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genome-wide rna-seq & microarray data  (Allen Institute for Brain Science)

 
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    Allen Institute for Brain Science genome-wide rna-seq & microarray data
    Genome Wide Rna Seq & Microarray Data, 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/rna-seq+and+microarray+data/rna+seq+datasets/pm29601049-80-38-100
    Average 90 stars, based on 1 article reviews
    genome-wide rna-seq & microarray data - by Bioz Stars, 2026-10
    90/100 stars

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    other:

    Article Title: PAUSE: principled feature attribution for unsupervised gene expression analysis.
    Article Snippet: The ACT RNA-Seq data20 was collected by the Allen Institute for Brain Science, Kaiser Permanente Washington Health Research Institute (KPWHRI), and the University of Washington (UW), and it was made available with Synapse ID syn5759376.

    Article Title: Mapping Human Neuronal Diversity in the Search for New Therapeutics: Using Real Human Neuron Data Sets to Build Student Quantitative Skills
    Article Snippet: Keywords: case study, epilepsy, Allen Institute for Brain Science, RNA-Seq, electrophysiology, hybrid learning, high-throughput data, quantitative skills, science process

    Article Title: Sex-stratified RNA-seq analysis reveals traumatic brain injury-induced transcriptional changes in the female hippocampus conducive to dementia
    Article Snippet: We conducted our genome-wide RNA sequencing analysis on the open-source dataset from the Aging, Dementia, and Traumatic Brain Injury Project conducted by the Allen Institute for Brain Science ( ).

    Article Title: Cell-specific expression of key mitochondrial enzymes limits OXPHOS in astrocytes of the adult human neocortex and hippocampal formation
    Article Snippet: Likewise, we also found that in mouse brain, RNA-Seq data fetched from the Allen Institute for Brain Science suggested that the mRNAs of Cox IV subunits are expressed in neurons and non-neuronal cell types to a similar degree (Supplementary Fig. ).

    RNA sequencing:

    Article Title: Ferroptosis of microglia in aging human white matter injury
    Article Snippet: .. We analyzed a publicly available bulk RNAseq data set from the Allen Institute for Brain Science ( https://aging.brain-map.org/rnaseq/search ). ..

    Article Title: Ferroptosis of microglia in aging human white matter injury
    Article Snippet: .. Gene expression was variably enhanced for seven markers associated with distinct ferroptosis pathways (GCLC, HMOX1, TFRC, IREB2, MR1G, AKRC1c and SLC1A5) quantified by qRT-PCR and normalized to 18S rRNA. ( B ) Analysis of bulk RNAseq data set from the Allen Institute for Brain Science of gene expression in 110 cases enrolled in the ACT study diagnosed with a spectrum of mVBI or ADNC. ..

    Article Title: Ferroptosis of microglia in aging human white matter injury
    Article Snippet: .. We next analyzed a publicly available bulk RNAseq data set from the Allen Institute for Brain Science that analyzed gene expression in 110 cases diagnosed with a spectrum of ADNC and VBI. ..

    Article Title: Cell-specific expression of key mitochondrial enzymes limits OXPHOS in astrocytes of the adult human neocortex and hippocampal formation.
    Article Snippet: .. Likewise, we also found that in mouse brain, RNASeq data fetched from the Allen Institute for Brain Science suggested that the mRNAs of Cox IV subunits are expressed in neurons and nonneuronal cell types to a similar degree (Supplementary Fig. 8). .. Heatmaps of mRNA expression levels in neuronal (Neu) and non-neuronal (N-N) cells based on single cell sequencing by the Allen Institute for Brain Science for all subunits participating inOXPHOS in humans and mice is provided in the Supplementary Data 2 (Dataset homo vs mus, respectively).

    Gene Expression:

    Article Title: Ferroptosis of microglia in aging human white matter injury
    Article Snippet: .. Gene expression was variably enhanced for seven markers associated with distinct ferroptosis pathways (GCLC, HMOX1, TFRC, IREB2, MR1G, AKRC1c and SLC1A5) quantified by qRT-PCR and normalized to 18S rRNA. ( B ) Analysis of bulk RNAseq data set from the Allen Institute for Brain Science of gene expression in 110 cases enrolled in the ACT study diagnosed with a spectrum of mVBI or ADNC. ..

