Sequence biases in large scale gene expression profiling data

We present the results of a simple, statistical assay that measures the G+C content sensitivity bias of gene expression experiments without the requirement of a duplicate experiment. We analyse five gene expression profiling methods: Affymetrix GeneChip, Long Serial Analysis of Gene Expression (LongSAGE), LongSAGELite, ‘Classic’ Massively Parallel Signature Sequencing (MPSS) and ‘Signature’ MPSS. We demonstrate the methods have systematic and random errors leading to a different G+C content sensitivity. The relationship between this experimental error and the G+C content of the probe set or tag that identifies each gene influences whether the gene is detected and, if detected, the level of gene expression measured. LongSAGE has the least bias, while Signature MPSS shows a strong bias to G+C rich tags and Affymetrix data show different bias depending on the data processing method (MAS 5.0, RMA or GC-RMA). The bias in the Affymetrix data primarily impacts genes expressed at lower levels. Despite the larger sampling of the MPSS library, SAGE identifies significantly more genes (60% more RefSeq genes in a single comparison)

LongSAGE profiling of nine human embryonic stem cell lines

Analysis of a 2.6 million longSAGE sequence tag resource generated from nine human embryonic stem cell lines reveals an enrichment of RNA binding proteins and novel ES-specific transcripts

Analysis of undifferentiated human embryonic stem cell lines using Serial Analysis of Gene Expression

Since the first reported isolation of immortalized human embryonic stem cell (hESC) lines in 1998 (Thomson et al., 1998), methods for directing their differentiation to various specialized derivatives has been extensively demonstrated and provides hope for future therapeutic applications. Characterization of the key molecular factors governing hESC self-renewal and pluripotency is necessary for ongoing efforts in deriving therapeutically useful cell types and in modelling human embryonic and oncogenic development. To this end the GSC Gene Expression Laboratory has generated 11 global gene expression profiles of 8 undifferentiated hESC lines using long Serial Analysis of Gene Expression (long SAGE) (NIH stem cell registry code BG01, ES03, ES04, WA01, WA07, WA09, WA13, and WA14). I analysed a database of the hESC long SAGE data consisting of 2,613,475 total tags corresponding to 379,465 transcripts. By employing various comprehensive tag-togene mapping resources I have provided a detailed survey of the genes expressed and differentially expressed in multiple hESC lines. A suite of sternness-associated factors was observed in the hESC SAGE data. We also observed molecular components of several pathways involved in embryonic development, the cell cycle, and programmed cell death. Comprehensive interspecies pair-wise comparisons between the hESC libraries and publicly available human SAGE libraries identified up-regulated transcripts in embryonic stem cells. A robust computational approach was designed and identified tags expressed solely in hESCs compared to 247 normal and malignant cells. A key feature of the approach was to isolate tags derived from sequences conserved across the human, mouse and rat genomes; this led to the identification of 301 candidate novel transcripts that may be integral to human pluripotent stem cells. These studies represent an important step in the development of high throughput approaches to an analysis of early human developmental processes and will be a strategic element in more comprehensive interspecies comparisons of E S cells to identify preserved control mechanisms.Medicine, Faculty ofMedical Genetics, Department ofGraduat

The Histone Demethylase KDM5b/JARID1b Plays a Role in Cell Fate Decisions by Blocking Terminal Differentiation ▿ †

The histone demethylase lysine demethylase 5b (KDM5b) specifically demethylates lysine 4 of histone H3 (meH3K4), thereby repressing gene transcription. KDM5b regulates cell cycle control genes in cancer and is expressed in the early epiblast. This suggests that KDM5b plays a developmental role by maintaining uncommitted progenitors. Here we show that transient overexpression of KDM5b in embryonic stem cells decreases the expression of at least three different modulators of cell fate decisions, Egr1, p27KIP1, and BMI1, by demethylation of their promoters. Constitutively increased KDM5b expression results in an increased mitotic rate and a decreased global 3meH3K4 but no change in cell identity. Results of two separate differentiation assays, neural differentiation and embryoid body EB (EB) formation, showed that KDM5b reduced the terminally differentiated cells and increased proliferating progenitors. These were achieved by two mechanisms, blocking of the upregulation of cell lineage markers and maintenance of cyclins, that allowed cells to escape differentiation and remain uncommitted. Additionally, EBs maintain high levels of Oct4 and Nanog and can be dissociated to reestablish highly proliferative cultures. The persistence of uncommitted progenitors may be due to the direct regulation of the Tcf/Lef family member mTcf3/hTcf7L1, an upstream regulator of Nanog expression. These findings demonstrate a role for KDM5b in the choice between proliferation and differentiation during development

Oligonucleotide Microarray Analysis of Genomic Imbalance in Children with Mental Retardation

The cause of mental retardation in one-third to one-half of all affected individuals is unknown. Microscopically detectable chromosomal abnormalities are the most frequently recognized cause, but gain or loss of chromosomal segments that are too small to be seen by conventional cytogenetic analysis has been found to be another important cause. Array-based methods offer a practical means of performing a high-resolution survey of the entire genome for submicroscopic copy-number variants. We studied 100 children with idiopathic mental retardation and normal results of standard chromosomal analysis, by use of whole-genome sampling analysis with Affymetrix GeneChip Human Mapping 100K arrays. We found de novo deletions as small as 178 kb in eight cases, de novo duplications as small as 1.1 Mb in two cases, and unsuspected mosaic trisomy 9 in another case. This technology can detect at least twice as many potentially pathogenic de novo copy-number variants as conventional cytogenetic analysis can in people with mental retardation

Expression of selected transcripts during embryoid body differentiation

qPCR was used to monitor expression of selected transcripts in ESCs stimulated to differentiate into embryoid bodies. Three control markers, Oct4, Lin28 and Msx1, were included. Expression levels are reported as the mean of triplicate measurements and are normalized to GAPDH.<p><b>Copyright information:</b></p><p>Taken from "LongSAGE profiling of nine human embryonic stem cell lines"</p><p>http://genomebiology.com/2007/8/6/R113</p><p>Genome Biology 2007;8(6):R113-R113.</p><p>Published online 14 Jun 2007</p><p>PMCID:PMC2394759.</p><p></p