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Allen Institute for Brain Science transcriptomic reference dataset
Transcriptomic Reference Dataset, supplied by Allen Institute for Brain Science, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/transcriptomic+reference+dataset/transcriptomics+explorer/pm39353431-47-3-20
Average 90 stars, based on 1 article reviews
transcriptomic reference dataset - by Bioz Stars, 2026-10
90/100 stars

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Related Articles

Gene Expression:

Article Title: Over-integration of visual network in major depressive disorder and its association with gene expression profiles.
Article Snippet: .. In this study, we integrated an R-fMRI dataset of 559 individuals with transcriptomic data from the brains of six donors provided by the Allen Human Brain Atlas (AHBA) from the Allen Institute for Brain Science (AIBS) [34, 39], to investigate the modular connectome patterns of brain networks in MDD and their relationships with gene expression profiles. ..

other:

Article Title: Cell-specific expression of key mitochondrial enzymes limits OXPHOS in astrocytes of the adult human neocortex and hippocampal formation.
Article Snippet: These data are corroborated by queries of transcriptomes (107 brains) of neuronal versus non-neuronal cells fetched from the Allen Institute for Brain Science for genes coding for amuch larger repertoire of entities contributing to OXPHOS, showing that human non-neuronal elements barely expressed mRNAs coding for such proteins.

Article Title: Transcriptomic cell-type specificity of local cortical circuits.
Article Snippet: We used a transcriptomic reference dataset composed of uninfected nuclei collected from V1 with cell-type annotations established according to the Allen Institute for Brain Science (AIBS) celltype taxonomy.5,26 This dataset has been previously shown to enable accurate characterization of rabies-infected cortical neurons.27 SingleR was used to conduct supervised label transfer annotation of cell types, and this annotation method was selected for its robustness against cell-type similarity and increased cell-type number compared with other computational methods.28 Input neurons were classified at the class level (glutamatergic, GABAergic, or non-neuronal), subclass level (e.g., L2/3, L4, L5 IT; Sst, Pvalb, Vip, etc.), and at the subtype level (e.g., Sst Chodl, Sst Esm1, etc.) (Figure 1B).

Transcriptomics:

Article Title: Cell-specific expression of key mitochondrial enzymes limits OXPHOS in astrocytes of the adult human neocortex and hippocampal formation
Article Snippet: .. Subsequently, they were queried using the Transcriptomics Explorer of the Allen Institute for Brain Science human and mouse brain transcriptome (RNA-seq) repository ( https://portal.brain-map.org/atlases-and-data/rnaseq ). ..

Article Title: Cell-specific expression of key mitochondrial enzymes limits OXPHOS in astrocytes of the adult human neocortex and hippocampal formation.
Article Snippet: Analysis of transcripts deposited in the Allen Institute for Brain Science coding for mitochondrially-localized proteins in individual brain cells The gene symbols ofmitochondrially-localized subunits of proteins enlisted inMitoCarta 2.065 curated to include newer data reported inMitoCarta 3.066 were filtered to include only those that are involved in OXPHOS (respiratory chain components, transporters of adenine nucleotides, Pi and substrates, and the citric acid cycle dehydrogenases MDH2, IDH2 and IDH3). .. Subsequently, they were queried using the Transcriptomics Explorer of the Allen Institute for Brain Science human and mouse brain transcriptome (RNA-seq) repository (https://portal.brain-map.org/atlases-and-data/ rnaseq). ..

RNA Sequencing:

Article Title: Cell-specific expression of key mitochondrial enzymes limits OXPHOS in astrocytes of the adult human neocortex and hippocampal formation
Article Snippet: .. Subsequently, they were queried using the Transcriptomics Explorer of the Allen Institute for Brain Science human and mouse brain transcriptome (RNA-seq) repository ( https://portal.brain-map.org/atlases-and-data/rnaseq ). ..

Article Title: Cell-specific expression of key mitochondrial enzymes limits OXPHOS in astrocytes of the adult human neocortex and hippocampal formation.
Article Snippet: Analysis of transcripts deposited in the Allen Institute for Brain Science coding for mitochondrially-localized proteins in individual brain cells The gene symbols ofmitochondrially-localized subunits of proteins enlisted inMitoCarta 2.065 curated to include newer data reported inMitoCarta 3.066 were filtered to include only those that are involved in OXPHOS (respiratory chain components, transporters of adenine nucleotides, Pi and substrates, and the citric acid cycle dehydrogenases MDH2, IDH2 and IDH3). .. Subsequently, they were queried using the Transcriptomics Explorer of the Allen Institute for Brain Science human and mouse brain transcriptome (RNA-seq) repository (https://portal.brain-map.org/atlases-and-data/ rnaseq). ..

