell lines compared to immortalized HOSE cells

hose ovarian cdna semi-quantitative northern
Aberrations of the p14(ARF) and p16(INK4a) genes in renal cell carcinomas.

PMID 11749694 · PMC5926680 · Japanese journal of cancer research : Gann · 2001 · 7 claims · 6 setups

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Homozygous co-deletion of p14ARF and p16INK4a is frequent in RCC cell lines (5 of 6 lines)

rcc differential methylation-specific immunohistochemistry
Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo.

PMID 16231974 · PMC1262628 · PLoS biology · 2005 · 8 claims · 8 setups

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Distinct combinations of pre-mRNA splicing factors are recruited to sites of alternatively spliced transcripts in intact cells, providing the first in vivo evidence for differential splicing factor association.

cos-1 cos-7 tau10-1 rt-pcr quantitative rna-fish
Identification of common genetic variation that modulates alternative splicing.

PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

ceph lcls skipped additional rt-pcr snp resequencing
Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer.

PMID 18418848 · PMC6668724 · Genes, chromosomes & cancer · 2008 · 6 claims · 5 setups

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Emulsion PCR combined with picotiter plate pyrosequencing (454 sequencing) enables high-resolution, high-throughput detection of low-frequency sequence variants among the many individual copies of an amplified gene.

erbb2-amplified erbb2-positive plasmid cos-7 emulsion serial immune-complex
Characterization of novel isoforms and evaluation of SNF2L/SMARCA1 as a candidate gene for X-linked mental retardation in 12 families linked to Xq25-26.

PMID 18302774 · PMC2266716 · BMC medical genetics · 2008 · 8 claims · 4 setups

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The SNF2L gene spans 77 kb and is encoded by 25 exons that undergo alternative splicing to generate multiple distinct transcripts.

lines genomic 293hek rt-pcr genomic indirect
Functional redundancy of exon 12 of BRCA2 revealed by a comprehensive analysis of the c.6853A>G (p.I2285V) variant.

PMID 19795481 · PMC3501199 · Human mutation · 2009 · 7 claims · 8 setups

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BRCA2 c.6853A>G (p.I2285V) co-occurs in trans with the deleterious founder mutation c.5946delT, supporting classification as a neutral variant

lymphocytes brca2 brca2-null ashkenazi rt-pcr splicing allelic
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
Single-cell transcriptomics reveals maturation of transplanted stem cell-derived retinal pigment epithelial cells toward native state.

PMID 37339216 · PMC10293804 · Proceedings of the National Academy of Sciences of the United States of America · 2023 · 8 claims · 8 setups

Has reproduction · 59

Subretinally transplanted stem cell-derived RPE (ESC- and iPSC-derived) retain RPE identity and survive in vivo for at least 30 days in immunocompetent rabbit eyes

hpsc-derived day esc dutch qrt-pcr immunofluorescence transepithelial
The human homologue of unc-93 maps to chromosome 6q27 - characterisation and analysis in sporadic epithelial ovarian cancer.

PMID 12381271 · PMC134458 · BMC genetics · 2002 · 7 claims · 8 setups

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UNC93A maps within the minimal region of allele loss on 6q27 between D6S264 and D6S149, centromeric to D6S149

panel 293-t malignant same rt-pcr northern fluorescence
The absence of Mth1 inactivation and DNA polymerase kappa overexpression in rat mammary carcinomas with frequent A:T to C:G transversions.

PMID 12036445 · PMC5927037 · Japanese journal of cancer research : Gann · 2002 · 8 claims · 5 setups

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SNI (elevated spontaneous point mutation rate without microsatellite instability) is present in rat mammary carcinoma cell lines and human breast cancer cell lines

mammary same normal pcr-sscp direct quantitative
Genetic and epigenetic analyses of MBD3 in colon and lung cancer.

PMID 15138480 · PMC2410281 · British journal of cancer · 2004 · 7 claims · 5 setups

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MBD3 is not a major target of genetic or epigenetic alteration in colon and lung cancer

colon normal pcr-sscp rt-pcr northern
Expression analysis of candidate breast tumour suppressor genes on chromosome 16q.

