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Rattus norvegicus
18 Downloadable Samples
Affymetrix Rat Expression 230A Array (rae230a), Affymetrix Rat Expression 230B Array (rae230b)
Description
Hypertensive congenic kidney - 21 week Salt RAE230A and B
Publication Title
Microarray analysis of rat chromosome 2 congenic strains.
Sample Metadata Fields
Age, Specimen part, Disease
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Transcriptome analysis of two Ph+ acute lymphoblastic leukemia cell lines after doxycycline induced silencing of MYB.
Publication Title
Targeting CDK6 and BCL2 Exploits the "MYB Addiction" of Ph<sup>+</sup> Acute Lymphoblastic Leukemia.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 29 Downloadable Samples
Illumina HiSeq 2500
Description
To probe the tissue source (cancer cell VS stromal cell) of gene expression in the mixed tumor samples, we took advantage of a set of Urothelial Cancer patient-derived xenograft (PDX) models given that the transcriptome in these models is a mixture of human RNA (derived from cancer cells) and mouse RNA (derived from stromal cells). Overall design: The cohort includes 5 different patient-derived PDX models, 3 replicates for each model, and thus a total of 15 samples
Publication Title
EMT- and stroma-related gene expression and resistance to PD-1 blockade in urothelial cancer.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 15 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
First experiment: Cells were cultured in sulfur amino acid-free DMEM supplemented with 0.1 mM methionine + 0.1 mM cysteine (complete) or supplemented only with 0.1 mM methionine (cysteine-free). Cells were cultured in either medium for 42 h (Long + Cys; Long -Cys) or in cysteine-free medium for 36 h followed by 6 h in complete medium (Short +Cys)
Publication Title
HepG2/C3A cells respond to cysteine deprivation by induction of the amino acid deprivation/integrated stress response pathway.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
HepG2/C3A cells cultured for 42 h in complete or leucine-devoid medium
Publication Title
HepG2/C3A cells respond to cysteine deprivation by induction of the amino acid deprivation/integrated stress response pathway.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus, Homo sapiens, Saccharomyces cerevisiae
- 9 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.
Sample Metadata Fields
Specimen part, Cell line, Treatment
View Samples- Saccharomyces cerevisiae
- 9 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
Inactivation of the yeast IME4 gene, the yeast homologue of METTL3, was shown to result in the loss of m6A in mRNA of mutant cells grown in sporulation medium. We attempted to characterize the effects of ime4 deletion on gene expression under vegetative and meiosis-inducing conditions. The results show that in vegetatively-growing ime4-/- cells there is an increased expression of the RME1 gene (repressor of meiosis) which prevents precocious entry into the meiotic program. Mutant yeast cells showed reduced expression levels of genes involved in ribosome biogenesis and gene expression processes. Surprisingly, despite the fact that a diploid strain was analyzed, there was also a striking change in the expression level of haploid-specific genes, suggesting that RNA methylation may be used to enforce the sexual identity of diploid cells, required for the implementation of the gametogenesis program. Consistently, when cells were induced to undergo meiosis, ime4-/- diploids failed to undergo the meiotic divisions. Among the genes showing reduced expression in the mutant were IME1 and IME2, the two known inducers of meiosis. Thus, the yeast IME4 gene plays an important role in the regulation of the developmental switch from vegetative cells into gametogenesis.
Publication Title
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
We developed a novel approach, m6A-seq, for high-resolution mapping of the transcriptome-wide m6A landscape, based on antibody-mediated capture followed by massively parallel sequencing. Overall design: Identification of m6A modified sequences in HepG2 cells. HepG2 cells were incubated with either IFNg (200ng/ml) or HGF/SF (10 ng/ml) over night. Stress effects were tested in HepG2 cells by either 30 minutes incubation at 43ºC (heat shock) or UV irradiation of 0.04 J/cm2 followed by 4 hours of recovery in normal growing conditions prior to harvesting using Trypsin.
Publication Title
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples
SRP012096- Homo sapiens
- 4 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
To gain insight into possible processes that require m6A for their function, METTL3 was knocked down (KD) in HepG2 cells by siRNA transfections Overall design: Differential expression analysis of METTL3 KD versus mock-transfected HepG2 cells, in 2 biological replicates
Publication Title
Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
Current pipelines used to map genetrap insertion sites are based on inverse- or splinkerette-PCR methods, which despite their efficacy are prone to artifacts and do not provide information on the impact of the genetrap on the expression of the targeted gene. We developed a new method, which we named TrapSeq, for the mapping of genetrap insertions based on paired-end RNA sequencing. By recognizing chimeric mRNAs containing genetrap sequences spliced to an endogenous exon, our method identifies insertions that lead to productive trapping. Overall design: We conducted two independent screenings for sensitivity against 6-thioguanine (6TG) and an ATR inhibitor (ATRi). We applied our RNAseq-based pipeline (TrapSeq) to identify mutations that provide resistance to these reagents. Importantly, and besides its use for screenings, when applied to individual clones our method provides a fast and cost-effective way that not only identifies the insertion site of the genetrap but also reveals the impact of the insertion on the expression of the trapped gene. Please note that HAP1, haploid for all chromosomes, derives from near-haploid KBM7 parent line which was in turn obtained from a chronic myeloid leukemia patient in blast crisis phase (Carette et al. Nature 477:340-343, 2011).
Publication Title
Trap<sup>Seq</sup>: An RNA Sequencing-Based Pipeline for the Identification of Gene-Trap Insertions in Mammalian Cells.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples