Filters
Technology
Platform
SRP042647
Homo sapiens
10 Downloadable Samples
Illumina Genome Analyzer II
Description
Specific mutations in the XPD subunit of transcription factor IIH result in combined xeroderma pigmentosum (XP)/Cockayne syndrome (CS), a severe DNA repair disorder characterized at the cellular level by a transcriptional arrest following UV irradiation. This transcriptional arrest has always been thought to be the result of faulty transcription-coupled repair. In the present study, we investigate the transcriptional dysregulation that follows UV irradiation in XP-D/CS compared with “pure” XP-D cells or WT cells. We also study how this process is affected by the inhibition of the histone deacetylase Sirt1.
Publication Title
Sirt1 suppresses RNA synthesis after UV irradiation in combined xeroderma pigmentosum group D/Cockayne syndrome (XP-D/CS) cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Escherichia coli str. k-12 substr. mg1655
- 4 Downloadable Samples
Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
Promoter recognition by bacterial RNA polymerase is mediated by subunits, which assemble transiently to RNA polymerase core enzyme (E) during transcription initiation. subunits drive transcription of specific sets of genes by allowing RNA polymerase to interact with different promoter sequences. However, 70, the housekeeping subunit, and S, an alternative subunit mainly active during slow growth and in response to cellular stresses, appear to recognize almost identical promoter sequences, raising the question of how promoter selectivity is achieved in the bacterial cell. To identify sequence determinants for selective promoter recognition, we performed a run-off/microarray experiment (ROMA): in vitro transcription experiments were carried out with RNA polymerase saturated either with 70 (E70) or with S (ES) using the whole Escherichia coli genome as DNA template, and transcript levels were determined by microarray analysis. We found that several genes associated with bacterial growth (e.g., ribosomal operons) were transcribed more efficiently by E70. In contrast, ES transcribed preferentially genes involved in stress responses, secondary metabolism, as well as regulatory RNAs and intergenic regions with yet unknown function. Genes preferentially recognized in vitro by ES showed reduced expression in ES -deficient mutant strain of E. coli. Sequence comparison of E70- versus ES dependent promoters confirms that the presence of a -35 sequence and the relative location of UP elements affect promoter interaction with either form of RNA polymerase, and suggests that a G/C bias in the -2/+1 nucleotides would favour efficient promoter recognition by E70.
Publication Title
In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements.
Sample Metadata Fields
Disease
View Samples- Escherichia coli str. k-12 substr. mg1655
- 58 Downloadable Samples
- Affymetrix E. coli Genome 2.0 Array (ecoli2)
Description
The widespread use of electricity raises the question of whether or not 50 Hz (power line frequency in Europe) magnetic fields (MFs) affect organisms. We investigated the transcription of Escherichia coli K-12 MG1655 in response to extremely low-frequency (ELF) MFs. Fields generated by three signal types (sinusoidal continuous, sinusoidal intermittent, and power line intermittent; all at 50 Hz, 1 mT), were applied and gene expression was monitored at the transcript level using an Affymetrix whole-genome microarray. Bacterial cells were grown continuously in a chemostat (dilution rate D = 0.4 h-1) fed with glucose-limited minimal medium and exposed to 50 Hz MFs with a homogenous flux density of 1 mT. For all three types of MFs investigated, neither bacterial growth (determined using optical density) nor culturable counts were affected. Likewise, no statistically significant change (fold-change > 2, P 0.01) in the expression of 4,358 genes and 714 intergenic regions represented on the gene chip was detected after MF exposure for 2.5 h (1.4 generations) or 15 h (8.7 generations). Moreover, short-term exposure (8 min) to the sinusoidal continuous and power line intermittent signal neither affected bacterial growth nor showed evidence for reliable changes in transcription. In conclusion, our experiments did not indicate that the different tested MFs (50 Hz, 1 mT) affected the transcription of E. coli.
Publication Title
Genome-wide transcription analysis of Escherichia coli in response to extremely low-frequency magnetic fields.
Sample Metadata Fields
Treatment
View Samples- Homo sapiens
- 10 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Gene expression profile in CS1AN deficient and CSBwt restored cell lines after 24 hours of UV or alphe-amanitin treatment (only for restored). The comaprison of expression profile between 0 and 24 hours revealed
Publication Title
Regulatory interplay of Cockayne syndrome B ATPase and stress-response gene ATF3 following genotoxic stress.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
The goal of this experiment was to compare gene expression after t-RA treatment in cells with or without the presence of the PolyADP ribose Glycohydrolase protein (PARG)
Publication Title
Poly (ADP-ribose) glycohydrolase regulates retinoic acid receptor-mediated gene expression.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 2 Downloadable Samples
- IlluminaHiSeq2500
Description
Diploidy is a fundamental genetic feature in mammals, in which haploid cells normally arise only as post-meiotic germ cells that serve to insure a diploid genome upon fertilization. Gamete manipulation has yielded haploid embryonic stem (ES) cells from several mammalian species, but as of yet not from humans. Here we analyzed a large collection of human parthenogenetic ES cell lines originating from haploid oocytes, leading to the successful isolation and maintenance of human ES cell lines with a normal haploid karyotype. Haploid human ES cells exhibited typical pluripotent stem cell characteristics such as self-renewal capacity and a pluripotency-specific molecular signature. Although haploid human ES cells resembled their diploid counterparts, they also displayed distinct properties including differential regulation of X chromosome inactivation and genes involved in oxidative phosphorylation, alongside reduction in absolute gene expression levels and cell size. Intriguingly, we found that a haploid genome is compatible not only with the undifferentiated pluripotent state, but also with differentiated somatic fates representing all three embryonic germ layers, despite a persistent dosage imbalance between the autosomes and X chromosome. We expect that haploid human ES cells will provide novel means for studying human functional genomics, development and evolution. Overall design: RNA sequencing analysis was performed on a total of 2 samples of in vitro fertilization (IVF) control embryonic stem cell lines.
Publication Title
Derivation and differentiation of haploid human embryonic stem cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 2 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Diploidy is a fundamental genetic feature in mammals, in which haploid cells normally arise only as post-meiotic germ cells that serve to insure a diploid genome upon fertilization. Gamete manipulation has yielded haploid embryonic stem (ES) cells from several mammalian species, but as of yet not from humans. Here we analyzed a large collection of human parthenogenetic ES cell lines originating from haploid oocytes, leading to the successful isolation and maintenance of human ES cell lines with a normal haploid karyotype. Haploid human ES cells exhibited typical pluripotent stem cell characteristics such as self-renewal capacity and a pluripotency-specific molecular signature. Although haploid human ES cells resembled their diploid counterparts, they also displayed distinct properties including differential regulation of X chromosome inactivation and genes involved in oxidative phosphorylation, alongside reduction in absolute gene expression levels and cell size. Intriguingly, we found that a haploid genome is compatible not only with the undifferentiated pluripotent state, but also with differentiated somatic fates representing all three embryonic germ layers, despite a persistent dosage imbalance between the autosomes and X chromosome. We expect that haploid human ES cells will provide novel means for studying human functional genomics, development and evolution.
Publication Title
Derivation and differentiation of haploid human embryonic stem cells.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 89 Downloadable Samples
- Illumina HiSeq 2500
Description
We developed a technique for generating hypothalamic neurons from human pluripotent stem cells. Here, as proof-of-principle, we examine the use of these cells in modeling of a monogenic form of severe obesity: PCSK1 deficiency. We generated PCSK1 (PC1/3)-deficient human embryonic stem cell (hESC) lines using both shRNA and CRISPR-Cas9, and investigated pro-opiomelanocortin (POMC) processing using hESC-differentiated hypothalamic neurons. Overall design: We tried to idenitify transcripitional profiles and specific transcription factors that involved in of different stages during hypothalamic neuron differentiation from single cell sequencing for hESC-derived Day27 hypothalamic neurons, Day 12 neuron progenitors and undifferentiated stem cells
Publication Title
PC1/3 Deficiency Impacts Pro-opiomelanocortin Processing in Human Embryonic Stem Cell-Derived Hypothalamic Neurons.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Homo sapiens
- 16 Downloadable Samples
- Illumina HumanRef-8 v3.0 expression beadchip
Description
Gene expression of sibling human ES cell lines are more similar to each other than unrelated cell lines.
Publication Title
Optimal timing of inner cell mass isolation increases the efficiency of human embryonic stem cell derivation and allows generation of sibling cell lines.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 37 Downloadable Samples
- Illumina mouseRef-8 v1.1 expression beadchip
Description
Although nuclear transfer allows the reprogramming of somatic cells to totipotency, little is known concerning the kinetics by which it takes place or the minimum requirements for its success. Here, we demonstrate that reprogramming can be achieved within a few hours and a single cell-cycle as long as two key constraints on reprogramming are satisfied. First, the recipient cell chromosomes must be removed during mitosis. Second, the nuclear envelope of the donor cell must be broken down and its chromosomes condensed, allowing an embryonic nucleus to be constructed around the incoming chromosomes. If these requirements are not met, then reprogramming fails and embryonic development arrests. These results point to a central role for processes intimately linked to cell division in mediating efficient transitions between transcriptional programs.
Publication Title
Reprogramming within hours following nuclear transfer into mouse but not human zygotes.
Sample Metadata Fields
Specimen part
View Samples