Omics · study · 2026
Single-nucleus multiome ATAC-seq and RNA-seq analysis of GCM1 knockout in rotational human tropholast organoids
Listed in NCBI GEO
Single nuclei were isolated from organoids to investigate the effects of GCM1 knockout and AAVS1 knockout (as control) on chromatin accessibility and gene expression profiles.
Description
Approximately 10,000 nuclei per sample were processed using 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit, enabling simultaneous profiling of chromatin accessibility and gene expression from individual nuclei. Raw sequencing data were processed using Cell Ranger ARC to generate filtered feature-barcode matrices.
Data analysis was performed in R (v4.3+) using Seurat (v4) and Signac packages.
Links
Get the data
- GEO FTP directory ftp.ncbi.nlm.nih.gov/geo/series/GSE305nnn/GSE305070 ↗
download · from NCBI GEO
Where it is published
- GEO accession page ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE305070 ↗
landing page · from NCBI GEO
Documentation and papers
- PRJNA1304391 ncbi.nlm.nih.gov/bioproject/PRJNA1304391 ↗
project · from NCBI GEO
Topics
- Stated by source
- Expression profiling by high throughput sequencing · Genome binding/occupancy profiling by high throughput sequencing · Homo sapiens
- From keywords
- Life Sciences
- Inferred from text
- RNA sequencing 65% · Sequencing 75%
Provenance · 1 source records, 10 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| NCBI GEO | GSE305070 | 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:expression-profiling-by-high-throughput-sequencing | source · NCBI GEO | connector:ncbi_geo@1.0.0 | /gdstype |
| 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%) |
| 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 |