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 58

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

Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

bac genome metaphase overlapping manual repeat fluorescence
Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

PMID 11991808 · PMC107843 · BMC genetics · 2002 · 6 claims · 5 setups

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The genomic organization of human CCS was characterized, with the 823 bp coding region organized into 8 exons spanning 12798 bp of genomic DNA.

bac heart ccs genomic genomic rt-pcr transcription
The DNA sequence and analysis of human chromosome 13.

PMID 15057823 · PMC2665288 · Nature · 2004 · 8 claims · 8 setups

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95.5 Mb of finished sequence from chromosome 13 was completed, containing 633 genes and 296 pseudogenes.

chromosome rpci-11 genomic comparative fluorescence
Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

PMID 17406619 · PMC2688820 · Nature protocols · 2007 · 8 claims · 7 setups

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Combining three human-optimized DOP-PCR primers before a secondary amino-labeled PCR increases array hybridization sensitivity and reproducibility sixfold compared to the standard 6MW DOP-PCR primer

large-insert patients test genomic array-cgh manual automated
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
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 and analysis of human chromosome 9.

PMID 15164053 · PMC2734081 · Nature · 2004 · 8 claims · 8 setups

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The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs, representing >99.6% of the region.

bac chromosome fibres chimpanzee clone-based restriction computational
The DNA sequence of the human X chromosome.

PMID 15772651 · PMC2665286 · Nature · 2005 · 8 claims · 8 setups

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The euchromatic sequence of the human X chromosome was determined to 99.3% completeness (~155 Mb total)

pac selected chromosome clone-based shotgun comparative
Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis.

PMID 18492229 · PMC2408590 · BMC microbiology · 2008 · 8 claims · 6 setups

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The mcrA gene serves as a useful biomarker for methanogen detection in the human gut

faecal mcra pure pcr rflp 16s
Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

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Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

c57bl orthologous alpha-defensin defensin manual comparative sequence
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
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
Improved tagging strategy for protein identification in mammalian cells.

PMID 16138932 · PMC1250225 · BMC genomics · 2005 · 7 claims · 7 setups

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EGFP tagging via the artificial exon did not affect the subcellular localization of the tagged endogenous proteins

osteosarcoma hos 293t lentiviral flow confocal
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
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
Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.

PMID 18226259 · PMC2268926 · BMC genomics · 2008 · 8 claims · 7 setups

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GOLGA8E and WHDC1L1 are characterized for the first time as protein-coding transcripts from the PWS proximal breakpoint region.

genomic chromosome lymphoblasts multi-tissue bioinformatic fish rt-pcr
Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

PMID 18193213 · PMC2206249 · Immunogenetics · 2008 · 8 claims · 6 setups

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Comparison of eight HLA-homozygous MHC haplotype sequences identified >44,000 variations (substitutions and indels), submitted to dbSNP

hla-homozygous same mhc indel clone-by-clone gene hla
Twin peaks: the draft human genome sequence.

PMID 11276423 · PMC138909 · Genome biology · 2001 · 8 claims · 8 setups

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The predicted number of human genes (~26,000-40,000) is far lower than the widely assumed ~100,000, though downstream RNA/protein complexity can still generate substantial biological complexity.

genome genomic genes yeast whole-genome bac computational
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
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

Experiments

Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

Human CCS gene: genomic organization and exclusion as a candidate for amyotrophic lateral sclerosis (ALS).

The DNA sequence and analysis of human chromosome 13.

Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

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

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

DNA sequence and analysis of human chromosome 9.

The DNA sequence of the human X chromosome.

Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis.

Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

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

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

Improved tagging strategy for protein identification in mammalian cells.

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

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

Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region.

Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

Twin peaks: the draft human genome sequence.

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

Survey of transcripts in the adult Drosophila brain.