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 70

System / cell line: bac ✕ Assay: sequence ✕ Clear

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
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
Dcode.org anthology of comparative genomic tools.

PMID 15980535 · PMC1160116 · Nucleic acids research · 2005 · 8 claims · 7 setups

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The dcode.org suite (zPicture, Mulan, eShadow, rVista 2.0, multiTF, Creme 2.0, ECR Browser) provides integrated tools for comparative genomic analysis and non-coding regulatory element discovery.

dlx1 hoxa prothrombin gene comparative multi-species phylogenetic
Using comparative genomics to reorder the human genome sequence into a virtual sheep genome.

PMID 17663790 · PMC2323240 · Genome biology · 2007 · 8 claims · 6 setups

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A sheep BAC library (CHORI-243) with ~13.5-fold genome coverage was constructed and end-sequenced.

sheep genome bac sequence randomization
Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

PMID 16759380 · PMC1525190 · BMC genomics · 2006 · 8 claims · 6 setups

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Overall pairwise genomic divergences among cattle, dog and human are relatively constant (0.32–0.37 change/site)

orthologous random cattle aligned three-way pairwise bac
Structure of the intergenic spacers in chicken ribosomal DNA.

PMID 31655542 · PMC6815422 · Genetics, selection, evolution : GSE · 2019 · 7 claims · 6 setups

Has reproduction · 80

Long-read PacBio sequencing of a chicken NOR-containing BAC clone resolved three complete IGS sequences plus rRNA gene clusters that are otherwise missing from genome assemblies.

wag137g04 pacbio gallus_gallus-5.0 chicken long-read novo comparative
Evolutionary toggling of the MAPT 17q21.31 inversion region.

PMID 19165922 · PMC2684794 · Nature genetics · 2008 · 8 claims · 6 setups

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The H2 (inverted) orientation is the most likely ancestral great ape/human configuration at 17q21.31

chimpanzee lymphoblastoid donor whole-genome reciprocal bac
Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.

PMID 17565693 · PMC1920519 · BMC genomics · 2007 · 8 claims · 4 setups

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42 different CNVs were detected in 27 phenotypically normal individuals using 1 Mb resolution BAC array-CGH

genomic metaphase computational array-cgh fish real-time
New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus.

PMID 16340004 · PMC1310899 · Nucleic acids research · 2005 · 7 claims · 8 setups

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Long pure palindromes (>~200 bp) cannot be stably cloned in E.coli due to cruciform-driven instability, and no E.coli mutant fully overcomes this cloning block.

individuals e.coli cerevisiae yeast pcr plasmid phi-29
Stable in a genome of instability: an interview with Evan Eichler. Interview by Jane Gitschier.

PMID 18654618 · PMC2442658 · PLoS genetics · 2008 · 8 claims · 5 setups

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Loss of AGG interruptions in CGG repeat tracts predisposes FMR1 alleles to instability and faster progression toward premutation/disease state

fmr1 xq28 genome agg fluorescence genome-wide
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
Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

PMID 16440057 · PMC1331980 · PLoS genetics · 2006 · 7 claims · 6 setups

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Complete 4.25-Mb sequence of the QBL haplotype was determined by BAC shotgun sequencing and compared with PGF (reference) and COX haplotypes

qbl pgf classical ceph bac comparative gene
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
Analysis of human sarcospan as a candidate gene for CFEOM1.

PMID 11180757 · PMC29083 · BMC genetics · 2001 · 7 claims · 5 setups

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Sarcospan sequence is unmutated in all six CFEOM1 families studied

yac genomic extraocular genome pcr direct immunofluorescence
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
DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

PMID 16625196 · PMC2610434 · Nature · 2006 · 8 claims · 7 setups

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A finished sequence of human chromosome 17 (78,839,971 bases, ~2.8% of the euchromatic genome) was generated.

chromosome dog macaque genomic comparative segmental
Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

PMID 18282289 · PMC2270265 · BMC genomics · 2008 · 8 claims · 6 setups

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The sheep TRG1 and TRG2 loci evolved through a series of duplication events involving either entire V-J-J-C recombinational cassettes or single V genes

sheep bac dot tandem
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
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

Experiments

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

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

Dcode.org anthology of comparative genomic tools.

Using comparative genomics to reorder the human genome sequence into a virtual sheep genome.

Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

Structure of the intergenic spacers in chicken ribosomal DNA.

Evolutionary toggling of the MAPT 17q21.31 inversion region.

Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.

New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus.

Stable in a genome of instability: an interview with Evan Eichler. Interview by Jane Gitschier.

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

DNA sequence and analysis of human chromosome 9.

Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

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

Analysis of human sarcospan as a candidate gene for CFEOM1.

The DNA sequence and analysis of human chromosome 13.

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

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

The DNA sequence of the human X chromosome.