Omics · study · 2026
The long noncoding RNA Malat1 contains an internal ribosome entry site mediating micropeptide translation
Listed in NCBI GEO
To determine the structure of the Malat1 IRES, fbDMS-MaP structure probing experiments were performed in BV2 cells for endogenous mouse Malat1 probing, and N2a cells for probing of reporter constructs pDual-GFP-(1-739) IRES-RFP and pDual-GFP-(558-695) IRES-RFP.
Description
Two biological replicates were collected for each probing target. For each replicate, fbDMS-MaP includes a sample treated with dimethyl sulfate (modified), and one sample treated with ethanol (unmodified).
DMS reacts with the Watson-Crick face of unpaired bases in RNA, covalently modifying them with a methyl adduct. These modifications are encoded as mutations during reverse transcription with MarathonRT. Amplicons are then PCR amplified, next-generation sequencing libraries are prepared, and sequenced using an Illumina NextSeq 2000 platform.
Read the rest (1 more)
The sequencing data are aligned to the reference sequence, and a reactivity profile of 'modified' and 'unmodified' samples is used to calculate the DMS reactivity values of each base. These data can subsequently be used for RNA secondary structure modelling.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE310nnn/GSE310313 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE310313 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1365748 ncbi.nlm.nih.gov/bioproject/PRJNA1365748 ↗
project · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Mus musculus
- From keywords
- Life Sciences
- Inferred from text
- Sequencing 75%
Provenance · 1 source records, 8 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE310313 | 13 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:expression-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| concepts[modality].local:modality:sequencing | enrichment · NCBI GEO | keyword-concept-rules@1.0.0 | title+description (75%) |
| concepts[organism].NCBITaxon:10090 | 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 |