https://www.atlasxomics.com/knowledge-center daily 0.75 2026-03-19 https://www.atlasxomics.com/knowledge-center/ikp2p81jm92g7oxkgb74mtwvpw8b2g-alzr2-cpd28-e4ntr-7yg44-yp32y-yn2tn-8b43e-4eyp9-w8687-ngwfx-fnjl2-fmgm8-rfsaa monthly 0.5 2026-03-03 https://images.squarespace-cdn.com/content/v1/628294411c64ff2b9b83b05b/82e347a3-2fb4-4238-90b0-22eeb9deebc4/Screenshot+2026-03-03+at+10.31.55%E2%80%AFAM.png Knowledge Center - AGBT 2026 Poster - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.atlasxomics.com/knowledge-center/oncology-case-study-ycehl-pstwf-er57k monthly 0.5 2026-01-29 https://images.squarespace-cdn.com/content/v1/628294411c64ff2b9b83b05b/53e3ee3b-6e64-4043-8f65-ab804b2cf9ab/Screenshot+2026-01-29+125312+v3.png Knowledge Center - Spatial CUT&amp;Tag: High-Resolution Chromatin Profiling with Spatial Context​ - Make it stand out Introduction Spatial CUT&Tag enables high-resolution mapping of histone modifications and chromatin-associated proteins directly within intact tissue, preserving native architecture while revealing regulatory patterns that bulk methods cannot capture. Developed in the Fan Lab and published in Science, the method delivers reproducible, low-background chromatin profiles with strong concordance to ENCODE ChIP-seq. This white paper highlights how Spatial CUT&Tag uncovers spatially distinct regulatory states—such as tumor-specific chromatin features and localized enhancer activity—to provide deeper insight into tissue heterogeneity and disease biology. https://www.atlasxomics.com/knowledge-center/oncology-case-study-ycehl-pstwf monthly 0.5 2026-03-19 https://images.squarespace-cdn.com/content/v1/628294411c64ff2b9b83b05b/1ba21808-9836-48e1-81b9-41b35569d6ec/copro_white_paper_summaryv2.png Knowledge Center - Spatial CoProfiling: Integrated ATAC + RNA Mapping from the Same Tissue Section - Make it stand out This case study demonstrates how AtlasXomics Spatial CoProfiling simultaneously captures chromatin accessibility (ATAC) and whole-transcriptome RNA expression from the same tissue section, preserving spatial context for regulatory inference. Using fresh-frozen mouse cerebellum, the analysis reveals distinct cellular architectures, strong accessibility–expression correlations for active regulatory programs, and clear examples where chromatin and RNA diverge to indicate poised or alternative regulatory states. These results highlight how Spatial CoProfiling enables researchers to interrogate regulatory logic in situ—connecting epigenomic state to transcriptional output with spatial precision. https://www.atlasxomics.com/knowledge-center/4ih3ijdk4tuldjmclstql476ctrbi8 monthly 0.5 2026-01-15 https://www.atlasxomics.com/knowledge-center/cell-type-annotation-video monthly 0.5 2026-01-15 https://www.atlasxomics.com/knowledge-center/gngtjiwdlzwxmal2ojm2oji65j2vc4 monthly 0.5 2026-01-15 https://www.atlasxomics.com/knowledge-center/oncology-case-study-ycehl-kjs9s-hy2zk-e8k37-9ly6n-73fgb monthly 0.5 2026-01-30 https://images.squarespace-cdn.com/content/v1/628294411c64ff2b9b83b05b/f54d01e5-c666-4218-b465-2afcc81fca8f/FFPE_sample_ops.png Knowledge Center - Predicting Spatial ATAC Success in FFPE tissue with AtlasVerify - Make it stand out This case study highlights how AtlasXomics’ in-situ bulk qualification assay (AtlasVerify) provides a high throughput method to evaluate FFPE tissue suitability before committing to a full spatial