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GSE26212
Homo sapiens
82 Downloadable Samples
Illumina HumanHT-12 V3.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
The effects of EBV transformation on gene expression levels and methylation profiles.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Homo sapiens
- 187 Downloadable Samples
- Illumina HumanHT-12 V3.0 expression beadchip
Description
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. We have previously shown that gene expression profiles of newly established LCLs maintain a strong individual component. Here, we extend our study to investigate the effect of freeze-thaw cycles on gene expression patterns in mature LCLs, especially in the context of inter-individual variation in gene regulation. We found a profound difference in the gene expression profiles of newly established and mature LCLs. Once newly established LCLs undergo a freeze-thaw cycle, the individual specific gene expression signatures become much less pronounced as the gene regulatory programs in LCLs from different individuals converge to a more uniform profile, which reflects a mature transformed B cell phenotype. As expected, previously identified eQTLs are enriched among the relatively few genes whose regulations in mature LCLs maintain marked individual signatures. We thus conclude that findings and insight drawn from gene regulatory studies in mature LCLs are generally not affected by artificial nature of the LCL model system and are likely to faithfully reflect regulatory interactions in primary tissues. However, our data indicate that many aspects of primary B cell biology cannot be observed and studied in mature LCL cultures.
Publication Title
The effect of freeze-thaw cycles on gene expression levels in lymphoblastoid cell lines.
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 82 Downloadable Samples
- Illumina HumanHT-12 V3.0 expression beadchip
Description
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. To evaluate the validity of this concern, we compared global gene expression profiles between CD20+ primary B cells and CD3+ primary T cells sampled from six individuals. Six independent replicates of transformed LCLs were derived from each sample.
Publication Title
The effects of EBV transformation on gene expression levels and methylation profiles.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Homo sapiens
- 40 Downloadable Samples
IlluminaHiSeq2000
Description
The use of low quality RNA samples in whole-genome gene expression profiling remains controversial. It is unclear if transcript degradation in low quality RNA samples occurs uniformly, in which case the effects of degradation can be normalized, or whether different transcripts are degraded at different rates, potentially biasing measurements of expression levels. This concern has rendered the use of low quality RNA samples in whole-genome expression profiling problematic. Yet, low quality samples are at times the sole means of addressing specific questions – e.g., samples collected in the course of fieldwork.
Publication Title
RNA-seq: impact of RNA degradation on transcript quantification.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 20 Downloadable Samples
- Illumina HiSeq 2500
Description
Elucidating the top of the mammary epithelial cell hierarchy is highly important for understanding its regeneration capabilities and identifying target cells for transformation. Aiming for enriched mammary epithelial stem cell population, CD200highCD200R1high epithelial cells were identified. These cells represent ~50% of the mammary repopulating units (MRUs, CD49fhigh CD24med ) and termed MRUCD200/CD200R1. Gene expression of these cells was compared to all other MRU cells, termed MRUnot CD200/CD200R1, as well as individual CD200+ population (MRU-CD200R1-) and CD200R1+ population (MRU-CD200-). Overall design: Gene expression from mammary epithelial cells carrying sorted by CD200, CD200R1 markers and MRU markers. Four populations were sequenced: MRU-positive CD200 positive and CD200R1 positive; MRU-positive and not CD200 positive CD200R1 positive; not MRU CD200 positive CD200R1 negative; not MRU CD200 negative CD200R1 positive. There are 5 replicates from 5 individual mice.
Publication Title
High Expression of CD200 and CD200R1 Distinguishes Stem and Progenitor Cell Populations within Mammary Repopulating Units.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
mRNA expression differences between the liver and kidney of an adult male (homo sapien) were investigated using three technical replicates.
Publication Title
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 309 Downloadable Samples
- IlluminaHiSeq2500
Description
A new method to measure elongation and intitiation rates Overall design: Reversal inhibition of transcription with DRB and tagging newly transcribed RNA with 4-thiouridine (4sU)
Publication Title
4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 259 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Identification of genetic polymorphisms associated with inter-individual variation in immune response to Mycobacterium tuberculosis infection.
Publication Title
Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 71 Downloadable Samples
- IlluminaHiSeq2500
Description
Genetic variants that impact gene regulation are important contributors to human phenotypic variation. For this reason, considerable efforts have been made to identify genetic associations with differences in mRNA levels of nearby genes, namely, cis expression quantitative trait loci (eQTLs). The phenotypic consequences of eQTLs are presumably due, in most cases, to their ultimate effects on protein expression levels. Yet, only few studies have quantified the impact of genetic variation on proteins levels directly. It remains unclear how faithfully eQTLs are reflected at the protein level, and whether there is a significant layer of cis regulatory variation acting primarily on translation or steady state protein levels. To address these questions, we measured ribosome occupancy by high-throughput sequencing, and relative protein levels by high-resolution quantitative mass spectrometry, in a panel of lymphoblastoid cell lines (LCLs) in which we had previously measured transcript expression using RNA sequencing. We then mapped genetic variants that are associated with changes in transcript expression (eQTLs), ribosome occupancy (rQTLs), or protein abundance (pQTLs). Most of the QTLs we detected are associated with transcript expression levels, with consequent effects on ribosome and protein levels. However, we found that eQTLs tend to have significantly reduced effect sizes on protein levels, suggesting that their potential impact on downstream phenotypes is often attenuated or buffered. Additionally, we confirmed the presence of a class of cis QTLs that specifically affect protein abundance with little or no effect on mRNA levels; most of these QTLs have little effect on ribosome occupancy, and hence may arise from differences in post-translational regulation. Overall design: We measured level of translation transcriptome-wide in lymphoblastoid cell lines derived from 72 HapMap Yoruba individuals using ribosome profiling assay, for which we have transcript level, protein level (62 out of 72) and genotype information collected.
Publication Title
Genomic variation. Impact of regulatory variation from RNA to protein.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 4 Downloadable Samples
- IlluminaGenomeAnalyzerII
Description
Next-generation sequencing has become an important tool for genome-wide quantification of DNA and RNA. However, a major technical hurdle lies in the need to map short sequence reads back to their correct locations in a reference genome. Here we investigate the impact of SNP variation on the reliability of read-mapping in the context of detecting allele-specific expression (ASE).We generated sixteen million 35 bp reads from mRNA of each of two HapMap Yoruba individuals. When we mapped these reads to the human genome we found that, at heterozygous SNPs, there was a significant bias towards higher mapping rates of the allele in the reference sequence, compared to the alternative allele. Masking known SNP positions in the genome sequence eliminated the reference bias but, surprisingly, did not lead to more reliable results overall. We find that even after masking, $\sim$5-10\% of SNPs still have an inherent bias towards more effective mapping of one allele. Filtering out inherently biased SNPs removes 40\% of the top signals of ASE. The remaining SNPs showing ASE are enriched in genes previously known to harbor cis-regulatory variation or known to show uniparental imprinting. Our results have implications for a variety of applications involving detection of alternate alleles from short-read sequence data. Scripts, written in Perl and R, for simulating short reads, masking SNP variation in a reference genome, and analyzing the simulation output are available upon request from JFD. Overall design: RNA-Seq on two YRI Hapmap cell lines. Each individual sequenced on two lanes of the Illumina Genome Analyzer
Publication Title
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.
Sample Metadata Fields
No sample metadata fields
View Samples