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Mendeley | Further Information

{"title"=>"A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells", "type"=>"journal", "authors"=>[{"first_name"=>"Je-Hyuk", "last_name"=>"Lee"}, {"first_name"=>"In-Hyun", "last_name"=>"Park"}, {"first_name"=>"Yuan", "last_name"=>"Gao"}, {"first_name"=>"Jin Billy", "last_name"=>"Li"}, {"first_name"=>"Zhe", "last_name"=>"Li"}, {"first_name"=>"George Q.", "last_name"=>"Daley"}, {"first_name"=>"Kun", "last_name"=>"Zhang"}, {"first_name"=>"George M.", "last_name"=>"Church"}], "year"=>2009, "source"=>"PLoS Genetics", "identifiers"=>{"pmid"=>"19911041", "doi"=>"10.1371/journal.pgen.1000718", "isbn"=>"1553-7390", "issn"=>"1553-7404"}, "id"=>"21200764-e271-3f05-bbb1-733ee4a35b8d", "abstract"=>"Normal variation in gene expression due to regulatory polymorphisms is often masked by biological and experimental noise. In addition, some regulatory polymorphisms may become apparent only in specific tissues. We derived human induced pluripotent stem (iPS) cells from adult skin primary fibroblasts and attempted to detect tissue-specific cis-regulatory variants using in vitro cell differentiation. We used padlock probes and high-throughput sequencing for digital RNA allelotyping and measured allele-specific gene expression in primary fibroblasts, lymphoblastoid cells, iPS cells, and their differentiated derivatives. We show that allele-specific expression is both cell type and genotype-dependent, but the majority of detectable allele-specific expression loci remains consistent despite large changes in the cell type or the experimental condition following iPS reprogramming, except on the X-chromosome. We show that our approach to mapping cis-regulatory variants reduces in vitro experimental noise and reveals additional tissue-specific variants using skin-derived human iPS cells.", "link"=>"http://www.mendeley.com/research/robust-approach-identifying-tissuespecific-gene-expression-regulatory-variants-using-personalized-hu-8", "reader_count"=>93, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>7, "Researcher"=>35, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>30, "Student > Postgraduate"=>2, "Other"=>4, "Student > Master"=>4, "Student > Bachelor"=>5, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>7, "Researcher"=>35, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>30, "Student > Postgraduate"=>2, "Other"=>4, "Student > Master"=>4, "Student > Bachelor"=>5, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>8, "Agricultural and Biological Sciences"=>69, "Medicine and Dentistry"=>8, "Neuroscience"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Physics and Astronomy"=>1, "Chemistry"=>3, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>8}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>3}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>69}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"United States"=>9, "Japan"=>1, "United Kingdom"=>1, "France"=>1, "Germany"=>1, "Russia"=>1}, "group_count"=>6}

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CrossRef

• http://doi.org/10.1002/wsbm.1380
• http://doi.org/10.1038/nrg2951
• http://doi.org/10.1186/1471-2164-12-518
• http://doi.org/10.1016/j.tig.2010.10.006
• http://doi.org/10.15252/msb.20145508
• http://doi.org/10.7554/eLife.53278
• http://doi.org/10.1093/nar/gku1246
• http://doi.org/10.1093/nar/gkw1076
• http://doi.org/10.1002/wsbm.124
• http://doi.org/10.3382/ps.2010-01295
• http://doi.org/10.1016/j.jviromet.2011.09.008
• http://doi.org/10.1002/9780470151808.sc05a08s35
• http://doi.org/10.1038/nature09805
• http://doi.org/10.1016/j.stemcr.2015.04.009
• http://doi.org/10.1186/s13040-014-0032-2
• http://doi.org/10.1371/journal.pgen.1004857
• http://doi.org/10.1371/journal.pone.0117102
• http://doi.org/10.1038/nprot.2014.191
• http://doi.org/10.1038/ng.3432
• http://doi.org/10.1093/hmg/ddt350
• http://doi.org/10.1038/nrg2815
• http://doi.org/10.1002/stem.1155
• http://doi.org/10.1261/rna.058347.116
• http://doi.org/10.1002/wsbm.1369
• http://doi.org/10.1186/ar4262
• http://doi.org/10.1371/journal.pgen.1000977
• http://doi.org/10.1371/journal.pgen.1001279
• http://doi.org/10.1126/science.1250212
• http://doi.org/10.1073/pnas.1018979108
• http://doi.org/10.1073/pnas.1201904109
• http://doi.org/10.1007/s00439-012-1240-9
• http://doi.org/10.1016/j.devcel.2020.11.020
