atac seq data raw sequencing fastq files (Biotechnology Information)
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atac seq data raw sequencing fastq files
Atac Seq Data Raw Sequencing Fastq Files, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/atac-seq+data/data+rna+seq+%E2%80%A2/pm42118837-364-1-31
Average 86 stars, based on 1 article reviews
Atac Seq Data Raw Sequencing Fastq Files, supplied by Biotechnology Information, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/atac-seq+data/data+rna+seq+%E2%80%A2/pm42118837-364-1-31
Average 86 stars, based on 1 article reviews
atac seq data raw sequencing fastq files - by Bioz Stars,
2026-11
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Sequencing:Article Title: Adaptive responses to mTOR gene targeting in hematopoietic stem cells reveal a proliferative mechanism evasive to mTOR inhibition Article Snippet: Article Title: Chromatin accessibility of circulating CD8 + T cells predicts treatment response to PD-1 blockade in patients with gastric cancer Article Snippet: Raw ATAC-seq data retrieved from the National Center for Article Title: Transcription factor Zhx2 restricts NK cell maturation and suppresses their antitumor immunity Article Snippet: The RNA-seq data and ATAC-seq data in this publication have been deposited in the National Center for Article Title: The developmental impacts of natural selection on human pelvic morphology Article Snippet: In addition, all ATAC-seq data raw sequencing fastq files and processed peak bed files and RNA-seq data raw sequencing fastq files and processed read count files have been deposited on National Center for Article Title: The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development Article Snippet: ATAC-seq data were deposited at the National Center for Article Title: Cell-lineage controlled epigenetic regulation in glioblastoma stem cells determines functionally distinct subgroups and predicts patient survival Article Snippet: All raw data ATAC-seq data from human GSC and mouse GSC generated in this study have been deposited in Gene Expression Omnibus of National Center for Article Title: Evolution of vertebrate gill covers via shifts in an ancient Pou3f3 enhancer Article Snippet: Article Title: Evolution of vertebrate gill covers via shifts in an ancient Pou3f3 enhancer Article Snippet: The ATAC-seq data reported in this paper have been deposited in the National Center for RNA Sequencing:Article Title: Adaptive responses to mTOR gene targeting in hematopoietic stem cells reveal a proliferative mechanism evasive to mTOR inhibition Article Snippet: Article Title: Chromatin accessibility of circulating CD8 + T cells predicts treatment response to PD-1 blockade in patients with gastric cancer Article Snippet: Raw ATAC-seq data retrieved from the National Center for Article Title: Transcription factor Zhx2 restricts NK cell maturation and suppresses their antitumor immunity Article Snippet: The RNA-seq data and ATAC-seq data in this publication have been deposited in the National Center for Article Title: The developmental impacts of natural selection on human pelvic morphology Article Snippet: In addition, all ATAC-seq data raw sequencing fastq files and processed peak bed files and RNA-seq data raw sequencing fastq files and processed read count files have been deposited on National Center for Article Title: The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development Article Snippet: ATAC-seq data were deposited at the National Center for Article Title: Cell-lineage controlled epigenetic regulation in glioblastoma stem cells determines functionally distinct subgroups and predicts patient survival Article Snippet: All raw data ATAC-seq data from human GSC and mouse GSC generated in this study have been deposited in Gene Expression Omnibus of National Center for Article Title: Evolution of vertebrate gill covers via shifts in an ancient Pou3f3 enhancer Article Snippet: Article Title: Evolution of vertebrate gill covers via shifts in an ancient Pou3f3 enhancer Article Snippet: The ATAC-seq data reported in this paper have been deposited in the National Center for Gene Expression:Article Title: Adaptive responses to mTOR gene targeting in hematopoietic stem cells reveal a proliferative mechanism evasive to mTOR inhibition Article Snippet: Article Title: Chromatin accessibility of circulating CD8 + T cells predicts treatment response to PD-1 blockade in patients with gastric cancer Article Snippet: Raw ATAC-seq data retrieved from the National Center for Article Title: Transcription factor Zhx2 restricts NK cell maturation and suppresses their antitumor immunity Article Snippet: The RNA-seq data and ATAC-seq data in this publication have been deposited in the National Center for Article Title: The developmental impacts of natural selection on human pelvic morphology Article Snippet: In addition, all ATAC-seq data raw sequencing fastq files and processed peak bed files and RNA-seq data raw sequencing fastq files and processed read count files have been deposited on National Center for Article Title: The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development Article Snippet: ATAC-seq data were deposited at the National Center for Article Title: Cell-lineage controlled epigenetic regulation in glioblastoma stem cells determines functionally distinct subgroups and predicts patient survival Article Snippet: All raw data ATAC-seq data from human GSC and mouse GSC generated in this study have been deposited in Gene Expression Omnibus of National Center for Article Title: Evolution of vertebrate gill covers via shifts in an ancient Pou3f3 enhancer Article Snippet: Article Title: Evolution of vertebrate gill covers via shifts in an ancient Pou3f3 enhancer Article Snippet: The ATAC-seq data reported in this paper have been deposited in the National Center for Generated:Article Title: Adaptive responses to mTOR gene targeting in hematopoietic stem cells reveal a proliferative mechanism evasive to mTOR inhibition Article Snippet: Article Title: Chromatin accessibility of circulating CD8 + T cells predicts treatment response to PD-1 blockade in patients with gastric cancer Article Snippet: Raw ATAC-seq data retrieved from the National Center for Article Title: Transcription factor Zhx2 restricts NK cell maturation and suppresses their antitumor immunity Article Snippet: The RNA-seq data and ATAC-seq data in this publication have been deposited in the National Center for Article Title: The developmental impacts of natural selection on human pelvic morphology Article Snippet: In addition, all ATAC-seq data raw sequencing fastq files and processed peak bed files and RNA-seq data raw sequencing fastq files and processed read count files have been deposited on National Center for Article Title: The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development Article Snippet: ATAC-seq data were deposited at the National Center for Article Title: Cell-lineage controlled epigenetic regulation in glioblastoma stem cells determines functionally distinct subgroups and predicts patient survival Article Snippet: All raw data ATAC-seq data from human GSC and mouse GSC generated in this study have been deposited in Gene Expression Omnibus of National Center for Article Title: Evolution of vertebrate gill covers via shifts in an ancient Pou3f3 enhancer Article Snippet: Article Title: Evolution of vertebrate gill covers via shifts in an ancient Pou3f3 enhancer Article Snippet: The ATAC-seq data reported in this paper have been deposited in the National Center for Chromatin Immunoprecipitation:Article Title: Adaptive responses to mTOR gene targeting in hematopoietic stem cells reveal a proliferative mechanism evasive to mTOR inhibition Article Snippet: Article Title: Chromatin accessibility of circulating CD8 + T cells predicts treatment response to PD-1 blockade in patients with gastric cancer Article Snippet: Raw ATAC-seq data retrieved from the National Center for Article Title: Transcription factor Zhx2 restricts NK cell maturation and suppresses their antitumor immunity Article Snippet: The RNA-seq data and ATAC-seq data in this publication have been deposited in the National Center for Article Title: The developmental impacts of natural selection on human pelvic morphology Article Snippet: In addition, all ATAC-seq data raw sequencing fastq files and processed peak bed files and RNA-seq data raw sequencing fastq files and processed read count files have been deposited on National Center for Article Title: The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development Article Snippet: ATAC-seq data were deposited at the National Center for Article Title: Cell-lineage controlled epigenetic regulation in glioblastoma stem cells determines functionally distinct subgroups and predicts patient survival Article Snippet: All raw data ATAC-seq data from human GSC and mouse GSC generated in this study have been deposited in Gene Expression Omnibus of National Center for Article Title: Evolution of vertebrate gill covers via shifts in an ancient Pou3f3 enhancer Article Snippet: Article Title: Evolution of vertebrate gill covers via shifts in an ancient Pou3f3 enhancer Article Snippet: The ATAC-seq data reported in this paper have been deposited in the National Center for |
