GEO DataSets

(Submitter supplied) Purpose: We examined the extent and nature of non-genetic variability at the gene regulatory activity and gene expression levels in isogenic LCLs, highlighting features of the LCL model that might aid the rational design of genetic association studies. Brief method: H3K27ac ChIP-Seq: Crosslinked chromatin corresponding to 5 million cells was immunoprecipitated with 2.5 ug anti-histone H3 (acetyl K27) antibody (Abcam, cat. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

26 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Expression profiling by array; Genome variation profiling by SNP array

4 related Platforms

862 Samples

Download data: CEL

(Submitter supplied) Radiation therapy is used to treat half of all cancer patients. Response to radiation therapy varies widely among patients. Therefore, we performed a genome-wide association study (GWAS) to identify biomarkers to help predict radiation response using 277 ethnically defined human lymphoblastoid cell lines (LCLs). Basal gene expression levels (Affymetrix) and 1.3 million genome-wide SNP markers (Illumina) were assayed for all 277 human LCLs. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platform:

GPL6987

95 Samples

Download data: CSV

(Submitter supplied) Radiation therapy is used to treat half of all cancer patients. Response to radiation therapy varies widely among patients. Therefore, we performed a genome-wide association study (GWAS) to identify biomarkers to help predict radiation response using 277 ethnically defined human lymphoblastoid cell lines (LCLs). Basal gene expression levels (Affymetrix) and 1.3 million genome-wide SNP markers (Illumina) were assayed for all 277 human LCLs. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platform:

GPL6434

192 Samples

Download data: CSV

(Submitter supplied) Radiation therapy is used to treat half of all cancer patients. Response to radiation therapy varies widely among patients. Therefore, we performed a genome-wide association study (GWAS) to identify biomarkers to help predict radiation response using 277 ethnically defined human lymphoblastoid cell lines (LCLs). Basal gene expression levels (Affymetrix) and 1.3 million genome-wide SNP markers (Illumina) were assayed for all 277 human LCLs. more...

Organism:

Homo sapiens

Type:

SNP genotyping by SNP array; Genome variation profiling by SNP array

Platform:

GPL6988

288 Samples

Download data: CSV

(Submitter supplied) We used microarrays to identify the variation of basal gene expression level among 287 lymphoblastoid cell lines. Radiation therapy is used to treat half of all cancer patients. Response to radiation therapy varies widely among patients. Therefore, we performed a genome-wide association study (GWAS) to identify biomarkers to help predict radiation response using 277 ethnically defined human lymphoblastoid cell lines (LCLs). more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

287 Samples

Download data: CEL

(Submitter supplied) We report single-cell RNA sequencing datasets for three lymphoblastoid cell lines (LCLs) prepared by infection of primary B cells with Epstein-Barr Virus (EBV). Inter- and intra-sample transcriptional variance is observed with respect to immunoglobulin heavy chain class; host gene sets involved in survival, proliferation and differentiation; and viral replication state. We propose that the observed heterogeneity arises from the dynamic nature of host-pathogen interactions, donor-specific compositions of primary B cells, and other experimental factors such as stochastic clonal evolution in cell culture conditions.

Organism:

human gammaherpesvirus 4; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23362

3 Samples

Download data: MTX, TSV

(Submitter supplied) Here we present single-cell RNA sequencing (scRNA-seq) data of two LCLs: GM12878 and GM18502, produced from the blood of two female donors with European and African ancestry, respectively.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: MTX, TSV

(Submitter supplied) Epstein-Barr virus (EBV) transformed lymphoblastoid cell lines (LCLs) are a widely used renewable resource for functional genomic studies in humans. The ability to accumulate multidimensional data pertaining to the same individual cell lines, from complete genomic sequences to detailed gene regulatory profiles, further enhances the utility of LCLs as a model system. However, the extent to which LCLs are a faithful model system is relatively unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL10558 GPL6947

187 Samples

Download data: TXT

(Submitter supplied) DNA was isolated from whole red blood cells from various lines and crosses of broiler chickens. DNA was genotyped using Axiom genome-wide chicken array and cel files were analyzed using Axiom Analysis Suite Software (version 3.0.1) with Gallus gallus 5.0 using the software's Best Practices for agricultural animals. The results were exported (Genotyping_Data-3-21-2018.vcf) for all genotype calls and text file of all SNPs with >= 97% call rate rate was also produced for filtering the VCF file (ALL_SNPSs_with_Call_Rate_97_Plus_3-21-2018).