• http://doi.org/10.1371/journal.pone.0169506
• http://doi.org/10.1126/science.1232033

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• {"month"=>"3", "year"=>"2018", "pdf_views"=>"3", "xml_views"=>"1", "html_views"=>"10"}
• {"month"=>"4", "year"=>"2018", "pdf_views"=>"5", "xml_views"=>"2", "html_views"=>"9"}
• {"month"=>"5", "year"=>"2018", "pdf_views"=>"0", "xml_views"=>"0", "html_views"=>"5"}
• {"month"=>"6", "year"=>"2018", "pdf_views"=>"19", "xml_views"=>"1", "html_views"=>"7"}
• {"month"=>"7", "year"=>"2018", "pdf_views"=>"1", "xml_views"=>"3", "html_views"=>"6"}
• {"month"=>"8", "year"=>"2018", "pdf_views"=>"30", "xml_views"=>"3", "html_views"=>"16"}
• {"month"=>"9", "year"=>"2018", "pdf_views"=>"7", "xml_views"=>"0", "html_views"=>"7"}
• {"month"=>"10", "year"=>"2018", "pdf_views"=>"4", "xml_views"=>"1", "html_views"=>"6"}
• {"month"=>"11", "year"=>"2018", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"7"}
• {"month"=>"12", "year"=>"2018", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"8"}
• {"month"=>"1", "year"=>"2019", "pdf_views"=>"13", "xml_views"=>"0", "html_views"=>"13"}
• {"month"=>"2", "year"=>"2019", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"2"}
• {"month"=>"3", "year"=>"2019", "pdf_views"=>"7", "xml_views"=>"1", "html_views"=>"7"}
• {"month"=>"4", "year"=>"2019", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"10"}
• {"month"=>"5", "year"=>"2019", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"10"}
• {"month"=>"6", "year"=>"2019", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"16"}
• {"month"=>"7", "year"=>"2019", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"12"}
• {"month"=>"8", "year"=>"2019", "pdf_views"=>"19", "xml_views"=>"1", "html_views"=>"16"}
• {"month"=>"9", "year"=>"2019", "pdf_views"=>"24", "xml_views"=>"0", "html_views"=>"29"}
• {"month"=>"10", "year"=>"2019", "pdf_views"=>"11", "xml_views"=>"0", "html_views"=>"6"}
• {"month"=>"11", "year"=>"2019", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"5"}
• {"month"=>"12", "year"=>"2019", "pdf_views"=>"15", "xml_views"=>"0", "html_views"=>"17"}
• {"month"=>"1", "year"=>"2020", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"10"}
• {"month"=>"2", "year"=>"2020", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"20"}
• {"month"=>"3", "year"=>"2020", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"10"}
• {"month"=>"4", "year"=>"2020", "pdf_views"=>"11", "xml_views"=>"1", "html_views"=>"27"}
• {"month"=>"5", "year"=>"2020", "pdf_views"=>"14", "xml_views"=>"0", "html_views"=>"8"}
• {"month"=>"6", "year"=>"2020", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"2"}
• {"month"=>"7", "year"=>"2020", "pdf_views"=>"0", "xml_views"=>"0", "html_views"=>"6"}
• {"month"=>"8", "year"=>"2020", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"7"}
• {"month"=>"9", "year"=>"2020", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"8"}
• {"month"=>"10", "year"=>"2020", "pdf_views"=>"6", "xml_views"=>"0", "html_views"=>"16"}
• {"month"=>"11", "year"=>"2020", "pdf_views"=>"9", "xml_views"=>"1", "html_views"=>"13"}
• {"month"=>"12", "year"=>"2020", "pdf_views"=>"18", "xml_views"=>"4", "html_views"=>"5"}
• {"month"=>"1", "year"=>"2021", "pdf_views"=>"1", "xml_views"=>"0", "html_views"=>"6"}

Figshare

• {"files"=>["https://ndownloader.figshare.com/files/876342"], "description"=>"<p>(A) In order to see if mappable ASE loci depended on the tissue type being examined, we examined 317 expression SNPs present in at least 16 out of 20 samples. Mapped ASE loci (red), unmapped ASE loci (black) and missing ASE loci (gray) were hierarchical clustered to reveal tissue-specific sample clustering. (B) When one of the most significant cluster mapping nodes (0.72 correlation) were examined, we found 29 expression SNPs that were consistently mapped in >80% of the cell types derived from PGP1.</p>", "links"=>[], "tags"=>["mapped", "ase", "loci"], "article_id"=>546784, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.g008", "stats"=>{"downloads"=>4, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Visualizing_the_mapped_ASE_loci_in_multiple_tissue_types_/546784", "title"=>"Visualizing the mapped ASE loci in multiple tissue types.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-13 01:53:04"}
• {"files"=>["https://ndownloader.figshare.com/files/877136"], "description"=>"<p>Padlock capture statistics.</p>", "links"=>[], "tags"=>["genetics and genomics/functional genomics", "genetics and genomics/gene expression"], "article_id"=>547579, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.t002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Padlock_capture_statistics_/547579", "title"=>"Padlock capture statistics.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-13 02:06:19"}
• {"files"=>["https://ndownloader.figshare.com/files/875878"], "description"=>"<p>(A) The ASE ratio measurement from the PGP1 fibroblast cDNA (1,021 SNPs) was plotted as a function of the total number of mapped reads (reference + alternative alleles), demonstrating a relationship between the ASE ratio variance and the read count. (B) Twelve random SNPs were examined in PGP1 fibroblasts and lymphocytes using quantitative Sanger sequencing, in which the height of each sequencing trace was used to calculate the allelic ratio in the cDNA. These values were then compared against the ASE ratio determined using padlock probes. (C) The correlation among the ASE ratios with less than 100 observations remained high (R² = 0.799) in technical replicates (PGP1 EB7b and EB7c). (D) Among the ASE ratios with more than 100 observations, the correlation improved to R² = 0.905.</p>", "links"=>[], "tags"=>["reproducibility", "padlock-based", "ase"], "article_id"=>546323, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.g003", "stats"=>{"downloads"=>9, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Noise_and_reproducibility_in_padlock_based_ASE_measurements_/546323", "title"=>"Noise and reproducibility in padlock-based ASE measurements.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-13 01:45:23"}
• {"files"=>["https://ndownloader.figshare.com/files/875789"], "description"=>"<p>(A) Padlock probes were used to capture approximately 19,000 SNPs from the genomic DNA. The number of mapped heterozygous reads (1.2 million) was then used to calculate the allelic ratio (reference:alternative) in 4,721 SNPs. The observed distribution of ASE ratios was symmetrically distributed around a mean of 0.51, suggesting little sequencing and/or mapping bias. (B) The heterozygous sequencing reads for both reference and alternative alleles were binned according to the observation counts. Their distribution probability was then plotted against the sequencing read counts, showing a nearly identical distribution pattern.</p>", "links"=>[], "tags"=>["heterozygous", "genotyping"], "article_id"=>546229, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.g002", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_heterozygous_genotyping_calls_/546229", "title"=>"Distribution of heterozygous genotyping calls.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-13 01:43:49"}
• {"files"=>["https://ndownloader.figshare.com/files/876116"], "description"=>"<p>The 186 expression SNPs were then normalized to reduce both genotyping and probe-specific biases. First, direct allelic ratios from the cDNA were normalized by those from the genomic DNA. Second, we calculated the mean ASE ratio across all samples derived from each individual and used the distance from the mean for hierarchical clustering. The normalized ASE predicted the sample relationship and the tissue-specificity with high accuracy, confirming the presence of tissue-specific regulatory expression variants.</p>", "links"=>[], "tags"=>["tissue-specific", "variations"], "article_id"=>546566, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.g006", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Normalized_tissue_specific_variations_in_ASE_/546566", "title"=>"Normalized tissue-specific variations in ASE.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-13 01:49:26"}
