# \#rna-seq **URL:** https://community.brain-map.org/tag/rna-seq/55.md [Latest](https://community.brain-map.org/latest.md) · [Categories](https://community.brain-map.org/categories.md) · [Tags](https://community.brain-map.org/tags.md) --- ## [How to start/do WGCNA of microarray datasets?](https://community.brain-map.org/t/how-to-start-do-wgcna-of-microarray-datasets/5073)
**Author:** [@Navy](https://community.brain-map.org/u/Navy)\ **Replies:** 3\ **Last updated:** [September 29, 2026, 9:32am UTC](https://community.brain-map.org/t/how-to-start-do-wgcna-of-microarray-datasets/5073 "2026-09-29T09:32:26Z")
i have four datasets whcih i worked on, i used limma as they were mcroarray platforms. then i did GSE for each dataset, also did several other downstream in silico test etc. but my guide said she want me to perform wgcna… --- ## [Clarification of SEA-AD MTG layer-level IBA1–6E10 colocalization percentage](https://community.brain-map.org/t/clarification-of-sea-ad-mtg-layer-level-iba1-6e10-colocalization-percentage/5068)
**Author:** [@Alexy](https://community.brain-map.org/u/Alexy)\ **Replies:** 0\ **Last updated:** [September 5, 2026, 9:23pm UTC](https://community.brain-map.org/t/clarification-of-sea-ad-mtg-layer-level-iba1-6e10-colocalization-percentage/5068 "2026-09-05T21:23:09Z")
Hello SEA-AD team, I am preparing a donor-level secondary analysis using the publicly released June 2026 SEA-AD quantitative neuropathology summary and processed MTG endothelial pseudobulk data. I would appreciate clari… --- ## [Replicating Fig 3c — request for lmplots source from helper\_functions.py](https://community.brain-map.org/t/replicating-fig-3c-request-for-lmplots-source-from-helper-functions-py/4963)
**Author:** [@granzota](https://community.brain-map.org/u/granzota)\ **Replies:** 2\ **Last updated:** [June 23, 2026, 10:07am UTC](https://community.brain-map.org/t/replicating-fig-3c-request-for-lmplots-source-from-helper-functions-py/4963 "2026-06-23T10:07:47Z")
Dear all, I am writing for clarification on the implementation of the lmplots function used to generate Figure 3c of Gabitto et al. 2024 (Nature Neuroscience). In the context of a project on a subpopulation in MTG, I h… --- ## [Freezing of isolated nuclei](https://community.brain-map.org/t/freezing-of-isolated-nuclei/1081)
**Author:** [@Martina17](https://community.brain-map.org/u/Martina17)\ **Replies:** 2\ **Last updated:** [May 11, 2026, 1:54pm UTC](https://community.brain-map.org/t/freezing-of-isolated-nuclei/1081 "2026-05-11T13:54:26Z")
Hi, I am isolating nuclei from snap frozen brain tissue (prefrontal cortex). The nuclei are then used to perform single-nuclei RNA seq using 10x genomics technology. I normally extract the nuclei from the tissue and th… --- ## [Histogram for a specific gene on ABC atlas](https://community.brain-map.org/t/histogram-for-a-specific-gene-on-abc-atlas/4877)
**Author:** [@Sora](https://community.brain-map.org/u/Sora)\ **Replies:** 2\ **Last updated:** [April 10, 2026, 5:09am UTC](https://community.brain-map.org/t/histogram-for-a-specific-gene-on-abc-atlas/4877 "2026-04-10T05:09:36Z")
Dear Allen Brain Institute team I am currently analyzing gene expression data from the Allen Brain Cell Atlas and have a question regarding the histograms provided for individual genes. I noticed that the bin widths in… --- ## [Were neurons and non-neurons sequenced using the same protocol?](https://community.brain-map.org/t/were-neurons-and-non-neurons-sequenced-using-the-same-protocol/4845)
**Author:** [@noamiz](https://community.brain-map.org/u/noamiz)\ **Replies:** 1\ **Last updated:** [February 6, 2026, 9:58pm UTC](https://community.brain-map.org/t/were-neurons-and-non-neurons-sequenced-using-the-same-protocol/4845 "2026-02-06T21:58:29Z")
Hi, Quick question about the dataset: were neurons and non-neurons processed and sequenced using the exact same protocol (library prep, chemistry, sequencing, etc.), or were there any differences between them? asking b… --- ## [Question on muscarinic receptor gene expression in WHB-10Xv3 dataset](https://community.brain-map.org/t/question-on-muscarinic-receptor-gene-expression-in-whb-10xv3-dataset/4708)
**Author:** [@xyaous](https://community.brain-map.org/u/xyaous)\ **Replies:** 6\ **Last updated:** [November 13, 2025, 8:53pm UTC](https://community.brain-map.org/t/question-on-muscarinic-receptor-gene-expression-in-whb-10xv3-dataset/4708 "2025-11-13T20:53:12Z")
Hi, I retrieved expression data of muscarinic receptor gene CHRM1 - 5 in all neuron cells from the WHB-10Xv3 dataset. Attached figure 1 plotted gene expression in CPM and percent of detection, where CHRM4 expression was… --- ## [ISH false discovery rate (fdr)](https://community.brain-map.org/t/ish-false-discovery-rate-fdr/4728)
**Author:** [@AKAnderson](https://community.brain-map.org/u/AKAnderson)\ **Replies:** 0\ **Last updated:** [October 24, 2025, 6:26pm UTC](https://community.brain-map.org/t/ish-false-discovery-rate-fdr/4728 "2025-10-24T18:26:33Z")
In the ISH dataset of mice, there is a fold change data for each gene, but there is not false discovery rate data (fdr). Is there a way to get this information? I am trying to generate a volcano plot. Thanks for any insi… --- ## [Bulk RNA-seq TPM values?](https://community.brain-map.org/t/bulk-rna-seq-tpm-values/4719)
**Author:** [@irene](https://community.brain-map.org/u/irene)\ **Replies:** 1\ **Last updated:** [October 10, 2025, 10:23pm UTC](https://community.brain-map.org/t/bulk-rna-seq-tpm-values/4719 "2025-10-10T22:23:54Z")
Hi team, I downloaded two bulk RNA-seq datasets (H0351.2001, H0351.2002) from this link: Microarray Data Download :: Allen Brain Atlas: Human Brain . I was planning to comparing to use the TPM values to check my gene o… --- ## [Ensembl ID and gene name not matching](https://community.brain-map.org/t/ensembl-id-and-gene-name-not-matching/4706)
**Author:** [@maddym](https://community.brain-map.org/u/maddym)\ **Replies:** 1\ **Last updated:** [September 26, 2025, 6:45pm UTC](https://community.brain-map.org/t/ensembl-id-and-gene-name-not-matching/4706 "2025-09-26T18:45:42Z")
Hello there, I am trying to process some specific gene data and it looks like there are some discrepancies in Ensembl IDs and gene names between the Allen Atlas and other sources. I am curious if there is a way to troubl… --- ## [Metadata/Publication for SMART-Seq v4 DFC M1C Dataset](https://community.brain-map.org/t/metadata-publication-for-smart-seq-v4-dfc-m1c-dataset/4553)
**Author:** [@berilerdogdu](https://community.brain-map.org/u/berilerdogdu)\ **Replies:** 1\ **Last updated:** [July 29, 2025, 3:18pm UTC](https://community.brain-map.org/t/metadata-publication-for-smart-seq-v4-dfc-m1c-dataset/4553 "2025-07-29T15:18:29Z")
Hello! I recently came across a dataset uploaded by your group to the Brain Knowledge Platform (nemo:dat-72qka5t), available at: This dataset contains SMART-Seq v4 RNA-Seq reads from human cortical areas M1C and DFC,… --- ## [Differential Gene Expression in RNA-seq TBI cohort](https://community.brain-map.org/t/differential-gene-expression-in-rna-seq-tbi-cohort/4326)
**Author:** [@kelseyaw](https://community.brain-map.org/u/kelseyaw)\ **Replies:** 3\ **Last updated:** [July 25, 2025, 11:20pm UTC](https://community.brain-map.org/t/differential-gene-expression-in-rna-seq-tbi-cohort/4326 "2025-07-25T23:20:02Z")
I am trying to download differentially expressed genes in each brain region of those having TBI vs those not having TBI. I keep getting the 403 Forbidden page and I am not sure what to do at this point. I have tried priv… --- ## [Downloading scRNA-Seq data for mouse developing brain](https://community.brain-map.org/t/downloading-scrna-seq-data-for-mouse-developing-brain/4532)
