Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

63 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profiling of the whole mouse brain using transcriptome tomography

ABSTRACT: We developed a novel framework to assess comprehensive endogenous gene expression maps in a broad and isotropic 3D-anatomical context using a relatively small number of original data points: transcriptome tomography. Using this method, we produced a dataset of gene expression maps of the whole mouse brain, computationally reconstructed from fraction data. A total of 61 fraction samples obtained with body axes-based slicing preparation conjugated with anatomical image acquisition were analysed. There are two sets of body axes-based preparation series: the S series, composed of 9 fractions/ C of 13 fractions/ H of 6 fractions , and the So series, composed of 10 fractions/ Co of 16 fractions/ Ho of 7 fractions.

ORGANISM(S): Mus musculus

SUBMITTER: Yuko Okamura-Oho

PROVIDER: E-GEOD-36408 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gene expression profiling of the whole mouse brain using transcriptome tomography

Project description:We developed a novel framework to assess comprehensive endogenous gene expression maps in a broad and isotropic 3D-anatomical context using a relatively small number of original data points: transcriptome tomography. Using this method, we produced a dataset of gene expression maps of the whole mouse brain, computationally reconstructed from fraction data.

2012-09-21 | GSE36408 | GEO

Gene expression profiling of the whole mouse brain at 7 days post-natal age using transcriptome tomography

Project description:We developed a novel framework to assess comprehensive endogenous gene expression maps in a broad and isotropic 3D-anatomical context using a relatively small number of original data points: transcriptome tomography. Using this method, we produced a dataset of gene expression maps of the whole mouse brain at 7 days after birth, computationally reconstructed from fraction data.

2018-08-07 | GSE118177 | GEO

Gene expression profiling of the whole mouse brain at 3 days post-natal age using transcriptome tomography

Project description:We developed a novel framework to assess comprehensive endogenous gene expression maps in a broad and isotropic 3D-anatomical context using a relatively small number of original data points: transcriptome tomography. Using this method, we produced a dataset of gene expression maps of the whole mouse brain at 3 days after birth, computationally reconstructed from fraction data.

2018-08-07 | GSE118176 | GEO

Gene expression profiling of the whole mouse brain at 3 weeks of post-natal age using transcriptome tomography

Project description:We developed a novel framework to assess comprehensive endogenous gene expression maps in a broad and isotropic 3D-anatomical context using a relatively small number of original data points: transcriptome tomography. Using this method, we produced a dataset of gene expression maps of the whole mouse brain at 3 weeks after birth, computationally reconstructed from fraction data.

2018-08-07 | GSE118178 | GEO

Colon cancer progression-polysomal difference

Project description:Two colon cancer cell lines are under study. SW480 and SW620. The first one is derived from primary cancer, SW620 are from lymphnode metastatic sites. they both comes from the sampe patient. Polisomal RNA fractions from the two isogenic colon cancer cells lines was purified by sucrose gradient and hybridized on affymetrix hgu133a chips. this study is complementary to the series GSE1323 were total RNA was used instead. Comparison between the polysomal fraction chips and the total RNA chips is performed and the analysis proposed in a paper from the authors (at the moment in preparation). Keywords: other

2005-11-08 | GSE2509 | GEO

Unique extracellular RNA profiles in different fractions of plasma

Project description:Circulating extracellular RNAs (exRNAs) have great promise as novel clinically plasma-based biomarkers for cancer diagnosis and prognosis. knowledge of the difference or association between these different sources of exRNAs is very limited. We performed a sequential physical and biochemical precipitation to receive 4 plasma fractions (platelets and cell debris, Thrombin-treated fraction, extracellular vesicles and supernatant) from each plasma sample. After total RNA extraction, we made ligation-free libraries and performed RNA-seq to evaluate full spectrum of RNA abundance in each fraction. All RNAs were included without size selection during the library preparation. We utilized a successive stepwise alignment strategy to map the RNA sequences to different RNA categories. We found that each plasma fraction had its own unique distribution of RNA species. Hierarchical cluster analysis showed similarity in samples with same fraction and significant differences between different fractions. In addition, we also observed abundance difference of unique transcript. Furthermore, a considerable proportion of exogenous RNAs and novel predicted miRNAs in all plasma fractions were detected. These results demonstrate that thorough inspection of all plasma fractions is necessary for exRNA-based biomarker study and appropriate sampling processes is needed for illustrating the complexity of plasma-based EVs study.

2021-06-07 | GSE145767 | GEO

Transcription profiling of two human colon cancer cell lines derived from a primry tumor and a lypmh node metastatsis from a single patient reveals global alterations in mRNA polysomal recruitment in a cell model of colorectal cancer progression to metastasis.

Project description:Two colon cancer cell lines are under study. SW480 and SW620. The first one is derived from primary cancer, SW620 are from lymphnode metastatic sites. they both come from the sample patient. Polysomal RNA fractions from the two isogenic colon cancer cells lines was purified by sucrose gradient and hybridized on affymetrix hgu133a chips. this study is complementary to the series GSE1323 where total RNA was used instead. Comparison between the polysomal fraction chips and the total RNA chips is performed and the analysis proposed in a paper from the authors (at the moment in preparation).

2007-10-27 | E-GEOD-2509 | biostudies-arrayexpress

CRISPR Phenotypic enrichment screen for epigenetic regulators of MEIS1 expression in acute myeloid leukemia (AML) [CRISPRScreens]

Project description:We perfomed CRISPR screens to investigate the upstream epigenetic regulators of MEIS1 expression, using a pooled CRISPR library targeting chromatin modifiers (~600 genes). We constructed the pooled library and used it to transduce U937 cells modified with a GFP knock-in in the MEIS1 locus. The cells were sampled at "Day 0" and kept in culture for 5 days, then sorted to harvest the top- and bottom- 20% fractions by GFP signal. Genomic DNA was then prepared from each fraction, as well as the Day 0 sample. We then performed library preparation and next generation sequencing to compare the relative abundance of sgRNA sequences in the fractions of interest.

2023-11-10 | GSE217778 | GEO

De novo protein identification in mammalian sperm using high-resolution in situ cryo-electron tomography

Project description:Understanding molecular mechanisms of cellular pathways regularly requires knowledge of the identities of participating proteins, their cellular localization and their 3D structures. Contemporary workflows typically require multiple techniques to identify target proteins, track their localization using fluorescence microscopy, followed by in vitro structure determination. To identify mammal-specific sperm proteins and understand their functions, we developed a visual proteomics workflow to directly address these challenges. Our in situ cryo-electron tomography analyses of mouse and human sperm revealed key microtubule structures at 6.0 Å resolution via subtomogram averaging. The well-resolved secondary and tertiary structures allowed us to unbiasedly match novel densities discovered in our 3D reconstruction maps with 21615 protein models from the library of the mouse proteome generated by AlphaFold2. Additional biochemical and mass spectrometry analyses helped validate potential candidates. Not only was it possible to de novo identify novel mammal-specific sperm proteins using this label-free structural approach, but their cellular localizations and molecular interactions could be determined in situ. Specifically, the novel sperm proteins form an extensive interaction network crosslinking the lumen of microtubules, suggesting they could modulate the mechanical and elastic properties of the microtubule filaments required for the vigorous beating motions of flagella. This project includes global protein abundance data from five biochemical fractionations of mouse sperm cells.

2024-05-21 | PXD036885 | Pride

Initiation Pausing of 80S Ribosome on mRNA Is Governed by 5’UTR and Responsive to mTORC1 Signaling (Microarray)

Project description:Recent studies have revealed that the mRNA translation is punctuated by ribosomal pauses through the body of transcripts. However, little is known about its physiological significance and regulatory aspects. Here we present a multi-dimensional ribosome profiling approach to quantify the dynamics of initiation and elongation of 80S ribosomes across the entire transcriptome in mammalian cells. We show that a subset of transcripts have a significant pausing of 80S ribosome around the start codon, creating a major barrier to the commitment of translation elongation. Intriguingly, genes encoding ribosome proteins themselves exhibit an exceptionally high initiation pausing on their transcripts. Our studies also reveal that the initiation pausing is dependent on the 5’ untranslated region (5’ UTR) of mRNAs and subject to the regulation of mammalian target of rapamycin complex 1 (mTORC1). Thus, the initiation pausing of 80S ribosome represents a novel regulatory step in translational control mediated by nutrient signaling pathway. Untreated TSC2 WT MEFs, TSC2 KO MEFs and TSC2 WT MEFs, TSC2 KO MEFs treated with 20nM rapamycin for 30 minutes or 3hours were harvested for ribosme profiling. The fraction samples were pooled into three groups based on velocity sedimentation: single ribosome fraction (Small group), fractions with 2 ~ 4 ribosomes (Medium group), and the one with ≥5 ribosomes (Large group). RNA were extracted from the whole cell lysis and each fraction group.

2011-11-12 | E-GEOD-25331 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data