ATAC-seq run. Using an FFPE pancreatic neuroendocrine tumor sample, the workflow generated nucleosome-free profiles, TSS enrichment, FRiP scores, and IGV peak traces that accurately predicted the performance of the downstream spatial assay. The spatial ATAC results closely mirrored the bulk QC metrics—demonstrating matched chromatin accessibility patterns, strong fragment counts, and clear pathology-aligned clusters. This predictive QC step empowers researchers to select the right samples, reduce failure risk, and confidently advance their spatial studies. https://www.atlasxomics.com/knowledge-center/ikp2p81jm92g7oxkgb74mtwvpw8b2g-alzr2-cpd28-e4ntr-7yg44-yp32y-yn2tn-8b43e-4eyp9-w8687-ngwfx-fnjl2-fmgm8-x64mt-rpw65-fesrb monthly 0.5 2025-10-17 https://images.squarespace-cdn.com/content/v1/628294411c64ff2b9b83b05b/223d8f52-e7df-49ec-a54a-050e7b7e137b/Screenshot+2025-10-17+at+10.09.45%E2%80%AFAM.png Knowledge Center - ASHG Poster 2025 - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.atlasxomics.com/knowledge-center/atac-tissue-preparation-blue-clamp-fsb7z-4jkdt-cjdtl-65adk-als5r-bktm8 monthly 0.5 2025-10-15 https://images.squarespace-cdn.com/content/v1/628294411c64ff2b9b83b05b/9c89952b-7e73-403a-9494-3b2bd22f02ce/Screenshot+2025-10-15+at+4.20.25%E2%80%AFPM.png Knowledge Center - FFPE tissue Sample Preparation and Tissue Mounting Instructions - 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CUT&amp;Tag Library Preparation - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.atlasxomics.com/knowledge-center/atac-tissue-preparation-blue-clamp-fsb7z-4jkdt monthly 0.5 2025-07-09 https://images.squarespace-cdn.com/content/v1/628294411c64ff2b9b83b05b/a4865c1f-0d8a-4879-bfa8-f5050c1a8ef5/Screenshot+2024-09-04+at+11.08.33%E2%80%AFAM.png Knowledge Center - FlowGel Stamping and Lysis Protocol - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.atlasxomics.com/knowledge-center/atac-tissue-preparation-blue-clamp-fsb7z monthly 0.5 2025-07-09 https://images.squarespace-cdn.com/content/v1/628294411c64ff2b9b83b05b/9327052b-e6ef-468d-8f25-f484ddbc7b84/Screenshot+2024-09-04+at+11.06.40%E2%80%AFAM.png Knowledge Center - CUT&amp;Tag Tissue Preparation - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.atlasxomics.com/knowledge-center/atac-tissue-preparation-blue-clamp-fsb7z-4jkdt-cjdtl monthly 0.5 2025-07-09 https://images.squarespace-cdn.com/content/v1/628294411c64ff2b9b83b05b/7bfdc975-1c54-4e6e-81bf-8308e4e9152b/Screenshot+2024-09-04+at+11.09.43%E2%80%AFAM.png Knowledge Center - 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Sample Service Data Report - Make it stand out Unbiased genome-wide map of chromatin accessibility landscape https://images.squarespace-cdn.com/content/v1/628294411c64ff2b9b83b05b/e9bbbf29-8ff2-435d-8c23-16f1fbf58ba6/Slide3.PNG Knowledge Center - Sample Service Data Report - Make it stand out Clustering is verified with the tissue morphology https://images.squarespace-cdn.com/content/v1/628294411c64ff2b9b83b05b/5d618f24-6e3b-46ff-88ab-6549f5d65c11/Slide6.PNG Knowledge Center - Sample Service Data Report - Make it stand out Clusters are annotated based on gene accessibility https://images.squarespace-cdn.com/content/v1/628294411c64ff2b9b83b05b/c65a1d86-06b7-4cfb-ad9a-fc76402a7e99/Slide7.PNG Knowledge Center - Sample Service Data Report - Make it stand out Spatial motifs are identified and mapped over the tissue