Global 50,332-region HDI-STARR-seq enhancer screen in mouse liver
HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivoA high-complexity STARR-TYC6 library of DNase-I-released mouse liver genomic fragments was delivered to mouse liver by hydrodynamic injection. Reporter activity was measured 7 days later in four untreated males, four TCPOBOP-treated males and three untreated females, with plasmid/DNA input normalization and condition-specific enhancer classifications.
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
Vehicle control or TCPOBOP (3 mg/kg, 24 h before collection) in male mice; untreated female control group
Episomal STARR-seq plasmid delivered in vivo by hydrodynamic tail-vein injection. The STARR-TYC6 reporter uses the modified minimal mouse Albumin promoter; inserts are orientation-independent DNase-I-released genomic fragments. The source reports normalized plasmid, liver DNA and reporter-RNA reads, per-condition mean enhancer activity, replicate-level QC classification, nearest gene/TAD annotations, and mm10 liftover coordinates.
Processed data
50 rows per page. Click a cell to inspect its full value.
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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 64 definitions
- element_id
- Unique global-library MACS2 peak identifier.
- chromosome
- Mouse mm9 chromosome.
- start_mm9
- Reported mm9 genomic start coordinate.
- end_mm9
- Reported mm9 genomic end coordinate.
- width_bp
- Peak width in base pairs (end minus start).
- chromosome_mm10
- Mouse mm10 chromosome after source UCSC liftover.
- start_mm10
- Lifted-over mm10 start coordinate.
- end_mm10
- Lifted-over mm10 end coordinate.
- plasmid_norm_reads_per_10m
- Input STARR-TYC6 plasmid reads normalized per 10 million mapped reads.
- dna_norm_tcpo_male
- TCPOBOP-male liver-extracted DNA reads normalized per 10 million mapped reads.
- dna_norm_vehicle_male
- Vehicle-male liver-extracted DNA reads normalized per 10 million mapped reads.
- dna_norm_vehicle_female
- Vehicle-female liver-extracted DNA reads normalized per 10 million mapped reads.
- rna_norm_tcpo_male_rep1
- TCPOBOP-male reporter-RNA reads normalized per 10 million mapped reads, replicate 1.
- rna_norm_tcpo_male_rep2
- TCPOBOP-male reporter-RNA reads normalized per 10 million mapped reads, replicate 2.
- rna_norm_tcpo_male_rep3
- TCPOBOP-male reporter-RNA reads normalized per 10 million mapped reads, replicate 3.
- rna_norm_tcpo_male_rep4
- TCPOBOP-male reporter-RNA reads normalized per 10 million mapped reads, replicate 4.
- rna_norm_vehicle_male_rep1
- Vehicle-male reporter-RNA reads normalized per 10 million mapped reads, replicate 1.
- rna_norm_vehicle_male_rep2
- Vehicle-male reporter-RNA reads normalized per 10 million mapped reads, replicate 2.
- rna_norm_vehicle_male_rep3
- Vehicle-male reporter-RNA reads normalized per 10 million mapped reads, replicate 3.
- rna_norm_vehicle_male_rep4
- Vehicle-male reporter-RNA reads normalized per 10 million mapped reads, replicate 4.
- rna_norm_vehicle_female_rep1
- Vehicle-female reporter-RNA reads normalized per 10 million mapped reads, replicate 1.
- rna_norm_vehicle_female_rep2
- Vehicle-female reporter-RNA reads normalized per 10 million mapped reads, replicate 2.
- rna_norm_vehicle_female_rep3
- Vehicle-female reporter-RNA reads normalized per 10 million mapped reads, replicate 3.
- n_rna_tcpo_male_ge20
- Number of TCPOBOP-male RNA replicates at or above the 20-read qualification threshold.
- mean_norm_rna_tcpo_male_qualified
- Mean normalized TCPOBOP-male RNA reads among qualified replicates.
- n_rna_vehicle_male_ge20
- Number of vehicle-male RNA replicates at or above the 20-read qualification threshold.
- mean_norm_rna_vehicle_male_qualified
- Mean normalized vehicle-male RNA reads among qualified replicates.
- n_rna_vehicle_female_ge20
- Number of vehicle-female RNA replicates at or above the 20-read qualification threshold.
- mean_norm_rna_vehicle_female_qualified
- Mean normalized vehicle-female RNA reads among qualified replicates.
- activity_class_any_condition
- Cleaned source class: Active, Stringently inactive, or Low/inconsistent.
- conditional_activity_class
- Source annotation for condition-specific activity patterns.
- activity_class_tcpo_male
- Source TCPOBOP-male activity classification (Active, Inactive or NA).
- activity_class_vehicle_male
- Source vehicle-male activity classification (Active, Inactive or NA).