Amplification:

Article Title: Cell-specific expression of key mitochondrial enzymes limits OXPHOS in astrocytes of the adult human neocortex and hippocampal formation.
Article Snippet: .. Here we show that astrocytes within formations of adult human brains exhibit barely detectable levels of enzymes that are critical forOXPHOS.The detection methods were amplified immunohistochemistry and imaging mass cytometry.Additionally, we compiled cell-specific transcriptomic data from the Allen Institute for Brain Science. ..

Immunohistochemistry:

Article Title: Cell-specific expression of key mitochondrial enzymes limits OXPHOS in astrocytes of the adult human neocortex and hippocampal formation.
Article Snippet: .. Here we show that astrocytes within formations of adult human brains exhibit barely detectable levels of enzymes that are critical forOXPHOS.The detection methods were amplified immunohistochemistry and imaging mass cytometry.Additionally, we compiled cell-specific transcriptomic data from the Allen Institute for Brain Science. ..

Imaging:

Article Title: Cell-specific expression of key mitochondrial enzymes limits OXPHOS in astrocytes of the adult human neocortex and hippocampal formation.
Article Snippet: .. Here we show that astrocytes within formations of adult human brains exhibit barely detectable levels of enzymes that are critical forOXPHOS.The detection methods were amplified immunohistochemistry and imaging mass cytometry.Additionally, we compiled cell-specific transcriptomic data from the Allen Institute for Brain Science. ..

Cytometry:

Article Title: Cell-specific expression of key mitochondrial enzymes limits OXPHOS in astrocytes of the adult human neocortex and hippocampal formation.
Article Snippet: .. Here we show that astrocytes within formations of adult human brains exhibit barely detectable levels of enzymes that are critical forOXPHOS.The detection methods were amplified immunohistochemistry and imaging mass cytometry.Additionally, we compiled cell-specific transcriptomic data from the Allen Institute for Brain Science. ..

RNA sequencing:

Article Title: Cell-specific expression of key mitochondrial enzymes limits OXPHOS in astrocytes of the adult human neocortex and hippocampal formation.
Article Snippet: Analysis of transcripts deposited in the Allen Institute for Brain Science coding for mitochondrially-localized proteins in individual brain cells The gene symbols ofmitochondrially-localized subunits of proteins enlisted inMitoCarta 2.065 curated to include newer data reported inMitoCarta 3.066 were filtered to include only those that are involved in OXPHOS (respiratory chain components, transporters of adenine nucleotides, Pi and substrates, and the citric acid cycle dehydrogenases MDH2, IDH2 and IDH3). .. Subsequently, they were queried using the Transcriptomics Explorer of the Allen Institute for Brain Science human and mouse brain transcriptome (RNA-seq) repository (https://portal.brain-map.org/atlases-and-data/ rnaseq). ..



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Allen Institute for Brain Science transcriptomic reference dataset
The schema of TransPilot server. (A) LLR-matrix coding for positive training nucleotide sequences. (B) LLR-matrix coding for negative training nucleotide sequences. (C) The ANN model and creation of the ranked and directed TF-target dataset. (D) Creation of ranked gene list from <t>transcriptome</t> data, identification of key TFs by TransPilot, and finally build the regulation network.
Transcriptomic Reference Dataset, supplied by Allen Institute for Brain Science, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/transcriptomic+reference+dataset/transcriptomics+explorer/pm39353431-47-3-20
Average 90 stars, based on 1 article reviews
transcriptomic reference dataset - by Bioz Stars, 2026-10
90/100 stars
  Buy from Supplier

Image Search Results


The schema of TransPilot server. (A) LLR-matrix coding for positive training nucleotide sequences. (B) LLR-matrix coding for negative training nucleotide sequences. (C) The ANN model and creation of the ranked and directed TF-target dataset. (D) Creation of ranked gene list from transcriptome data, identification of key TFs by TransPilot, and finally build the regulation network.

Journal: Bioinformatics Advances

Article Title: TransPilot: mining key transcription factors by correlating binding sites with differentially expressed genes

doi: 10.1093/bioadv/vbag145

Figure Lengend Snippet: The schema of TransPilot server. (A) LLR-matrix coding for positive training nucleotide sequences. (B) LLR-matrix coding for negative training nucleotide sequences. (C) The ANN model and creation of the ranked and directed TF-target dataset. (D) Creation of ranked gene list from transcriptome data, identification of key TFs by TransPilot, and finally build the regulation network.

Article Snippet: The TF-target pairs were ranked by the ANN score ( Y ANN , > 0.5) and the directions (positive or negative) of the regulatory relationships for each pair were determined by the correlation coefficient between their expression levels in a reference transcriptome dataset obtained from the Human Protein Atlas database ( Uhlén et al. 2015 ).

Techniques: