Omics · study · 2026
Characterizing circular and linear non-coding RNA in human aging brains and their association with dementia
Listed in NCBI GEO
Total RNA, depleted for ribosomal RNA, is commonly used for RNA sequencing to capture both polyadenylated and non-polyadenylated transcripts, while the poly(A) tail targeting protocols can either enrich (Poly(A)-selection) or deplete (Poly(A)-depletion) the polyadenylated fraction.
Description
To ascertain the best library strategy for capturing long non-coding RNAs (lncRNAs, >200nt) and circular RNAs (circRNAs) in aged brains, we applied three protocols (total ribo-depleted, poly(A)-selected, and poly(A)-depleted) to 128 human hippocampus samples.
Our results show that both ribo-depleted and poly(A)-depleted perform well for lncRNA and circRNA profiling, with poly(A)-depleted protocol generally having a slightly higher number of non-coding RNAs detected. Additionally, we compared poly(A)-selected and -depleted data for predicting the poly(A) status of hippocampus transcripts. The proportion of non-polyadenylated transcripts was higher than previously found.
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This study demonstrates how the choice of library construction impacts the outcomes, helping to make informed methodological choices when studying brain non-coding RNAs. In addition, we for the first time examined whether the poly(A) status of protein-coding mRNAs is associated with AD and AD-related dementias.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE339nnn/GSE339279 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE339279 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1498080 ncbi.nlm.nih.gov/bioproject/PRJNA1498080 ↗
project · from NCBI GEO
Topics
- Stated by source
- Homo sapiens · Non-coding RNA profiling by high throughput sequencing
- From keywords
- Life Sciences
- Inferred from text
- RNA sequencing 75% · Sequencing 75%
Provenance · 1 source records, 9 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE339279 | 14 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:non-coding-rna-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[modality].local:modality:rna-seq | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[modality].local:modality:sequencing | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[organism].NCBITaxon:9606 | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /taxon |
| description | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /summary |
| publication_date | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| title | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /title |