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rna-seq and microarray data  (Biotechnology Information)

 
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    Biotechnology Information rna-seq and microarray data
    Rna Seq And Microarray Data, supplied by Biotechnology Information, 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+microarray+data/rna+seq+data/pmc08994804-199-20-28
    Average 90 stars, based on 1 article reviews
    rna-seq and microarray data - by Bioz Stars, 2026-09
    90/100 stars

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    Related Articles

    other:

    Article Title: Genome-wide identification and functional analysis of PEL gene family in Brassica napus L.
    Article Snippet: The RNA-seq raw sequence data of B. napus have been deposited on the National Centre for Biotechnology Information (NCBI, h t t p s : / / w w w . n c b i . n l m . n i h . g o v /) repository with accession number PRJNA1235670 ( h t t p s : / / w w w . n c b i . n l m . n i h . g o v / s r a /PRJNA1235670).

    Article Title: Comprehensive resource for transcription readthrough events in healthy human tissues.
    Article Snippet: A comprehensive set of publicly available RNA-seq datasets and TRT data representing healthy human tissues was collected from National Center for Biotechnology Information (NCBI) and relevant published literature (https://doi.org/10.6084/m9.figshare.24848265.v3)22,25 (Supplementary Table S1).

    Article Title: Transcriptomic insights into the synergistic effects of darkness and mechanical stimulation on peanut pod development.
    Article Snippet: Data availability The raw RNA-seq sequencing data have been deposited at the National Center for Biotechnology Information (NCBI) under the Bio-Project accession PRJNA1045372.

    Article Title: Scaffold protein RhCASPL1D1 stabilizes RhPIP2 aquaporins and promotes flower recovery after dehydration in rose ( Rosa hybrida )
    Article Snippet: The raw data of RNA-seq used in the study were deposited into the National Center for Biotechnology Information (NCBI) database at Sequence Read Archive (SRA) with the accession number PRJNA1250776 and PRJNA1250784.

    Article Title: Supporting Information for HKDC1, a target of TFEB, is essential to maintain both mitochondrial and lysosomal homeostasis, preventing cellular senescence
    Article Snippet: RNA-seq data used in this study have been deposited to the National Center for Biotechnology Information Gene Expression Omnibus with accession number GSE226743.

    Article Title: Scalable modulation of CRISPR‒Cas enzyme activity using photocleavable phosphorothioate DNA.
    Article Snippet: RNA-seq data are available from theNational Center for Biotechnology Information Sequencing Read Archive (SRA) database, accession code PRJNA1249431.

    RNA sequencing:

    Article Title: Co-domestication of cold tolerance and female flower is determined by CsEIN2 in cucumber.
    Article Snippet: .. The RNAseq data have been deposited in the National Centre for Biotechnology Information under the project ID PRJNA1207901. ..

    Article Title: Cell-based ZNT8 assay
    Article Snippet: .. The RNAseq data are available under an accession number of GSE134122 from Gene Expression Omnibus (GEO) of National Center for Biotechnology Information. ..

    Gene Expression:

    Article Title: Cell-based ZNT8 assay
    Article Snippet: .. The RNAseq data are available under an accession number of GSE134122 from Gene Expression Omnibus (GEO) of National Center for Biotechnology Information. ..



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    Protein candidates proposed as potential prognostic markers for high and low risk of tumour recurrence in CRC-II patients.

    Journal: BJC Reports

    Article Title: Protein prognostic biomarkers in stage II colorectal cancer: implications for post-operative management

    doi: 10.1038/s44276-024-00043-z

    Figure Lengend Snippet: Protein candidates proposed as potential prognostic markers for high and low risk of tumour recurrence in CRC-II patients.

    Article Snippet: Candidate selection can be made via informatics approaches [ , ], DNA/RNA microarray data analyses [ ], protein involvement in key biochemical processes [ ], being differentially expressed through mass spectrometry (MS) analysis [ ], Olink proteomics assays [ ] or SomaLogic assays [ ] or as a diagnostic or prognostic marker for other tumour types [ ].

    Techniques: Biomarker Discovery, Expressing, Marker, Reverse Transcription Polymerase Chain Reaction, Microarray, Over Expression

    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