    Article Title: Ferroptosis of microglia in aging human white matter injury
    Article Snippet: .. We next analyzed a publicly available bulk RNAseq data set from the Allen Institute for Brain Science that analyzed gene expression in 110 cases diagnosed with a spectrum of ADNC and VBI. ..

    Quantitative RT-PCR:

    Article Title: Ferroptosis of microglia in aging human white matter injury
    Article Snippet: .. Gene expression was variably enhanced for seven markers associated with distinct ferroptosis pathways (GCLC, HMOX1, TFRC, IREB2, MR1G, AKRC1c and SLC1A5) quantified by qRT-PCR and normalized to 18S rRNA. ( B ) Analysis of bulk RNAseq data set from the Allen Institute for Brain Science of gene expression in 110 cases enrolled in the ACT study diagnosed with a spectrum of mVBI or ADNC. ..



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    FIGURE 3 Upregulation of IL4I1 infers an unfavorable prognosis for glioma. (A) Representative images (left) and quantification (right) showing IL4I1 staining of normal brain tissues (n = 16) and glioma tissues (n = 37) with the anti-IL4I1 antibody, with scale bars 100 µm (up) and 20 µm (down). (B–D) Kaplan– Meier analysis for OS based on three glioma datasets (CGGA, Rembrandt, and GSE16011). (E–G) ROC curves of OS in CGGA, Rembrandt, and GSE16011 datasets. (H, I) Univariate and multivariate analyses of OS based on CGGA-glioma datasets. ****p < 0.0001.

    Journal: Frontiers in immunology

    Article Title: IL4I1 in M2-like macrophage promotes glioma progression and is a promising target for immunotherapy.

    doi: 10.3389/fimmu.2023.1338244

    Figure Lengend Snippet: FIGURE 3 Upregulation of IL4I1 infers an unfavorable prognosis for glioma. (A) Representative images (left) and quantification (right) showing IL4I1 staining of normal brain tissues (n = 16) and glioma tissues (n = 37) with the anti-IL4I1 antibody, with scale bars 100 µm (up) and 20 µm (down). (B–D) Kaplan– Meier analysis for OS based on three glioma datasets (CGGA, Rembrandt, and GSE16011). (E–G) ROC curves of OS in CGGA, Rembrandt, and GSE16011 datasets. (H, I) Univariate and multivariate analyses of OS based on CGGA-glioma datasets. ****p < 0.0001.

    Article Snippet: Dataset Data type WHO grade II WHO grade III WHO grade IV CGGA RNA-seq 291 334 388 Rembrandt Microarray 98 85 130 GSE16011 Microarray 24 85 159 frontiersin.org (1:2000, 60143-1-Ig, Proteintech), CD163 (1:1,000, ab182422, Abcam), CD86 (1:1,000, ab239075, Abcam), and beta-tubulin (1:2000, DF7967, Affinity) overnight.

    Techniques: Staining

    FIGURE 4 Heightened IL4I1 expression is correlated with the malignant phenotype of gliomas. (A–D) IL4I1 shows a significant increase in GBM (WHO IV) in TCGA, Rembrandt, GSE16011, and CGGA datasets. Additionally, box plots visualizing the associations between IL4I1 and various clinical characteristics based on the CGGA dataset. Specifically: (E) Age. (F) Status. (G) Histology. (H, I) High expression of IL4I1 in IDH wild-type and 1p/19q non-codel gliomas.