• {"files"=>["https://ndownloader.figshare.com/files/875966"], "description"=>"<p>(A) We examined 1,124 genes in PGP1 fibroblast cDNA shared between Illumina's BeadChip Ref-8 V3 and our padlock probe set. To normalize for the probe-specific differences in capture, the cDNA capture reads were divided by the number of reads obtained from the genomic DNA. For those genes that were targeted by padlock probes more than once, we averaged the number of normalized reads from each probe. We generated a plot of the relative gene expression from BeadChip versus the normalized average capture counts, demonstrating only a weak correlation between the level of gene expression and the frequency of padlock capture. (B) We then examined the distribution of the gene expression level detected on BeadChip (green) versus those captured by padlock probes (red). Of the 18,630 genes, approximately 50% did not reach the detection criteria (<i>p</i>-value <0.01) on BeadChip. On the other hand, 14% of all digital RNA allelotyping calls were made using these ‘undetectable’ rare transcripts.</p>", "links"=>[], "tags"=>["genetics and genomics/functional genomics", "genetics and genomics/gene expression"], "article_id"=>546415, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.g004", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effect_of_the_gene_expression_level_on_ASE_/546415", "title"=>"Effect of the gene expression level on ASE.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-13 01:46:55"}
• {"files"=>["https://ndownloader.figshare.com/files/877090"], "description"=>"<p>Genotyping concordancy.</p>", "links"=>[], "tags"=>["genetics and genomics/functional genomics", "genetics and genomics/gene expression"], "article_id"=>547537, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.t003", "stats"=>{"downloads"=>2, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genotyping_concordancy_/547537", "title"=>"Genotyping concordancy.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-13 02:05:37"}
• {"files"=>["https://ndownloader.figshare.com/files/876989"], "description"=>"<p>ASE-associated with tissue-restricted transcripts.</p>", "links"=>[], "tags"=>["tissue-restricted"], "article_id"=>547439, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.t008", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ASE_associated_with_tissue_restricted_transcripts_/547439", "title"=>"ASE-associated with tissue-restricted transcripts.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-13 02:03:59"}
• {"files"=>["https://ndownloader.figshare.com/files/876457"], "description"=>"<p>(A) In the two iPS clones derived from PGP9, the X-chromosomal ASE ratio was highly reproducible, in which 7 out of 14 SNPs escaped complete silencing (R² = 0.9833). (B) When compared to their parental primary fibroblasts (clonally derived PGP9Bx1F1), we observed that the X-chromosomal ASE ratio was now inversely proportional (R² = 0.5199), strongly suggesting the re-activation of the random silencing mechanism. (C) Autosomal genes in the same pair showed a positive correlation (R² = 0.6343). (D) When PGP9Bx1F1 (clonally derived) was compared to PGP9Bx2F1 (non-clonal), the X-chromosomal ASE ratio confirmed the clonality of PGP9Bx1F1 used for iPS reprogramming.</p>", "links"=>[], "tags"=>["ase", "reflects", "x-chromosomal", "ips"], "article_id"=>546904, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.g009", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Changes_in_ASE_reflects_X_chromosomal_silencing_during_iPS_reprogramming_/546904", "title"=>"Changes in ASE reflects X-chromosomal silencing during iPS reprogramming.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-13 01:55:04"}
• {"files"=>["https://ndownloader.figshare.com/files/434670", "https://ndownloader.figshare.com/files/434709", "https://ndownloader.figshare.com/files/434732"], "description"=>"<div><p>Normal variation in gene expression due to regulatory polymorphisms is often masked by biological and experimental noise. In addition, some regulatory polymorphisms may become apparent only in specific tissues. We derived human induced pluripotent stem (iPS) cells from adult skin primary fibroblasts and attempted to detect tissue-specific <em>cis</em>-regulatory variants using <em>in vitro</em> cell differentiation. We used padlock probes and high-throughput sequencing for digital RNA allelotyping and measured allele-specific gene expression in primary fibroblasts, lymphoblastoid cells, iPS cells, and their differentiated derivatives. We show that allele-specific expression is both cell type and genotype-dependent, but the majority of detectable allele-specific expression loci remains consistent despite large changes in the cell type or the experimental condition following iPS reprogramming, except on the X-chromosome. We show that our approach to mapping <em>cis</em>-regulatory variants reduces <em>in vitro</em> experimental noise and reveals additional tissue-specific variants using skin-derived human iPS cells.