Excel · study · 2026
An Optimized Methods for Reconstruction of Transcriptional Regulatory Networks in Bacteria Using ChIP-exo and RNA-seq Datasets [ChIP-exo]
Listed in NCBI GEO
We propose an optimized protocol to reconstruct bacterial transcriptional regulatory networks (TRNs) using ChIP-exo and RNA-seq datasets.
Description
For the reconstruction of TRNs, the omics datasets were targeted to RpoS and generated in Escherichia coli K-12 MG1655 cultured at mid-exponential phase in M9 glucose media.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE271nnn/GSE271231 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE271231 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1130493 ncbi.nlm.nih.gov/bioproject/PRJNA1130493 ↗
project · from NCBI GEO
- PubMed 39527186 pubmed.ncbi.nlm.nih.gov/39527186 ↗
publication · from NCBI GEO
Topics
- Stated by source
- Genome binding/occupancy profiling by high throughput sequencing
- From keywords
- Life Sciences
- Inferred from text
- RNA sequencing 65% · Sequence analysis 76%
Provenance · 1 source records, 8 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE271231 | 13 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[field].anzsrc:field:310206 | enrichment · NCBI GEO | taxonomy-embedding@1.1.0 | title+keywords+description (76%) |
| concepts[field].local:field:life-sciences | mapping · NCBI GEO | connector:ncbi_geo@1.0.0 | |
| concepts[method].geo_series_type:genome-binding-occupancy-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 (65%) |
| 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 |