publication_authors:Sonabend AM Results

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Organism

Mus musculus (244)

Danio rerio (10)

Technology

Microarray (247)

Rna-seq (7)

Platform

Affymetrix Mouse Genome 430 2.0 Array (mouse4302) (244)

Illumina HiSeq 2000 (7)

Affymetrix Zebrafish Genome Array (zebrafish) (3)

Includes Publication (7)

GSE29458

Expression data from PDGF driven mouse tumors

Mus musculus
23 Downloadable Samples

Description

Background

Publication Title

Glioblastoma models reveal the connection between adult glial progenitors and the proneural phenotype.

Alternate Accession IDs

E-GEOD-29458

Sample Metadata Fields

Specimen part

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GSE107292

Expression data and genome-wide maps of chromatin in Phf8 knock out and wild type mice

Mus musculus
6 Downloadable Samples

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Phf8 histone demethylase deficiency causes cognitive impairments through the mTOR pathway.

Alternate Accession IDs

E-GEOD-107292

Sample Metadata Fields

Age, Specimen part

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GSE107210

Expression data from hippocampus of Phf8 knock out and wild type mice

Mus musculus
1 Downloadable Sample

Description

We used microarrays to detail the global programme gene expression of Phf8 knock out and wild type mice

Publication Title

Phf8 histone demethylase deficiency causes cognitive impairments through the mTOR pathway.

Alternate Accession IDs

E-GEOD-107210

Sample Metadata Fields

Age, Specimen part

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GSE83326

Hepatic gene expression data from cadmium-exposed mice

Mus musculus
10 Downloadable Samples

Description

Environmental cadmium, with a high average dietary intake, is a severe public health risk. However, the long-term health implications of environmental exposure to cadmium in different life stages remain unclear.

Publication Title

Sex-Dependent Effects of Cadmium Exposure in Early Life on Gut Microbiota and Fat Accumulation in Mice.

Alternate Accession IDs

E-GEOD-83326

Sample Metadata Fields

Sex, Specimen part

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GSE23821

Expression analysis of stimulated macrophages from CEBPB-knockout, CEBPE-knockout, and CEBPB/CEBPE double-knockout mice

Mus musculus
3 Downloadable Samples

Description

The CCAAT/enhancer-binding proteins (CEBPs) are transcription factors involved in hematopoietic cell development and induction of several inflammatory mediators. Here, we generated CEBP-beta (CEBPB) and CEBP-epsilon (CEBPE) double-knockout (bbee) mice and compared their phenotypes to those of single-deficient (bbEE and BBee) and wild-type (BBEE) mice.

Publication Title

In vivo deficiency of both C/EBPβ and C/EBPε results in highly defective myeloid differentiation and lack of cytokine response.

Alternate Accession IDs

E-GEOD-23821

Sample Metadata Fields

Sex, Specimen part, Treatment

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SRP018699

Gene expression profiling of zebrafish embryos at 5 days post fertilization [Illumina RNA-Seq]

Danio rerio
3 Downloadable Samples
IlluminaHiSeq2000

Description

We compared Agilent custom made expression microarrays with Illumina deep sequencing for RNA analysis of zebrafish embryos 5 days post fertilization, showing as expected a high degree of correlation of expression of a common set of 15,927 genes for untreated fish. The transcriptomes were also compared for fish injected in the yolk with Mycobacterium marinum Overall design: This RNA deep sequencing study was designed to determine the gene expression profile of zebrafish embryos 5 days post fertilization. We also have compared expression with embryos that were injected with Mycobacterium marinum in the yolk at 2 hours post fertilization. After injections embryos were transferred into fresh egg water and incubated at 28Â°C. 150 embryos of mock-injected embryos or 200 embryos injected with 12 CFU bacteria were snap-frozen in liquid nitrogen, and total RNA was isolated using TRIZOL reagent.

Publication Title

Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformatics.

Alternate Accession IDs

GSE44351

Sample Metadata Fields

No sample metadata fields

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SRP030657

Assessment of hematopoietic failure due to RPL11 deficiency in a zebrafish model of Diamond–Blackfan anemia by deep sequencing

Danio rerio
2 Downloadable Samples
IlluminaHiSeq2000

Description

To comprehensively reflect the impact of RPL11 deficiency on the transcriptome of zebrafish embryos, we collected 40–50 RPL11-deficient and MO control zebrafish embryos at 48 hpf from separate experiments and constructed two mRNA-seq sequencing libraries in parallel. High-throughput sequencing was performed on the Hi-Seq2000 sequencing platform in parallel. The number of sequenced gene transcript reads was 35–40 million. We found that hemoglobin biosynthetic and hematological defects in RPL11-deficient zebrafish were related to dysregulation of iron metabolism-related genes, including tfa, tfr1b, alas2 and slc25a37, which are involved in heme and hemoglobin biosynthesis. In addition, we found reduced expression of the hematopoietic stem cells (HSC) marker c-myb and HSC transcription factor tal1 and hoxb4a in RPL11-deficient zebrafish embryos, indicating that the hematopoietic defects may be related to impaired HSC differentiation and proliferation. However, RPL11 deficiency did not affect the development of other blood cell lineages such as granulocytes and myelocytes. Overall design: Compare 2 different transcriptomes of RPL11-deficient and MO control zebrafish embryos

Publication Title

Transcriptome analysis of Rpl11-deficient zebrafish model of Diamond-Blackfan Anemia.

Alternate Accession IDs

GSE51326

Sample Metadata Fields

No sample metadata fields

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GSE17667

Pou5f1 transcription targets in zebrafish

Danio rerio
3 Downloadable Samples

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Zebrafish Pou5f1-dependent transcriptional networks in temporal control of early development.

Alternate Accession IDs

E-GEOD-17667

Sample Metadata Fields

No sample metadata fields

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GSE47772

Expression data from subpopulations of Apc1638N/+ intestinal adeno tumors versus Apc1638N/+ / KRAS v12G intestinal adenocarcinomas tumors

Mus musculus
24 Downloadable Samples

Description

Constitutive activation of the Wnt pathway leads to adenoma formation, an obligatory step towards intestinal cancer. In view of the established role of Wnt in regulating stemness, we attempted the isolation of cancer stem cells (CSCs) from Apc- and Apc/KRAS-mutant intestinal tumours. Whereas CSCs are present in malignant Apc/KRASmutant carcinomas, they appear to be very rare (<10-6) in the benign Apcmutant adenomas. In contrast, the Lin-CD24hiCD29+ subpopulation of adenocarcinoma cells appear to be enriched in CSCs with increased levels of active -catenin. Expression profiling analysis of the CSC-enriched subpopulation confirmed their enhanced Wnt activity and revealed additional differential expression of other signalling pathways, growth factor binding proteins, and extracellular matrix components. As expected, genes characteristic of the Paneth cell lineage (e.g. defensins) are co-expressed together with stem cell genes (e.g. Lgr5) within the CSC-enriched subpopulation. This is of interest as it may indicate a cancer stem cell niche role for tumor-derived Paneth-like cells, similar to their role in supporting Lgr5+ stem cells in the normal intestinal crypt. Overall, our results indicate that oncogenic KRAS activation in Apc-driven tumours results in the expansion of the CSCs compartment by increasing b-catenin intracellular stabilization.