**Author:** [@ellie123](https://community.brain-map.org/u/ellie123)\ **Replies:** 1\ **Last updated:** [July 16, 2025, 10:48pm UTC](https://community.brain-map.org/t/downloading-scrna-seq-data-for-mouse-developing-brain/4532 "2025-07-16T22:48:38Z")
Hello! I’m looking to download the RNA-Seq genecode normalized expression values and metadata for the mouse developing brain (shown in the heatmaps). This is available for download with the developing human brain but I c… --- ## [Having trouble finding MET data all for the same cell from specific paper](https://community.brain-map.org/t/having-trouble-finding-met-data-all-for-the-same-cell-from-specific-paper/4405)
**Author:** [@dom\_pols](https://community.brain-map.org/u/dom_pols)\ **Replies:** 3\ **Last updated:** [June 20, 2025, 8:56pm UTC](https://community.brain-map.org/t/having-trouble-finding-met-data-all-for-the-same-cell-from-specific-paper/4405 "2025-06-20T20:56:39Z")
Thus far, I have been looking at all the data found on this page: Multimodal Characterization in Mouse Visual Cortex - brain-map.org for the combined morphology, electrophysiology, and transcriptome data for individual … --- ## [Data Download: Different Sample Numbers in Files](https://community.brain-map.org/t/data-download-different-sample-numbers-in-files/4430)
**Author:** [@ss3943](https://community.brain-map.org/u/ss3943)\ **Replies:** 3\ **Last updated:** [May 29, 2025, 4:33pm UTC](https://community.brain-map.org/t/data-download-different-sample-numbers-in-files/4430 "2025-05-29T16:33:40Z")
I downloaded the folder ‘RNA-seq Gencode v3c summarized to genes’ and loaded the dataframes into R. From what I understand, the columns in the ‘expression\_matrix.csv’ file are the samples listed in the ‘columns\_metadata.… --- ## [Mouse Brain Nuclei Isolation for 10X GEM-X Flex Gene Expression](https://community.brain-map.org/t/mouse-brain-nuclei-isolation-for-10x-gem-x-flex-gene-expression/4070)
**Author:** [@Andrea97](https://community.brain-map.org/u/Andrea97)\ **Replies:** 6\ **Last updated:** [February 27, 2025, 12:19am UTC](https://community.brain-map.org/t/mouse-brain-nuclei-isolation-for-10x-gem-x-flex-gene-expression/4070 "2025-02-27T00:19:45Z")
Dear All, I am a research assistant working in the neurologe field. As part of a project we are currently performing nuclei isolation for single-nuclei RNA sequencing from frozen mouse brain tissues. For the nuclei isol… --- ## [New abc\_atlas\_acces release with Aging Mouse Data](https://community.brain-map.org/t/new-abc-atlas-acces-release-with-aging-mouse-data/4003)
**Author:** [@morriscb](https://community.brain-map.org/u/morriscb)\ **Replies:** 0\ **Last updated:** [December 18, 2024, 11:28pm UTC](https://community.brain-map.org/t/new-abc-atlas-acces-release-with-aging-mouse-data/4003 "2024-12-18T23:28:10Z")
Hi everyone, We’re happy to announce the release of the Aging Mouse dataset via the abc\_atlas\_access tool. A full release through the ABC Atlas visualization will be coming in the future. This data release includes des… --- ## [Processed gene expression matrix for SEA-AD?](https://community.brain-map.org/t/processed-gene-expression-matrix-for-sea-ad/3964)
**Author:** [@willgryanv](https://community.brain-map.org/u/willgryanv)\ **Replies:** 1\ **Last updated:** [December 10, 2024, 5:57pm UTC](https://community.brain-map.org/t/processed-gene-expression-matrix-for-sea-ad/3964 "2024-12-10T17:57:00Z")
Hi there, Are there plans to generate a processed gene expression matrix for the latest SEA-AD dataset? I noted it’s absence on the S3 bucket and explore page. For example, the earlier Human MTG 10x SEA-AD explore page … --- ## [How can I optimize my snRNA-seq workflow—both experimentally and bioinformatically—to enable high-resolution transcriptomic cell type mapping?](https://community.brain-map.org/t/how-can-i-optimize-my-snrna-seq-workflow-both-experimentally-and-bioinformatically-to-enable-high-resolution-transcriptomic-cell-type-mapping/3902)
