# How to download a small of subset of single-cell multiomics (RNA/ATAC) of a small brain region? **URL:** \ **Category:** How To\ **Tags:** how-to\ **Created:** [November 15, 2025, 11:13pm UTC](https://community.brain-map.org/t/how-to-download-a-small-of-subset-of-single-cell-multiomics-rna-atac-of-a-small-brain-region/4768 "2025-11-15T23:13:42Z")\ **Posts on this page:** 1\ **Showing post:** 4
**Author:** ![SvenOtto](https://yyz1.discourse-cdn.com/flex027/user_avatar/community.brain-map.org/svenotto/32/893_2.png) [@SvenOtto](https://community.brain-map.org/u/SvenOtto)\ **Post date:** [December 4, 2025, 11:23pm UTC](https://community.brain-map.org/t/how-to-download-a-small-of-subset-of-single-cell-multiomics-rna-atac-of-a-small-brain-region/4768/4 "2025-12-04T23:23:50Z")
Hi Chris, Glad you found what you needed for now. It’d be helpful to understand what kind of search-to-download process you’d expected to guide future product development. So any feedback you have would be much appreciated. I’ll approach the rest of my answer as how I’d encourage folks to navigate the Brain Knowledge Platform’s (BKP) data ecosystem. I hope this helps 🙂 **Finding the right projects** I’d encourage anybody to start with the BKP’s Data Catalog on [Brain Knowledge Platform](https://knowledge.brain-map.org/data) and use the faceted search and text search options to narrow things down to projects that may fit your interests. Tutorials for how to use them can be found here: - [Updated search UI in Brain Knowledge Platform’s Data Catalog](https://community.brain-map.org/t/updated-search-ui-in-brain-knowledge-platform-s-data-catalog/3721) - [Scientists search projects using own search terms via Text Search in Brain Knowledge Platform’s Data Catalog](https://community.brain-map.org/t/scientists-search-projects-using-own-search-terms-via-text-search-in-brain-knowledge-platform-s-data-catalog/4607) The result may look something like this: ![FindingData0](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/d/de57be10a78c10c4a8846cbe2b687931f29a8438.jpeg) **Navigating projects, data collections and their files** Projects include data collections that capture their files. How many data collections and what other types of resources are associated with a project is visible via the content chips highlighted below. The first example includes four data collections. The second includes only one data collection but also offers data visualizations via ABC Atlas. ![FindingData1](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/9/9f35e672a59ea55552305b8409c5342abadf8c19.jpeg) One you click into a given project, you’ll see the list of data collections and their corresponding metadata. In most cases they include links to the data archives or S3 buckets where you can download the relevant files. Archive example: [Brain Knowledge Platform](https://knowledge.brain-map.org/data/MR9M3L8BU9PCOH3BHCV) S3 bucket example: [Brain Knowledge Platform](https://knowledge.brain-map.org/data/7CVKSF7QGAKIQ8LM5LC) ![FindingData2](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/b/b99664a7636581adf2ba80194e8679266f9ae1d5.jpeg) **Projects with detailed specimen inventories and file manifests** Some projects include detailed specimen inventories and file manifests that allow for more integrated subsetting of the data in BKP already. Example: [Brain Knowledge Platform](https://knowledge.brain-map.org/data/BUQ7G50XHDCFCJCQ03A/specimens) After you’ve filtered down to the specimens of interest, you can download the associated file manifest: ![FindingData3](https://canada1.discourse-cdn.com/flex027/uploads/brainobservatory/original/2X/1/104ef3b177f2328a6deacd8e6160490e557c3293.jpeg) Once you have the manifest in hand, you can follow processes like this one to download the files. > [@How to: Use BKP file manifest to access BICAN data at NeMO archive](https://community.brain-map.org/t/how-to-use-bkp-file-manifest-to-access-bican-data-at-nemo-archive/3505): > > [Manifest download and formatting](https://community.brain-map.org/t/how-to-use-bkp-file-manifest-to-access-bican-data-at-nemo-archive/3505#manifest-download-and-formatting-1)[NeMO Portal-Client tool for downloading files using file manifest](https://community.brain-map.org/t/how-to-use-bkp-file-manifest-to-access-bican-data-at-nemo-archive/3505#p-6179-nemo-portal-client-tool-for-downloading-files-using-file-manifest-2)[Portal-Client compatible manifest template](https://community.brain-map.org/t/how-to-use-bkp-file-manifest-to-access-bican-data-at-nemo-archive/3505#p-6179-portal-client-compatible-manifest-template-3)[Basic invocation](https://community.brain-map.org/t/how-to-use-bkp-file-manifest-to-access-bican-data-at-nemo-archive/3505#p-6179-basic-invocation-4)[NeMO data collection and landing pages](https://community.brain-map.org/t/how-to-use-bkp-file-manifest-to-access-bican-data-at-nemo-archive/3505#p-6179-nemo-data-collection-and-landing-pages-5)[Data accessible: restricted and open data](https://community.brain-map.org/t/how-to-use-bkp-file-manifest-to-access-bican-data-at-nemo-archive/3505#p-6179-data-accessible-restricted-and-open-data-6)[Accessing data](https://community.brain-map.org/t/how-to-use-bkp-file-manifest-to-access-bican-data-at-nemo-archive/3505#p-6179-accessing-data-7)[Open data](https://community.brain-map.org/t/how-to-use-bkp-file-manifest-to-access-bican-data-at-nemo-archive/3505#p-6179-open-data-8)[Restricted data](https://community.brain-map.org/t/how-to-use-bkp-file-manifest-to-access-bican-data-at-nemo-archive/3505#p-6179-restricted-data-9)[Data collections available in Rapid Releases](https://community.brain-map.org/t/how-to-use-bkp-file-manifest-to-access-bican-data-at-nemo-archive/3505#p-6179-data-collections-available-in-rapid-releases-10)[Accessing NeMO Collections from Brain Knowledge Platform (BKP)](https://community.brain-map.org/t/how-to-use-bkp-file-manifest-to-access-bican-data-at-nemo-archive/3505#p-6179-accessing-nemo-collections-from-brain-knowledge-platform-bkp-11)[HTTPS public browser access](https://community.brain-map.org/t/how-to-use-bkp-file-manifest-to-access-bican-data-at-nemo-archive/3505#p-6179-https-public-access-browser-12)Manifest download and formatting Scientists can download a project’s fil… **What’s currently not possible** You currently can’t define a set of projects in Data Catalog, e.g. Technique = “10X Genomics Multiome”, check a box, and click a download button that downloads all the files at their respective locations. --- _[View the full topic](https://community.brain-map.org/t/how-to-download-a-small-of-subset-of-single-cell-multiomics-rna-atac-of-a-small-brain-region/4768)._