Omics · study · 2026
Strand-specific RNA-seq of Escherichia coli Nissle 1917 delta_cra, delta_crp, and delta_cra_delta_crp knockout mutants
Listed in NCBI GEO
This study used prokaryotic strand-specific RNA sequencing to characterize transcriptomic changes associated with knockout of two global transcriptional regulator genes, cra and crp, encoding catabolite repressor/activator (CRA) and cAMP receptor protein (CRP), respectively, in Escherichia coli Nissle 1917.
Description
Four genotypes were profiled: wild-type strain, delta_cra mutant, delta_crp mutant, and delta_cra_delta_crp double-knockout mutant.
Cells were cultured in MS medium and harvested at OD600 = 0.6. Ribosomal RNA was depleted, strand-specific RNA-seq libraries were constructed, and paired-end sequencing reads were generated on an Illumina NovaSeq 6000 platform. Gene-level read count, RPKM, and TPM matrices were generated to compare expression profiles among genotypes.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE329nnn/GSE329458 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE329458 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1459272 ncbi.nlm.nih.gov/bioproject/PRJNA1459272 ↗
project · from NCBI GEO
- PubMed 42252666 pubmed.ncbi.nlm.nih.gov/42252666 ↗
publication · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing
- From keywords
- Life Sciences
- Inferred from text
- RNA sequencing 75% · Sequencing 75%
Provenance · 1 source records, 8 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE329458 | 15 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: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%) |
| 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 |