# Data Updates - December 13, 2023
**URL:** https://community.brain-map.org/t/data-updates-december-13-2023/2779
**Category:** Allen Brain Cell (ABC) Atlas
**Created:** [December 13, 2023, 4:09pm UTC](https://community.brain-map.org/t/data-updates-december-13-2023/2779 "2023-12-13T16:09:32Z")
**Posts on this page:** 11
**Page:** 1
### Author:  [@Elysha-AIBS](https://community.brain-map.org/u/Elysha-AIBS)
#### Post date: [December 13, 2023, 4:09pm UTC](https://community.brain-map.org/t/data-updates-december-13-2023/2779/1 "2023-12-13T16:09:32Z")
The Allen Brain Cell Atlas (ABC Atlas) has been updated with new data!
### Mouse Whole-Brain Transcriptomic Cell Type Atlas Data Updates
In conjunction with the publication of an associated paper in [Nature](https://www.nature.com/articles/s41586-023-06812-z), we have made some minor updates to the Merscope and 10x data sets. In addition, 7 new neighborhood embeddings are now fully explorable in the ABC Atlas:
- [10x scRNAseq HY-EA-Glut-GABA](https://knowledge.brain-map.org/data/LVDBJAW8BI5YSS1QUBG/explore?filterOptions%5Ba%5D=&genes=a%3ASult3a1&layoutState=Single&views=a~5.465494499999998-5.4018175_51.713441798387095-39.191444249999996_0_cartesian&visualizations=a~NV8UBPK6WDPCN2GZD1G%3AAK0J6HPECUVKE4BGVSD~METADATA%3AFS00DXV0T9R1X9FJ4QE%3Anull%3Anull%3Anull%3Afalse%3A0.5)
- [10x scRNAseq MB-HB-CB-GABA](https://knowledge.brain-map.org/data/LVDBJAW8BI5YSS1QUBG/explore?filterOptions%5Ba%5D=&genes=a%3ADynlt1c&layoutState=Single&views=a~6.0222005-3.999686500000003_48.425852059677425-36.69991815_0_cartesian&visualizations=a~CP32G2UIJ6VUPWUTHRA%3ADNXG3CRWLXRRLHV5IRH~METADATA%3AFS00DXV0T9R1X9FJ4QE%3Anull%3Anull%3Anull%3Afalse%3A0.5)
- [10x scRNAseq Subpallium-GABA](https://knowledge.brain-map.org/data/LVDBJAW8BI5YSS1QUBG/explore?filterOptions%5Ba%5D=&genes=a%3AKlk6&layoutState=Single&views=a~5.219618750000002-4.345906250000002_48.271872845967756-36.58322377500001_0_cartesian&visualizations=a~1JY9KF3V6Z0DSQ9OLH5%3AWINDIIG7DYY89BTXY48~METADATA%3AFS00DXV0T9R1X9FJ4QE%3Anull%3Anull%3Anull%3Afalse%3A0.5)
- [10x scRNAseq MB-HB-Glut-Sero-Dopa](https://knowledge.brain-map.org/data/LVDBJAW8BI5YSS1QUBG/explore?filterOptions%5Ba%5D=&genes=a%3AHhatl&layoutState=Single&views=a~7.415796499999999-5.863104499999999_49.66048721774194-37.63559625_0_cartesian&visualizations=a~QCTHOSC7UR6VUKOIP70%3AZDVQAUYQZM13HYPAZI8~METADATA%3AFS00DXV0T9R1X9FJ4QE%3Anull%3Anull%3Anull%3Afalse%3A0.5)
- [10x scRNAseq Pallium-Glut](https://knowledge.brain-map.org/data/LVDBJAW8BI5YSS1QUBG/explore?filterOptions%5Ba%5D=&genes=a%3AGm36406&layoutState=Single&views=a~6.725921500000002-4.818932499999999_50.618516062903225-38.36164605_0_cartesian&visualizations=a~F6OPS5MJHKCDXE3DTXU%3A488I12FURRB8ZY5KJ8T~METADATA%3AFS00DXV0T9R1X9FJ4QE%3Anull%3Anull%3Anull%3Afalse%3A0.5)
- [10x scRNAseq NN-IMN-GC](https://knowledge.brain-map.org/data/LVDBJAW8BI5YSS1QUBG/explore?filterOptions%5Ba%5D=&genes=a%3AGm35453&layoutState=Single&views=a~4.8400539999999985-5.129172999999998_49.37071742258065-37.415991899999995_0_cartesian&visualizations=a~40JXWIVV4DIVZ8I7XNP%3A7PS5E57VP5TQ6HE3VED~METADATA%3AFS00DXV0T9R1X9FJ4QE%3Anull%3Anull%3Anull%3Afalse%3A0.5)
- [10x scRNAseq TH-EPI-Glut](https://knowledge.brain-map.org/data/LVDBJAW8BI5YSS1QUBG/explore?filterOptions%5Ba%5D=&genes=a%3AGm31706&layoutState=Single&views=a~6.028312249999999-6.029600749999999_44.77850965725806-33.935750625_0_cartesian&visualizations=a~TTD51W48S5OD23X11EK%3AZZ71VL88BCGRGT1HABS~METADATA%3AFS00DXV0T9R1X9FJ4QE%3Anull%3Anull%3Anull%3Afalse%3A0.5)
Check out our [GitHub resources](https://alleninstitute.github.io/abc_atlas_access/intro.html) to learn more and download data.
