Home › Research › Laboratory science
An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex
Ye Zhang, Kenian Chen, Steven A. Sloan, Mariko L. Bennett, Anja R. Scholze, Sean O’Keeffe, Hemali P. Phatnani, Paolo Guarnieri, Christine Caneda, Nadine Ruderisch, Shuyun Deng, Shane A. Liddelow, Chaolin Zhang, Richard Daneman, Tom Maniatis, Ben A. Barres, Jia Qian Wu. Journal of Neuroscience, 2014-09-03
Topic: Brain proteins, microglia and lab models
The major cell classes of the brain differ in their developmental processes, metabolism, signaling, and function. To better understand the functions and interactions of the cell types that comprise these classes, we acutely purified representative populations of neurons, astrocytes, oligodendrocyte precursor cells, newly formed oligodendrocytes, myelinating oligodendrocytes, microglia, endothelial cells, and pericytes from mouse cerebral cortex. We generated a transcriptome database for these eight cell types by RNA sequencing and used a sensitive algorithm to detect alternative splicing events in each cell type. Bioinformatic analyses identified thousands of new cell type-enriched genes and splicing isoforms that will provide novel markers for cell identification, tools for genetic manipulation, and insights into the biology of the brain. For example, our data provide clues as to how neurons and astrocytes differ in their ability to dynamically regulate glycolytic flux and lactate generation attributable to unique splicing of PKM2, the gene encoding the glycolytic enzyme pyruvate kinase. This dataset will provide a powerful new resource for understanding the development and function of the brain. To ensure the widespread distribution of these datasets, we have created a user-friendly website (http://web.stanford.edu/group/barres_lab/brain_rnaseq.html) that provides a platform for analyzing and comparing transciption and alternative splicing profiles for various cell classes in the brain.
Why it matters
Describes a database of gene activity, built with RNA sequencing, for eight cell types purified from mouse cerebral cortex, including neurons, glia and blood vessel cells. The authors made it available on a website as a resource for studying how the brain develops and works.
How this study scored 58/100
Published in a peer-reviewed journal. Scored zero for study design, sample size, effect reported, studied in people and randomised / blinded because the record does not state it. We have no data on strength of evidence, so that was left out: it earned 55 of the 95 points we could judge it on, which is 58 out of 100.
| Component | Points | Why |
|---|---|---|
| Journal tier | 7 / 10 | Tier 3 — peer-reviewed journal (Journal of Neuroscience) |
| Journal's citation record | 4 / 4 | Journal of Neuroscience: journal h-index 651 (OpenAlex, 2026-10-29) |
| Study design | 0 / 12 | No study design recorded — scores zero, not guessed (not stated in the record — scored 0) |
| Strength of evidence | — / 5 | No evidence rating recorded — left out of this score |
| Peer-review validation | 10 / 10 | Peer-reviewed. Published as an article in a named peer-reviewed journal. |
| How recent | 1 / 5 | 2014 — within 20 year(s) of the newest study here |
| Sample size | 0 / 4 | Participant count not stated — scores zero (not stated in the record — scored 0) |
| Effect reported | 0 / 3 | No effect size reported — scores zero (not stated in the record — scored 0) |
| Studied in people | 0 / 3 | Not stated whether this was studied in people — scores zero (not stated in the record — scored 0) |
| Randomised / blinded | 0 / 2 | No randomisation or blinding stated — scores zero (not stated in the record — scored 0) |
| Times cited | 7 / 7 | Cited 5,024 times (OpenAlex, 2026-10-10) |
| Citations per year | 5 / 5 | 358.9 citations a year over 14 year(s) since 2014 |
| Impact for its field and year | 6 / 6 | Cited 94.3× the average for papers of its field and year (OpenAlex FWCI) |
| Cited by studies here | 0 / 6 | No other study in this library cites it |
| Still being cited | 4 / 4 | Cited 1,080 times in 2024–2026 (2026 still in progress; OpenAlex) |
| Senior author's track record | 2 / 4 | Last-listed author Jia Qian Wu: h-index 24 (OpenAlex, whole career) |
| Institution's track record | 3 / 3 | Stanford University: institution h-index 2,684 (OpenAlex) |
| Multi-centre collaboration | 2 / 3 | OpenAlex lists 8 institution(s) in 2 countries |
| Indexed in PubMed | 2 / 2 | Indexed in PubMed (PMID 25186741) |
| Free to read | 2 / 2 | Free to read |
| Points | 55 / 95 | Scored on 19 of 20 parts. We have no data for the rest, so they are left out: 55 of the 95 points we could judge it on is 58 out of 100. |
| Total | 58 / 100 | — |
What each of these 20 components measures, and what this score is not →
Read the original
- DOI: 10.1523/jneurosci.1860-14.2014
- PubMed: 25186741
- Original source →
- Free full text: Journal of Neuroscience →
Full text: free to read — OpenAlex lists this copy as free to read: the link above (checked 6 Feb 1020).
Cite this study APA, Vancouver, BibTeX · download .bib or .ris
Built from the record alzhub holds for this paper, not looked up. Volume, issue and page numbers are not held in the record. The record names 17 authors; APA and Vancouver show the first six, BibTeX and the downloads carry all of them. Check the citation against the original before you use it.
APA 7th
Zhang, Y., Chen, K., Sloan, S. A., Bennett, M. L., Scholze, A. R., O’Keeffe, S., et al. (2014). An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex. Journal of Neuroscience. https://doi.org/10.1523/jneurosci.1860-14.2014
Vancouver
Zhang Y, Chen K, Sloan SA, Bennett ML, Scholze AR, O’Keeffe S, et al. An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex. Journal of Neuroscience. 2014. doi:10.1523/jneurosci.1860-14.2014. PMID: 25186741.
BibTeX
@article{zhang2014-25186741,
author = {Zhang, Ye and Chen, Kenian and Sloan, Steven A. and Bennett, Mariko L. and Scholze, Anja R. and O’Keeffe, Sean and Phatnani, Hemali P. and Guarnieri, Paolo and Caneda, Christine and Ruderisch, Nadine and Deng, Shuyun and Liddelow, Shane A. and Zhang, Chaolin and Daneman, Richard and Maniatis, Tom and Barres, Ben A. and Wu, Jia Qian},
title = {{An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex}},
journal = {Journal of Neuroscience},
year = {2014},
doi = {10.1523/jneurosci.1860-14.2014},
pmid = {25186741},
url = {https://doi.org/10.1523/jneurosci.1860-14.2014}
}
Related studies in Laboratory science
Also tagged “cerebral”
900 studies in the library carry the topic tag “cerebral”; these are this study's neighbours in a fixed, alphabetical-by-hash tour of them, not the closest in content. All 900 tagged studies.