Organism:

Gallus gallus

Type:

Genome variation profiling by SNP array

Platform:

GPL23815

96 Samples

Download data: CEL, VCF

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL8490 GPL6947

192 Samples

Download data

(Submitter supplied) Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) provide a conveniently accessible and renewable resource for functional studies in humans. The ability to accumulate multidimensional data pertaining to the same individual cell lines, from complete genomic sequences to detailed gene regulatory profiles, further enhances the utility of LCLs as a model system. A lingering concern, however, is that the changes associated with EBV transformation of LCLs reduce the usefulness of LCLs as a surrogate model for primary tissues. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

96 Samples

Download data: TXT

(Submitter supplied) Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines (LCLs) provide a conveniently accessible and renewable resource for functional studies in humans. The ability to accumulate multidimensional data pertaining to the same individual cell lines, from complete genomic sequences to detailed gene regulatory profiles, further enhances the utility of LCLs as a model system. A lingering concern, however, is that the changes associated with EBV transformation of LCLs reduce the usefulness of LCLs as a surrogate model for primary tissues. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

96 Samples

Download data: TXT

(Submitter supplied) Statin-induced gene expression differences observed in LCLs may be influenced by their transformation, and thus differ from those observed in native B-cells. To assess this possibility, we prepared LCLs and purified B-cells from the same donors, and compared mRNA profiles after 24hr incubation with simvastatin (2µM) or sham buffer.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

48 Samples

Download data: TXT

(Submitter supplied) Next-generation sequencing has been widely used for the genome-wide profiling of histone modifications, transcription factor binding and gene expression through chromatin immunoprecipitated DNA sequencing (ChIP-seq) and cDNA sequencing (RNA-seq). Here, we describe a versatile library construction method that can be applied to both ChIP-seq and RNA-seq on the widely used Illumina platforms. Standard methods for ChIP-seq library construction require nanograms of starting DNA, substantially limiting its application to rare cell types or limited clinical samples. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

23 Samples

Download data: TXT, WIG

(Submitter supplied) Recent studies indicated that iPSCs retain an epigenetic memory relating to their cell of origin that affected their properties and their functions as PSCs. Then, we used microarrays to detail the global programme of gene expression reflecting the effect of cell type of origin, and carefully compared the characteristics of iPSCs from LCL, T-cell, and DF based on their expression profiles .

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

12 Samples

Download data: CEL

(Submitter supplied) Epstein-Barr Virus (EBV) encoded Nuclear Antigens (EBNAs) and virus activated NF-kB subunits mostly bind to enhancers in EBV transformed lymphoblastoid cells lines (LCLs). Using LCL 3D genome organization map that links EBV enhancers to promoters, we built the most comprehensive virus regulome. EBV regulome contained 1992 genes and enhancers directly linked to them. ~30% of genes essential for LCL growth were linked to EBV enhancers. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

8 Samples

Download data: BAM, TDF

(Submitter supplied) Genome wide association studies have identified >200 susceptibility loci accounting for much of the heritability of Multiple Sclerosis (MS). Epstein-Barr virus (EBV), a memory B cell tropic virus, has been identified as necessary but not sufficient for development of MS. The molecular and immunological basis for this has not been established. Infected B cell proliferation is driven by signalling through the EBV produced cell surface protein LMP1, a homologue of the MS risk gene CD40. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

10 Samples

Download data: TXT

(Submitter supplied) Purpose: There exists a rich bio-resource of numerous lymphoblastoid cell line (LCL) repositories generated from a wide array of patients, many of them with extensive genotypic and phenotypic data already generated. We have developed a highly efficient LCL to induced pluripotent stem cells (iPSC) reprogramming method and performed whole genome mRNA and miRNA analysis to understand mechanistic changes that take place at the transcriptome and cellular functional level during reprogramming of LCLs into iPSCs and further differentiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

36 Samples

Download data: TXT

(Submitter supplied) EBNA1 is the EBV-encoded nuclear antigen required for viral episome maintenance during latency. EBNA1 is a sequence specific DNA binding protein with high affinity binding sites for the viral genome, especially OriP. EBNA1 can also bind sequence specifically to a large number of sites in the host cellular genome, but the function of these binding sites has remained elusive. EBNA1 is also known to provide a host cell survival function, but the molecular mechanisms accounting for this function are not completely understood. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL9115

12 Samples

Download data: TXT