</p></div>", "links"=>[], "tags"=>["robust", "identifying", "tissue-specific", "variants", "personalized", "induced", "pluripotent", "cells"], "article_id"=>145742, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000718.s001", "https://dx.doi.org/10.1371/journal.pgen.1000718.s002", "https://dx.doi.org/10.1371/journal.pgen.1000718.s003"], "stats"=>{"downloads"=>3, "page_views"=>34, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Robust_Approach_to_Identifying_Tissue_Specific_Gene_Expression_Regulatory_Variants_Using_Personalized_Human_Induced_Pluripotent_Stem_Cells/145742", "title"=>"A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-11-13 01:35:42"}
• {"files"=>["https://ndownloader.figshare.com/files/877039"], "description"=>"<p>Illumina GA sequencing summary.</p>", "links"=>[], "tags"=>["ga", "sequencing"], "article_id"=>547483, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.t001", "stats"=>{"downloads"=>6, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illumina_GA_sequencing_summary_/547483", "title"=>"Illumina GA sequencing summary.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-13 02:04:43"}
• {"files"=>["https://ndownloader.figshare.com/files/876203"], "description"=>"<p>In order to call a specific locus as being associated with a potential <i>cis</i>-regulatory variant, we used a χ² -test to select the expression SNPs showing greater than a 60:40 allelic imbalance as well as having relatively higher read counts. (A) After making such confidence calls (‘mapping’) for each SNP, the reproducibility of ASE ratio measurements increased to R² = 0.9802. (B) We prepared two sequencing libraries from the same pool of total RNA (technical replicates). In order to estimate the error rate in ASE calling/mapping overall, we compared the ASE ratio in these replicate libraries using a χ² -test. We found that 1.6% of the statistically significant ASE calls were due to the sample processing and/or measurement error.</p>", "links"=>[], "tags"=>["ase"], "article_id"=>546652, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.g007", "stats"=>{"downloads"=>4, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Estimation_of_the_error_rate_in_ASE_mapping_/546652", "title"=>"Estimation of the error rate in ASE mapping.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-13 01:50:52"}
• {"files"=>["https://ndownloader.figshare.com/files/876625"], "description"=>"<p>iPS cells (A), retinoic acid (RA)-treated iPS cells (B), and embryoid bodies (C) were compared to another iPS clone from the same individual pair-wise. Two different types of statistical threshold were used to categorize ‘mappable’ ASE loci. Mono-allelic expression is defined as having an allelic preference of >90%. <i>N</i> is the number of observation from cDNA samples. Retinoic acid was added directly to newly suspended iPS colonies growing on a low-attachment plate for 12 hours. Embryoid bodies were cultured the same way without retinoic acid for 7 days.</p>", "links"=>[], "tags"=>["mappable", "ase", "loci", "ips"], "article_id"=>547065, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.g010", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Variations_in_the_mappable_ASE_loci_with_in_vitro_iPS_differentiation_/547065", "title"=>"Variations in the mappable ASE loci with <i>in vitro</i> iPS differentiation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-13 01:57:45"}
• {"files"=>["https://ndownloader.figshare.com/files/877314"], "description"=>"<p>(χ² >6.64; >60% allelic imbalance. Estimated false discovery rate  = 1.6%)</p>", "links"=>[], "tags"=>["ase"], "article_id"=>547765, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.t006", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_ASE_mapping_calls_/547765", "title"=>"Summary of ASE mapping calls.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-13 02:09:25"}
