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Resource: An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes
- Chong Li,
- Marc Jan Bonder,
- Sabriya Syed,
- Matthew Jensen,
- Human Genome Structural Variation Consortium (HGSVC),
- HGSVC Functional Analysis Working Group,
- Mark B. Gerstein,
- Michael C. Zody,
- Mark J.P. Chaisson,
- Michael E. Talkowski,
- Tobias Marschall,
- Jan O. Korbel,
- Evan E. Eichler,
- Charles Lee,
- and Xinghua Shi
Genome Res. December 2024 34: 2304-2318; Published in Advance December 5, 2024, doi:10.1101/gr.279419.124
...An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human s Chong Li1,2, Marc Jan Bonder3,4, Sabriya Syed5, Matthew Jensen6,7, Human Genome Structural Variation Consortium (HGSVC), HGSVC Functional Analysis Working Group, Mark B...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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Method: Predicting genotype-specific gene regulatory networks
- Deborah Weighill,
- Marouen Ben Guebila,
- Kimberly Glass,
- John Quackenbush,
- and John Platig
Genome Res. March 2022 32: 524-533; Published in Advance February 22, 2022, doi:10.1101/gr.275107.120
...et al. (2018) had previously analyzed RNA-seq data derived from three cell types: lymphoblastoid cell lines, induced pluripotent stem cells (iPSCs), and cardiomyocytes (CMs; differentiated from the iPSCs). They demonstrated that genes preferentially expressed in CMs were enriched for processes...
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Research: The motif composition of variable number tandem repeats impacts gene expression
- Tsung-Yu Lu,
- Paulina N. Smaruj,
- Geoffrey Fudenberg,
- Nicholas Mancuso,
- and Mark J.P. Chaisson
Genome Res. April 2023 33: 511-524; Published in Advance April 10, 2023, doi:10.1101/gr.276768.122
...://www.international.org/data-portal/data-collection/hgsvc2), and the matching residualized gene expression matrix for lymphoblastoid cell lines (GD462.GeneQuantRPKM.50FN.samplename.resk10.txt.gz) were retrieved directly from the Geuvadis portal at https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-GEUV-1 (Lappalainen et al. 2013).RPGG construction...
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Research: Gene essentiality in cancer cell lines is modified by the sex chromosomes
- Shahar Shohat,
- Ethel Vol,
- and Sagiv Shifman
Genome Res. November/December 2022 32: 1993-2002; Published in Advance November 23, 2022, doi:10.1101/gr.276488.121
...of the X and Y Chromosomes in external data sets, we compared our results with an expression microarray analysis performed on lymphoblastoid cell lines (LCLs) from individuals with diverse sex-chromosome aneuploidies (X0, XXX, XXY, XYY, and XXYY) (Raznahan et al. 2018). We compared the genes whose...
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Research: Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels
- Amanda J. Lea,
- Julie Peng,
- and Julien F. Ayroles
Genome Res. October 2022 32: 1826-1839; Published in Advance October 13, 2022, doi:10.1101/gr.276430.121
...changes in gene expression levelsWe exposed 544 lymphoblastoid cell lines (LCLs) derived from individuals included in the 1000 Genomes study (The 1000 Genomes Project Consortium 2012) to 12 cellular environments, including 10 treatment and two control conditions (Fig. 1A; Supplemental Table S1). We chose...
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Method: Highly accurate quantification of allelic gene expression for population and disease genetics
- Anna Saukkonen,
- Helena Kilpinen,
- and Alan Hodgkinson
Genome Res. August 2022 32: 1565-1572; Published in Advance July 6, 2022, doi:10.1101/gr.276296.121
...across a larger number of genes.Finally, to demonstrate the utility of PAC in finding biologically informative events, we attempted to identify cell type–specific ASE using gene expression data from Findley et al. (2021), who exposed three different cell types (lymphoblastoid cell lines [LCLs], induced...
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Resource: A cross-platform analysis of 14,177 expression quantitative trait loci derived from lymphoblastoid cell lines
- Liming Liang,
- Nilesh Morar,
- Anna L. Dixon,
- G. Mark Lathrop,
- Goncalo R. Abecasis,
- Miriam F. Moffatt,
- and William O.C. Cookson
Genome Res. April 2013 23: 716-726; Published in Advance January 23, 2013, doi:10.1101/gr.142521.112
...SNP and gene >1 Mb away from gene, either on the same chromosome or on different chromosomes (the equivalent of trans). Results The first sample (MRCA) contained 206 siblings of British descent (Dixon et al. 2007). Global gene expression in lymphoblastoid cell lines (LCLs) was measured using Affymetrix HG-U133...
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Research: Quantitative analysis of Y-Chromosome gene expression across 36 human tissues
- Alexander K. Godfrey,
- Sahin Naqvi,
- Lukáš Chmátal,
- Joel M. Chick,
- Richard N. Mitchell,
- Steven P. Gygi,
- Helen Skaletsky,
- and David C. Page
Genome Res. June 2020 30: 860-873; Published in Advance May 27, 2020, doi:10.1101/gr.261248.120
..., USA Corresponding author: dcpage@wi.mit.eduAbstractLittle is known about how human Y-Chromosome gene expression directly contributes to differences between XX (female) and XY (male) individuals in nonreproductive tissues. Here, we analyzed quantitative profiles of Y-Chromosome gene expression across...
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Research: Radiation pharmacogenomics: A genome-wide association approach to identify radiation response biomarkers using human lymphoblastoid cell lines
- Nifang Niu,
- Yuxin Qin,
- Brooke L. Fridley,
- Junmei Hou,
- Krishna R. Kalari,
- Minjia Zhu,
- Tse-Yu Wu,
- Gregory D. Jenkins,
- Anthony Batzler,
- and Liewei Wang
Genome Res. November 2010 20: 1482-1492; Published in Advance October 5, 2010, doi:10.1101/gr.107672.110
...using 277 ethnically defined human lymphoblastoid cell lines (LCLs). Basal gene expression levels and 1.3 million -wide single nucleotide polymorphism (SNP) markers from both Affymetrix and Illumina platforms were assayed for all 277 human LCLs. MTS [3-(4,5-dimethylthiazol-2-yl)-5...

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