**Author:** [@sbhamidipati](https://community.brain-map.org/u/sbhamidipati)\ **Replies:** 2\ **Last updated:** [December 4, 2024, 6:21pm UTC](https://community.brain-map.org/t/how-can-i-optimize-my-snrna-seq-workflow-both-experimentally-and-bioinformatically-to-enable-high-resolution-transcriptomic-cell-type-mapping/3902 "2024-12-04T18:21:39Z")
Hello! I’m writing to get some guidance on optimizing my snRNA-seq workflow to facilitate accurate mapping to the Allen Institute’s transcriptomic types at the highest granularity possible. Specifically, Is there an … --- ## [How to use "Mouse Whole Cortex and Hippocampus 10x" to annotate a spatial data set in seuart?](https://community.brain-map.org/t/how-to-use-mouse-whole-cortex-and-hippocampus-10x-to-annotate-a-spatial-data-set-in-seuart/2333)
**Author:** [@ivingan01](https://community.brain-map.org/u/ivingan01)\ **Replies:** 2\ **Last updated:** [June 1, 2023, 7:35pm UTC](https://community.brain-map.org/t/how-to-use-mouse-whole-cortex-and-hippocampus-10x-to-annotate-a-spatial-data-set-in-seuart/2333 "2023-06-01T19:35:40Z")
Hi Allen Brian Map Community, Long time listener, first time caller. I am a novice to coding and data analysis. I am working my way through the seurat tutorial to analyze spatial transcriptomic data (Analysis, visualiz… --- ## [V1C data from Seattle Alzheimer's Disease Cell Atlas](https://community.brain-map.org/t/v1c-data-from-seattle-alzheimers-disease-cell-atlas/3801)
**Author:** [@MPanday](https://community.brain-map.org/u/MPanday)\ **Replies:** 2\ **Last updated:** [October 23, 2024, 3:56pm UTC](https://community.brain-map.org/t/v1c-data-from-seattle-alzheimers-disease-cell-atlas/3801 "2024-10-23T15:56:21Z")
Hello, I’m trying to access V1C (primary visual cortex) data from the Seattle Alzheimer’s Disease Database. According to the documentation, V1C data should be available. However, when I check the AWS bucket for single-c… --- ## [SEA-AD snRNASeq dataset format and loading in R for analysis using Seuratv5](https://community.brain-map.org/t/sea-ad-snrnaseq-dataset-format-and-loading-in-r-for-analysis-using-seuratv5/3454)
**Author:** [@eitan.kaplan](https://community.brain-map.org/u/eitan.kaplan)\ **Replies:** 1\ **Last updated:** [July 17, 2024, 3:51pm UTC](https://community.brain-map.org/t/sea-ad-snrnaseq-dataset-format-and-loading-in-r-for-analysis-using-seuratv5/3454 "2024-07-17T15:51:44Z")
I am the Scientific Project Manager for the SEA-AD Consortium. I am posting a community question received via email related to working with SEA-AD data: I am trying to use the dataset: SEAAD\_MTG\_RNAseq\_final-nuclei.2024… --- ## [How to do a correlation analysis between two specific genes across different tissues](https://community.brain-map.org/t/how-to-do-a-correlation-analysis-between-two-specific-genes-across-different-tissues/3193)
**Author:** [@MNani](https://community.brain-map.org/u/MNani)\ **Replies:** 5\ **Last updated:** [April 3, 2024, 5:23pm UTC](https://community.brain-map.org/t/how-to-do-a-correlation-analysis-between-two-specific-genes-across-different-tissues/3193 "2024-04-03T17:23:16Z")
Hey everyone! I am new to the forum and It’s my first time using the Allen mouse brain atlas. I am looking to do an analysis where for each mice within the dataset I would need to extract the data (ISH or 10x) for the e… --- ## [Known protein not detected by RNA explorer](https://community.brain-map.org/t/known-protein-not-detected-by-rna-explorer/3109)
**Author:** [@jackp](https://community.brain-map.org/u/jackp)\ **Replies:** 1\ **Last updated:** [February 29, 2024, 7:31pm UTC](https://community.brain-map.org/t/known-protein-not-detected-by-rna-explorer/3109 "2024-02-29T19:31:50Z")
I recently used the RNA explorer (10x and SMART-seq) to view expression of the mechanosensitive channel Piezo1 which is known to be expressed in the motor cortex and hippocampus of mice. The heatmap results did not show … --- ## [Count data for Developmental Transcriptome Dataset (RNA-Seq Gencode v10 summarized to genes)](https://community.brain-map.org/t/count-data-for-developmental-transcriptome-dataset-rna-seq-gencode-v10-summarized-to-genes/2961)