• {"files"=>["https://ndownloader.figshare.com/files/876843"], "description"=>"<p>(A) A biological replicate of PGP1Bx1 iPS1 cells were used for <i>in vitro</i> differentiation, using 100-µM trans-retinoic acid for 12 hours or embryoid body formation for 7 days. ASE loci with high confidence scores are shown. The expression SNPs in the upper left and the lower right quadrant represent those that have significantly altered their preference of parental alleles (5–13%). (B) Variations in ASE across six differentiated samples (3 RA-induced and 3 EBs) were analyzed according to their chromosomal locations. The ASE ratio variance from Chromosome 6 was compared to the ASE ratio variance from all other chromosomes.</p>", "links"=>[], "tags"=>["ase", "ips"], "article_id"=>547288, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.g011", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Changes_in_ASE_during_iPS_differentiation_/547288", "title"=>"Changes in ASE during iPS differentiation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-13 02:01:28"}
• {"files"=>["https://ndownloader.figshare.com/files/877272"], "description"=>"<p>Observation frequency and ASE calling.</p>", "links"=>[], "tags"=>["ase"], "article_id"=>547717, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.t007", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Observation_frequency_and_ASE_calling_/547717", "title"=>"Observation frequency and ASE calling.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-13 02:08:37"}
• {"files"=>["https://ndownloader.figshare.com/files/875633"], "description"=>"<p>(A) We derived 2–3 iPS cell lines from two biopsy sites in each individual. iPS cells expressed molecular pluripotency markers (SSEA4, SSEA3, Tra1-60, Tra1-81, NANOG and OCT4) and stained for the alkaline phosphatase activity. (B) When injected into immune-deficient mice, iPS cells formed a teratoma, containing normal tissues from all three germ layers, including respiratory epithelium (endoderm), bone (mesoderm) and neuroectoderm (ectoderm).</p>", "links"=>[], "tags"=>["induced", "pluripotent"], "article_id"=>546075, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.g001", "stats"=>{"downloads"=>8, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PGP_induced_pluripotent_stem_cells_/546075", "title"=>"PGP induced pluripotent stem cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-13 01:41:15"}
• {"files"=>["https://ndownloader.figshare.com/files/877181"], "description"=>"<p>Tissue-specific ASE calls (χ²>6.64).</p>", "links"=>[], "tags"=>["ase", "calls"], "article_id"=>547631, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.t005", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Tissue_specific_ASE_calls_2_gt_6_64_/547631", "title"=>"Tissue-specific ASE calls (χ²>6.64).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-13 02:07:11"}
• {"files"=>["https://ndownloader.figshare.com/files/877228"], "description"=>"<p>Strand-specific padlock capture efficiency.</p>", "links"=>[], "tags"=>["padlock"], "article_id"=>547675, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.t004", "stats"=>{"downloads"=>3, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Strand_specific_padlock_capture_efficiency_/547675", "title"=>"Strand-specific padlock capture efficiency.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-11-13 02:07:55"}
• {"files"=>["https://ndownloader.figshare.com/files/876047"], "description"=>"<p>Of the 695 heterozygous expression SNPs commonly shared between PGP1 and PGP9, we selected 186 expression SNPs that were detectable in 17 out of 17 cDNA samples (three samples with a very low sequencing depth were excluded). Using log2-transformed ASE ratios derived directly from the sequencing counts, we performed hierarchical clustering of samples and expression SNPs (green: reference allele; red: alternative allele). We identified highly individual-specific clusters from the ASE ratio alone in the absence of any genotyping data. In addition, most tissue-specificity relationships were determined correctly from the ASE ratio.</p>", "links"=>[], "tags"=>["ase", "reveals", "tissue-", "person-specificity"], "article_id"=>546489, "categories"=>["Genetics"], "users"=>["Je-Hyuk Lee", "In-Hyun Park", "Yuan Gao", "Jin Billy Li", "Zhe Li", "George Q. Daley", "Kun Zhang", "George M. Church"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000718.g005", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_ASE_ratio_alone_reveals_tissue_and_person_specificity_of_regulatory_differences_/546489", "title"=>"The ASE ratio alone reveals tissue- and person-specificity of regulatory differences.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-11-13 01:48:09"}

PMC Usage Stats | Further Information

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F1000Prime