    Journal: Frontiers in immunology

    Article Title: IL4I1 in M2-like macrophage promotes glioma progression and is a promising target for immunotherapy.

    doi: 10.3389/fimmu.2023.1338244

    Figure Lengend Snippet: FIGURE 4 Heightened IL4I1 expression is correlated with the malignant phenotype of gliomas. (A–D) IL4I1 shows a significant increase in GBM (WHO IV) in TCGA, Rembrandt, GSE16011, and CGGA datasets. Additionally, box plots visualizing the associations between IL4I1 and various clinical characteristics based on the CGGA dataset. Specifically: (E) Age. (F) Status. (G) Histology. (H, I) High expression of IL4I1 in IDH wild-type and 1p/19q non-codel gliomas.

    Article Snippet: Dataset Data type WHO grade II WHO grade III WHO grade IV CGGA RNA-seq 291 334 388 Rembrandt Microarray 98 85 130 GSE16011 Microarray 24 85 159 frontiersin.org (1:2000, 60143-1-Ig, Proteintech), CD163 (1:1,000, ab182422, Abcam), CD86 (1:1,000, ab239075, Abcam), and beta-tubulin (1:2000, DF7967, Affinity) overnight.

    Techniques: Expressing

    FIGURE 6 IL4I1 is expressed in M2-like macrophages in glioma. (A) Summary of IL4I1 expression in 12 distinct single-cell datasets from glioma patients. (B) Association between IL4I1 and macrophages on XCELL, TIMER, and EPIC algorithms. (C) Association between IL4I1 expression and markers of M1 and M2 macrophages in CGGA and TCGA databases. Color depth and digital scale represent the strength of association. (D) Representative colocalization images from IF staining between IL4I1 and CD206 in clinical glioma specimens. DAPI (blue), IL4I1 (red) and CD206 (green). Scale bar: 20 mm. (E) Measurement of protein and mRNA expression levels for markers (CD11B, CD204, CD86, CD206, and CD163) of THP-1, M0, M1, and M2 macrophages using WB and RT-qPCR. (F) Assessment of IL4I1 expression in various macrophage subtypes (M0, M1, and M2) and glioma cells (U87, LN229, and U251). (G) Representative IF pictures of the difference of IL4I1 among M0, M1, and M2 macrophages, U87, and LN229 cells with DAPI (blue) and IL4I1 (red). *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001.

    Journal: Frontiers in immunology

    Article Title: IL4I1 in M2-like macrophage promotes glioma progression and is a promising target for immunotherapy.

    doi: 10.3389/fimmu.2023.1338244

    Figure Lengend Snippet: FIGURE 6 IL4I1 is expressed in M2-like macrophages in glioma. (A) Summary of IL4I1 expression in 12 distinct single-cell datasets from glioma patients. (B) Association between IL4I1 and macrophages on XCELL, TIMER, and EPIC algorithms. (C) Association between IL4I1 expression and markers of M1 and M2 macrophages in CGGA and TCGA databases. Color depth and digital scale represent the strength of association. (D) Representative colocalization images from IF staining between IL4I1 and CD206 in clinical glioma specimens. DAPI (blue), IL4I1 (red) and CD206 (green). Scale bar: 20 mm. (E) Measurement of protein and mRNA expression levels for markers (CD11B, CD204, CD86, CD206, and CD163) of THP-1, M0, M1, and M2 macrophages using WB and RT-qPCR. (F) Assessment of IL4I1 expression in various macrophage subtypes (M0, M1, and M2) and glioma cells (U87, LN229, and U251). (G) Representative IF pictures of the difference of IL4I1 among M0, M1, and M2 macrophages, U87, and LN229 cells with DAPI (blue) and IL4I1 (red). *p < 0.05, **p < 0.01, ***p < 0.001, and ****p < 0.0001.

    Article Snippet: Dataset Data type WHO grade II WHO grade III WHO grade IV CGGA RNA-seq 291 334 388 Rembrandt Microarray 98 85 130 GSE16011 Microarray 24 85 159 frontiersin.org (1:2000, 60143-1-Ig, Proteintech), CD163 (1:1,000, ab182422, Abcam), CD86 (1:1,000, ab239075, Abcam), and beta-tubulin (1:2000, DF7967, Affinity) overnight.

    Techniques: Expressing, Staining, Quantitative RT-PCR