https://www.atlasxomics.com/knowledge-center/oncology-case-study-ycehl-kjs9s-hy2zk monthly 0.5 2024-09-18 https://images.squarespace-cdn.com/content/v1/628294411c64ff2b9b83b05b/7390aa5c-02e7-4368-b7a9-cb9446ed32dc/Screenshot+2024-09-18+at+11.01.34%E2%80%AFAM.png Knowledge Center - 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EpiTrace: A Chromatin Clock to Map Cell Mitotic Age from scATAC‑seq - Fig. 1. a) Schematic of mitotic-age tracing via chromatin accessibility (ChrAcc) at ClockDML sites. b) DNAm on G8-group ClockDML inversely correlates with PBMC age (R = −0.98, P < 2.2 × 10⁻¹⁶; 95 % CI shaded). c) Enrichment odds ratios for mitosis-ClockDML, chronology-ClockDML and solo-WCGW loci across ATAC-seq peak sets from pan-cancer, bladder, normal, placenta and hematopoietic samples (Fisher’s exact test; whiskers = 95 % CI). d) Outline of the EpiTrace algorithm. e) UMAP of single-cell ATAC from early human embryos, colored by stage. f) ClockDML accessibility (raw and HMM-smoothed) and iterative EpiTrace age ranks across stages (sample counts in legend). Pearson correlations shown; P values < 2.2 × 10⁻¹⁶ reported. “tropho.” = trophoblast. https://www.atlasxomics.com/june-newsletter/spatial-atac-seq-uncovers-glial-epigenetic-alterations-in-early-alzheimers-disease-slaxd monthly 0.5 2025-06-25 https://images.squarespace-cdn.com/content/v1/628294411c64ff2b9b83b05b/3fad5861-ccc8-46de-9128-c00467b863df/F1.large.jpg June Newsletter - Spatial ATAC-seq Unmasks Early Glial Rewiring in Alzheimer’s - Fig. 1. Experimental workflow and key findings from spatial ATAC-seq in 5×FAD and control mouse brains. (A) Schematic of the experimental design. Spatial ATAC-seq was performed on sagittal brain sections from 5×FAD and C57BL/6J mice to profile chromatin accessibility across defined brain regions. (B) Key findings from the study include: (1) identification of major brain cell types and glial subtypes; (2) region-specific chromatin accessibility patterns; (3) cell-type-specific transcription factor motif enrichment; (4) differential chromatin accessibility in AD risk genes; and (5) experimental validation of Vsir expression in microglial subtypes. https://www.atlasxomics.com/june-newsletter/unveiling-hidden-drivers-how-atac-seq-illuminates-medulloblastoma-progression monthly 0.5 2025-06-12 https://images.squarespace-cdn.com/content/v1/628294411c64ff2b9b83b05b/324e3186-5309-4794-b2a7-f4df1a911136/Screenshot+2025-06-12+at+11.01.47%E2%80%AFAM.png June Newsletter - Chromosome-Scale Shifts, Not Single Genes, Ignite Medulloblastoma - Clonal proliferation and differentiation gradients are independent of oncogene expression https://www.atlasxomics.com/june-newsletter/chromatin-accessibility-reveals-gstm1-as-a-prognostic-marker-in-glioblastoma monthly 0.5 2025-06-12 https://images.squarespace-cdn.com/content/v1/628294411c64ff2b9b83b05b/7e8cf4e0-f426-443c-ac0c-aabfa201a07d/Screenshot+2025-06-12+at+11.19.34%E2%80%AFAM.png June Newsletter - Chromatin Accessibility Flags GSTM1 as an Early Prognostic Marker in Glioblastoma&nbsp; - Integrative chromatin and expression profiling highlights GSTM1 as a potential tumor biomarker By combining ATAC-seq and RNA-seq analyses across tumor vs. normal and short- vs. long-survival patient samples, the authors identified 11 genes with both elevated promoter accessibility and gene expression. 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