**Author:** [@pgraber](https://community.brain-map.org/u/pgraber)\ **Replies:** 2\ **Last updated:** [January 24, 2024, 10:23pm UTC](https://community.brain-map.org/t/count-data-for-developmental-transcriptome-dataset-rna-seq-gencode-v10-summarized-to-genes/2961 "2024-01-24T22:23:11Z")
I am working with the Developmental Transcriptome Dataset. https://www.brainspan.org/api/v2/well\_known\_file\_download/267666525 I was wondering if there is the raw count data available for this dataset? I would like to … --- ## [ABC raw data availablility](https://community.brain-map.org/t/abc-raw-data-availablility/2822)
**Author:** [@jkniehaus](https://community.brain-map.org/u/jkniehaus)\ **Replies:** 2\ **Last updated:** [January 3, 2024, 6:39pm UTC](https://community.brain-map.org/t/abc-raw-data-availablility/2822 "2024-01-03T18:39:24Z")
Hello, I would like to download raw fastq files from the latest cell taxonomy. It appears that the nemo data archive housing the raw sequencing files is currently down. I believe this was planned, but would like to know… --- ## [The method of "expression" in the below window of the "reference alta"](https://community.brain-map.org/t/the-method-of-expression-in-the-below-window-of-the-reference-alta/2675)
**Author:** [@zhang](https://community.brain-map.org/u/zhang)\ **Replies:** 1\ **Last updated:** [November 9, 2023, 9:51pm UTC](https://community.brain-map.org/t/the-method-of-expression-in-the-below-window-of-the-reference-alta/2675 "2023-11-09T21:51:22Z")
i wonder “mouse brain”, the subtitle “reference alta”. in the below window, it’s about the method of “expression”. thank you in advance. --- ## [Where to obtain Continuous Pseuo-progression scores (CPS) in SEA-AD data](https://community.brain-map.org/t/where-to-obtain-continuous-pseuo-progression-scores-cps-in-sea-ad-data/2599)
**Author:** [@tadeoye](https://community.brain-map.org/u/tadeoye)\ **Replies:** 1\ **Last updated:** [October 6, 2023, 5:43pm UTC](https://community.brain-map.org/t/where-to-obtain-continuous-pseuo-progression-scores-cps-in-sea-ad-data/2599 "2023-10-06T17:43:52Z")
Hello team, After reviewing the uploaded metadata and supplementary data for the SEA-AD data, I observed that the Continuous Pseudo-progression scores of AD severity (CPS scores) were not included. Would it be possible … --- ## [Will Mouse Patch-Seq data be available in NEMO Analytics?](https://community.brain-map.org/t/will-mouse-patch-seq-data-be-available-in-nemo-analytics/1969)
**Author:** [@shandran](https://community.brain-map.org/u/shandran)\ **Replies:** 5\ **Last updated:** [September 26, 2023, 9:27pm UTC](https://community.brain-map.org/t/will-mouse-patch-seq-data-be-available-in-nemo-analytics/1969 "2023-09-26T21:27:18Z")
I found the mouse patch-seq scRNA data on the NEMO archive, but in the NEMO Analytics tool (specifically, the Single Cell Workbench), I could not see the patch-seq data in the pull-down menu for public datasets. Are ther… --- ## [How rto download single cell RNAseq data in patchseq](https://community.brain-map.org/t/how-rto-download-single-cell-rnaseq-data-in-patchseq/2527)
**Author:** [@heather\_green](https://community.brain-map.org/u/heather_green)\ **Replies:** 8\ **Last updated:** [August 21, 2023, 11:31pm UTC](https://community.brain-map.org/t/how-rto-download-single-cell-rnaseq-data-in-patchseq/2527 "2023-08-21T23:31:11Z")
Hi Allen Community, I am trying to learn patch-seq data on your website, and I want to download patch-seq data for analysis. But I find the single-cell RNAseq data you put on NEMO is under control. How can I get access… [Next page](https://community.brain-map.org/tag/rna-seq/55.md?match_all_tags=true&page=1&tags%5B%5D=rna-seq)