PMID 16280054 · PMC1410740 · Breast cancer research : BCR · 2005 · 8 claims · 7 setups

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None of the six candidate genes (CBFA2T3, TERF2, TERF2IP, FBXL8, LRRC29, FANCA) showed inactivating mutations or expression differences clearly associated with 16q LOH status

breast quantitative fragment gene-expression
Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.

PMID 18772397 · PMC2848990 · Science (New York, N.Y.) · 2008 · 8 claims · 6 setups

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Pancreatic cancers contain an average of 63 genetic alterations, the majority of which are point mutations

pancreatic computational targeted prevalence snp
Additional EFNB1 mutations in craniofrontonasal syndrome.

PMID 18627045 · PMC2774847 · American journal of medical genetics. Part A · 2008 · 8 claims · 4 setups

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Loss-of-function mutations in EFNB1 (Xq13.1) are the cause of CFNS in the majority of patients

lymphoblastoid cfns patients additional pcr multiplex molecular
Loss of cyclin-dependent kinase inhibitor genes and chromosome 9 karyotypic abnormalities in human bladder cancer cell lines.

PMID 7577470 · PMC2033929 · British journal of cancer · 1995 · 8 claims · 4 setups

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Homozygous deletion of both p15 and p16 occurred in 7 of 13 (54%) independent bladder cancer cell lines tested

bladder pcr pcr cytogenetic arbitrary
Loss of heterozygosity at the 5,10-methylenetetrahydrofolate reductase locus in human ovarian carcinomas.

PMID 9099956 · PMC2222800 · British journal of cancer · 1997 · 8 claims · 7 setups

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No sequence mutations were found in the MTHFR gene in ovarian tumors and cell lines despite extensive SSCP screening

ovarian non-mucinous informative rt-pcr immunohistochemistry pcr-rflp
High frequency of deletions at the hypoxanthine-guanine phosphoribosyltransferase locus in an ataxia-telangiectasia lymphoblastoid cell line irradiated with gamma-rays.

PMID 11714443 · PMC5926665 · Japanese journal of cancer research : Gann · 2001 · 7 claims · 5 setups

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A high proportion (12/15, 80%) of gamma-ray-induced HPRT-deficient mutants in A-T (GM2783) cells are deletions

gm2783 mutant multiplex pcr long

Experiments

NovelFam3000--uncharacterized human protein domains conserved across model organisms.

Molecular genetic analysis of an endotoxin nonresponder mutant cell line: a point mutation in a conserved region of MD-2 abolishes endotoxin-induced signaling.

Decreased expression of the Id3 gene at 1p36.1 in ovarian adenocarcinomas.

Aberrations of the p14(ARF) and p16(INK4a) genes in renal cell carcinomas.

Differential recruitment of pre-mRNA splicing factors to alternatively spliced transcripts in vivo.

Identification of common genetic variation that modulates alternative splicing.

Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer.

Characterization of novel isoforms and evaluation of SNF2L/SMARCA1 as a candidate gene for X-linked mental retardation in 12 families linked to Xq25-26.

Functional redundancy of exon 12 of BRCA2 revealed by a comprehensive analysis of the c.6853A>G (p.I2285V) variant.

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.

Single-cell transcriptomics reveals maturation of transplanted stem cell-derived retinal pigment epithelial cells toward native state.

The human homologue of unc-93 maps to chromosome 6q27 - characterisation and analysis in sporadic epithelial ovarian cancer.

The absence of Mth1 inactivation and DNA polymerase kappa overexpression in rat mammary carcinomas with frequent A:T to C:G transversions.

Genetic and epigenetic analyses of MBD3 in colon and lung cancer.

Expression analysis of candidate breast tumour suppressor genes on chromosome 16q.

Core signaling pathways in human pancreatic cancers revealed by global genomic analyses.

Additional EFNB1 mutations in craniofrontonasal syndrome.

Loss of cyclin-dependent kinase inhibitor genes and chromosome 9 karyotypic abnormalities in human bladder cancer cell lines.

Loss of heterozygosity at the 5,10-methylenetetrahydrofolate reductase locus in human ovarian carcinomas.

High frequency of deletions at the hypoxanthine-guanine phosphoribosyltransferase locus in an ataxia-telangiectasia lymphoblastoid cell line irradiated with gamma-rays.