Promoter comparison for in vivo HDI-STARR-seq
HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivoThe same global liver-DNase fragment pool was cloned into STARR-TYC4 with an SCP1 promoter, STARR-TYC5 with an ORI promoter, or STARR-TYC6 with the minimal Albumin promoter. The promoter libraries were delivered to TCPOBOP-treated male mouse liver and assayed 7 days later; the available processed GEO table reports aggregate mapped RNA/DNA library activity by sample rather than element-level activities.
Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.
Perturbation & assay details
TCPOBOP (3 mg/kg, i.p., 1 day before collection); male mouse liver
Episomal promoter-comparison STARR-seq after hydrodynamic liver delivery. STARR-TYC4 used SCP1, STARR-TYC5 used ORI and STARR-TYC6 used the modified minimal Albumin promoter; DNA and reporter-RNA libraries were separately sequenced. The processed GEO value is total RNA reads divided by total DNA reads for the corresponding library/sample, not a per-enhancer score.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (10 of 10)
| Row | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ||||||||||
| 2 | ||||||||||
| 3 | ||||||||||
| 4 | ||||||||||
| 5 | ||||||||||
| 6 | ||||||||||
| 7 | ||||||||||
| 8 | ||||||||||
| 9 | ||||||||||
| 10 | ||||||||||
| 11 | ||||||||||
| 12 |
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 10 definitions
- sample_id
- Source processed-dataset sample identifier.
- geo_accession
- GEO sample accession mapped from the GEO family metadata.
- read_type
- RNA library or DNA library.
- replicate
- Biological/library replicate number parsed from the source sample description.
- sex
- Mouse sex reported for the sample.
- perturbation
- Treatment reported for the promoter-comparison liver collection.
- promoter_construct
- STARR-seq library and promoter used: SCP1, ORI or minimal Albumin.
- mapped_read_count
- Total properly paired uniquely mapped R1+R2 reads reported by GEO.
- relative_rna_activity_rna_over_dna
- Aggregate total RNA reads divided by total DNA reads for the same promoter library; reported for RNA samples only.
- qc_pass
- Packaging QC indicator: mapped read count was greater than zero (1=pass).
Quality control
GEO metadata reports Bowtie2 mapping to mm9 with uniquely aligned reads. The packaged table retains all 12 source samples with mapped read count greater than zero (six RNA and six DNA libraries); DNA samples correctly have NA for the aggregate RNA/DNA activity field.
Curation notes
This is a library-level promoter-performance experiment, not an element-level enhancer table. The source reports much higher aggregate RNA activity for the Albumin-promoter library than for SCP1 or ORI; do not interpret the rows as per-region enhancer effects.