- activity_class_vehicle_female
- Source vehicle-female activity classification (Active, Inactive or NA).
- stringently_inactive_all_conditions
- Indicator that normalized RNA was below 20 in every one of the 11 livers (1=yes, 0=no).
- robust_active_all_conditions
- Indicator that the enhancer met the active threshold in all three biological conditions (1=yes, 0=no).
- mean_enhancer_activity_tcpo_male
- Source mean DNA-normalized enhancer activity for qualified TCPOBOP-male replicates.
- sd_enhancer_activity_tcpo_male
- Source standard deviation of TCPOBOP-male enhancer activity.
- cv_enhancer_activity_tcpo_male
- Source coefficient of variation of TCPOBOP-male enhancer activity.
- mean_enhancer_activity_vehicle_male
- Source mean DNA-normalized enhancer activity for qualified vehicle-male replicates.
- sd_enhancer_activity_vehicle_male
- Source standard deviation of vehicle-male enhancer activity.
- cv_enhancer_activity_vehicle_male
- Source coefficient of variation of vehicle-male enhancer activity.
- mean_enhancer_activity_vehicle_female
- Source mean DNA-normalized enhancer activity for qualified vehicle-female replicates.
- sd_enhancer_activity_vehicle_female
- Source standard deviation of vehicle-female enhancer activity.
- cv_enhancer_activity_vehicle_female
- Source coefficient of variation of vehicle-female enhancer activity.
- tcpo_vs_vehicle_male_log2fc
- Derived log2 fold change of mean TCPOBOP-male enhancer activity divided by vehicle-male activity; NA when either mean is nonpositive or missing.
- female_vs_vehicle_male_log2fc
- Derived log2 fold change of mean vehicle-female enhancer activity divided by vehicle-male activity; NA when either mean is nonpositive or missing.
- tcpo_vs_vehicle_male_pvalue
- Source p-value for TCPOBOP-male versus vehicle-male enhancer activity.
- tcpo_vs_vehicle_male_fdr
- Source FDR-adjusted p-value for TCPOBOP-male versus vehicle-male activity.
- female_vs_vehicle_male_pvalue
- Source p-value for vehicle-female versus vehicle-male enhancer activity.
- female_vs_vehicle_male_fdr
- Source FDR-adjusted p-value for vehicle-female versus vehicle-male activity.
- sex_dhs_id
- Identifier of overlapping published sex-associated mouse liver DHS, when present.
- tcpo_dhs_id
- Identifier of overlapping published TCPOBOP-associated mouse liver DHS, when present.
- dhs_overlap_count
- Number of published DHS sets overlapping the region (0, 1 or 2).
- dhs_present
- Indicator that the region overlaps at least one published mouse liver DHS set (1=yes, 0=no).
- nearest_gene
- Nearest RefSeq or lncRNA gene assigned within the same TAD by the source analysis.
- gene_chromosome
- Chromosome of the assigned gene.
- gene_tss_start_mm9
- Assigned gene TSS start coordinate in mm9.
- gene_tss_end_mm9
- Assigned gene TSS end coordinate in mm9.
- distance_to_tss_bp
- Shortest distance from either end of the reporter region to the assigned gene TSS, in base pairs.
- tad_region
- Source topologically associating domain containing the region and assigned gene.
- enhanceratlas_chromosome
- Chromosome of overlapping EnhancerAtlas2.0 mouse-liver enhancer, when present.
- enhanceratlas_start
- Start coordinate of overlapping EnhancerAtlas2.0 enhancer, when present.
- enhanceratlas_end
- End coordinate of overlapping EnhancerAtlas2.0 enhancer, when present.
Quality control
The source pipeline aligned paired-end reads to mm9 with Bowtie2, retained uniquely aligned reads, called and merged MACS2 peaks across plasmid, DNA and RNA libraries, removed peaks represented only in RNA or overlapping ENCODE blacklisted regions, and reduced 117,122 merged peaks to 50,332 autosomal regions with more than 40 normalized plasmid reads per 10 million mapped reads. Reporter-RNA values below 20 normalized reads per 10 million were excluded from condition means; active enhancers required the threshold in at least 3 of 4 male, 3 of 4 TCPOBOP-male, or 3 of 3 female livers. Stringently inactive regions were below the threshold in all 11 livers. The packaged table retains all 50,332 source-qualified rows, including active, stringently inactive and low/inconsistent regions.
Curation notes
The global library was assembled from pooled DNase-I-released fragments and analyzed as an in vivo episomal STARR-seq assay. The source workbook has 50,332 data rows despite occasional narrative references to 50,322; this package follows the exact 50,332 qualified rows and preserves both mm9 coordinates and source mm10 liftover. The 117,122-peak starting set and the active/inactive definitions are documented in the raw supplementary workbook and GEO metadata.