![The ocrRBBR framework for OCR-driven Boolean rule inference explaining gene expression variability. ( A ) In the mouse multiome dataset, nine blood cell lineages—stromal cells, stem cells, DC, myeloid cells, ILC, B, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\alpha \beta$\end{document} T, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\gamma \delta$\end{document} T, and activated T (ActT) cells—are shown in distinct colors. ( B <t>)</t> <t>ATAC-seq</t> data are used to identify all OCRs within \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\pm$\end{document} 100 kb of gene promoters. ocrRBBR derives Boolean rules among OCRs to explain gene expression variability, as measured by RNA-seq, across 85 cell types spanning nine blood lineages. ( C ) Candidate models are constructed using all combinations of single-, double-, and triple-OCR subsets from the available OCR repertoire (e.g. \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\lbrace OCR_A, OCR_B, OCR_C, \dots , OCR_H, OCR_K, OCR_L\rbrace$\end{document} ). ( D ) Each OCR subset is transformed into a set of Boolean rules, which serve as inputs to a ridge regression model used to predict gene expression across cell types. For example, the double-OCR subset \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\lbrace OCR_A, OCR_D\rbrace$\end{document} yields rules such as \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $(OCR_A \wedge OCR_D)$\end{document} , \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $(\lnot OCR_A \wedge OCR_D)$\end{document} , and so on. Boolean rules receiving positive (orange) coefficients in the fitted model are associated with cell types where the gene is expressed, whereas those with negative (blue) coefficients correspond to cell types with low or no expression. ( E ) Fitted models and their associated Boolean rule sets—such as \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $(OCR_A \wedge OCR_D) \ \mathrm{or}\ (\lnot OCR_A \wedge OCR_D)$\end{document} , and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $(OCR_A \wedge OCR_B \wedge OCR_D) \ \mathrm{or}\ (\lnot OCR_A \wedge OCR_B \wedge OCR_D)$\end{document} —are ranked according to their BIC scores. ( F ) Boolean rules are categorized based on the cell types in which they act as active regulators of gene expression.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_8175/pmc13148175/pmc13148175__gkag230fig1.jpg)
![OCR-driven Boolean rules for Spi1 are associated with cell-type-specific chromatin structures involved in its regulation. ( A ) ATAC-seq readouts within \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\pm$\end{document} 100 kb of the Spi1 promoter identify candidate OCRs, and RNA-seq quantifies Spi1 expression levels across 85 cell types spanning nine blood lineages. ( B ) A double-OCR subset \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\lbrace \mathrm{E}_{-12}, \mathrm{Promoter}\rbrace$\end{document} —including an enhancer located 12 kb upstream of the TSS and the promoter—predicts gene expression variability with the optimal BIC. In the circular heatmap, blood lineages are color-coded similar to panel (A); OCR accessibility, Spi1 expression, and Boolean rule values are shown, with cold colors representing low levels and warm colors high levels. ( C, D ) MSE and Boolean rule coefficients are shown as a function of the regularization parameter \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\log (\lambda )$\end{document} in the fitted ridge regression model, where Boolean rules derived from the double-OCR subset are used as predictors of Spi1 expression. ( E ) Two boolean rules \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $(\mathrm{E}_{-12} \wedge \mathrm{Promoter}) \ \mathrm{or}\ (\lnot \mathrm{E}_{-12} \wedge \mathrm{Promoter})$\end{document} receive positive coefficients, corresponding to chromatin structures associated with gene regulation in myeloid and B cells.](https://pub-med-central-images-cdn.bioz.com/pub_med_central_ids_ending_with_8175/pmc13148175/pmc13148175__gkag230fig2.jpg)