As always, thank you for being part of the AIBS community. Please [let us know](https://docs.google.com/forms/d/e/1FAIpQLSeIaEalEJM-sz4PYMMXNtWvLXdGceqTdfP_Qvp3DIv7uEHSFg/viewform)how we can improve the ABC Atlas to better serve your needs.
---
### Author:  [@shawnfan19](https://community.brain-map.org/u/shawnfan19)
#### Post date: [February 15, 2024, 8:20pm UTC](https://community.brain-map.org/t/data-updates-december-13-2023/2779/2 "2024-02-15T20:20:22Z")
hello, than you for putting together such a nice dataset
in the was container, i noticed that there are .h5ad files for atac and rna data of the mtg cells. is there any chance that they can be made available for the dlpfc cells as well?
thank you
---
### Author:  [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)
#### Post date: [February 15, 2024, 9:09pm UTC](https://community.brain-map.org/t/data-updates-december-13-2023/2779/3 "2024-02-15T21:09:18Z")
@shawnfan19: if you are referring to the human SEA-AD work, all of the single nucleus -omics data from DLPFC and MTG (and spatial transcriptomics data from MTG) [are available on AWS](https://registry.opendata.aws/allen-sea-ad-atlas/).
---
### Author:  [@shawnfan19](https://community.brain-map.org/u/shawnfan19)
#### Post date: [February 15, 2024, 9:45pm UTC](https://community.brain-map.org/t/data-updates-december-13-2023/2779/4 "2024-02-15T21:45:49Z")
yes i am aware of that
in the aws bucket you provided the .h5ad files for MTG cells at sea-ad-single-cell-profiling/MTG/ATACseq/SEAAD\_MTG\_ATACseg\_all-nuclei.2024-02-13.h5ad and sea-ad-single-cell-profiling/MTG/RNAseq/SEAAD\_MTG\_RNAseq\_all-nuclei.2024-02-13.h5ad.
i was wondering if similar .h5ad files can be made available for the DLPFC cells as well
thank you
---
### Author:  [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)
#### Post date: [February 15, 2024, 9:51pm UTC](https://community.brain-map.org/t/data-updates-december-13-2023/2779/5 "2024-02-15T21:51:31Z")
The are [already available](https://sea-ad-single-cell-profiling.s3.amazonaws.com/index.html#DLPFC/) for DLPFC. Let us know if you have any more issues.
---
### Author:  [@shawnfan19](https://community.brain-map.org/u/shawnfan19)
#### Post date: [February 15, 2024, 10:04pm UTC](https://community.brain-map.org/t/data-updates-december-13-2023/2779/6 "2024-02-15T22:04:54Z")
i found sea-ad-single-cell-profiling/DLPFC/RNAseq/SEAAD\_DLPFC\_RNAseq\_all-nuclei.2024-02-13.h5ad but could not find any .h5ad files in sea-ad-single-cell-profiling/DLPFC/ATACseq.
is there a .h5ad file for ATACseq data?
---
### Author:  [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)
#### Post date: [February 15, 2024, 11:09pm UTC](https://community.brain-map.org/t/data-updates-december-13-2023/2779/7 "2024-02-15T23:09:06Z")
Correct, for ATAC-Seq h5ad files are available only for MTG, as we have not yet analyzed DLPFC this way. For RNA-seq h5ad files are available in both regions. Sorry for the confusion.
---
### Author:  [@jerem](https://community.brain-map.org/u/jerem)
#### Post date: [March 1, 2024, 3:17pm UTC](https://community.brain-map.org/t/data-updates-december-13-2023/2779/8 "2024-03-01T15:17:11Z")
Hello,
Do you plan to analyze the DLPFC ATAC-Seq data in the same way soon? To have an idea if I can expect to have DLPFC ATAC-Seq h5ad files in the near future. Thank you in advance and have a nice day
---
### Author:  [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)
#### Post date: [March 4, 2024, 7:19pm UTC](https://community.brain-map.org/t/data-updates-december-13-2023/2779/9 "2024-03-04T19:19:28Z")
Hi @jerem. These ATAC-seq data are actively being analyzed. While we don’t currently have a timeline for release, we will post to the Community Forum when these (or other SEA-AD) data become available.
---
### Author:  [@jerem](https://community.brain-map.org/u/jerem)
#### Post date: [October 3, 2024, 12:58pm UTC](https://community.brain-map.org/t/data-updates-december-13-2023/2779/10 "2024-10-03T12:58:52Z")
Hi @jeremyinseattle, do the DLPFC ATAC-seq data have been analyzed? If yes, where could I find them please? They are not available on [AWS S3 Explorer](https://sea-ad-single-cell-profiling.s3.amazonaws.com/index.html#DLPFC/)
Thank you and have a nice day
---
### Author:  [@jeremyinseattle](https://community.brain-map.org/u/jeremyinseattle)
#### Post date: [October 7, 2024, 11:39pm UTC](https://community.brain-map.org/t/data-updates-december-13-2023/2779/11 "2024-10-07T23:39:41Z")
This is something we are still working on. When we have a timeline for release or a location for newly released ATAC-seq data, we’ll post on the Community Forum. More soon, I hope.
As for some good news (related to the original post but not the replies), we now have imputed genes available for the whole mouse brain data set in the ABC Atlas (see [this post](https://community.brain-map.org/t/new-imputed-gene-data-for-the-whole-mouse-brain-now-explorable-in-abc-atlas/3723) for details).