Hsp68 promoter CRX CRE MPRA in mouse retinal explants
Pathogenic variants in CRX have distinct cis-regulatory effects on enhancers and silencers in photoreceptorsHsp68-promoter episomal MPRA testing 3,747 synthetic 164-bp library members (1,723 CRX-bound CREs, CRX motif mutants, and controls) in mouse retinal explants across WT, R90W, E168d2, and Crx-null genotypes. Each member is summarized separately for six genotype conditions using barcode RNA/DNA activity.
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
No exogenous treatment; Crx genotype panel
Hsp68 promoter library: each 164-bp CRE or control sequence was cloned upstream of a minimal promoter driving DsRed, with a unique barcode in the DsRed 3-prime UTR. Plasmids were electroporated into postnatal day 8 mouse retina explants; reporter RNA was normalized to input plasmid DNA. The study used three biological electroporations of three retinas each per genotype and promoter library, with four barcodes per library member; the GEO archive includes the corresponding barcode-count inputs.
Processed data
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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 · 79 definitions
- promoter_library
- MPRA library/promoter backbone: rho (Rho promoter) or hsp68 (Hsp68 promoter).
- library_id
- Unique identifier for one tested 164-bp library member.
- variant_type
- Library-member class (basal, scrambled control, wild-type CRE, or CRX motif mutant).
- chip_peak_id
- CRX ChIP-seq peak identifier for genomic CRE members; blank for non-genomic controls.
- chrom
- mm9 chromosome for the source CRX-bound peak; blank for controls.
- start_mm9
- 0-based mm9 start coordinate of the source CRX-bound peak.
- stop_mm9
- mm9 end coordinate of the source CRX-bound peak.
- epigenome_group
- Chromatin/epigenome group assigned to the source CRX peak.
- atac_crx_dependent
- Whether peak accessibility was classified as CRX-dependent or independent.
- num_crx_sites
- Number of CRX motif sites in the source peak.
- strand
- Strand annotation for the source CRX peak.
- CRE_sequence
- 164-bp DNA sequence cloned into the indicated MPRA library.
- predicted_occupancy_CRX
- Predicted CRX binding occupancy for the library sequence.
- predicted_occupancy_GFI1
- Predicted GFI1 binding occupancy for the library sequence.
- predicted_occupancy_MAZ
- Predicted MAZ binding occupancy for the library sequence.
- predicted_occupancy_MEF2D
- Predicted MEF2D binding occupancy for the library sequence.
- predicted_occupancy_NDF1
- Predicted NDF1 binding occupancy for the library sequence.
- predicted_occupancy_NRL
- Predicted NRL binding occupancy for the library sequence.
- predicted_occupancy_RORB
- Predicted RORB binding occupancy for the library sequence.
- predicted_occupancy_RAX
- Predicted RAX binding occupancy for the library sequence.
- total_occupancy
- Sum of predicted transcription-factor occupancies.
- diversity
- Number of transcription-factor models contributing predicted occupancy.
- info_content
- Sequence information-content score from the authors library annotation.
- nearby_gene_names_mm39
- Semicolon-separated nearby gene names from the authors GRCm39/mm39 TSS annotation.
- nearest_gene_name_mm39
- Nearest annotated gene by absolute TSS-to-peak-midpoint distance in the authors mm39 annotation.
- nearest_gene_tss_distance_mm39
- Absolute distance in bp from the mm39 peak midpoint to the nearest annotated gene TSS.
- activity_mean_WT
- Mean RNA/DNA reporter activity for the WT genotype, from the authors processed S1 table.
- activity_std_WT
- Standard deviation of barcode-level RNA/DNA activity for the WT genotype.
- n_observations_WT
- Number of retained barcode observations contributing to the WT library-member summary.
- activity_mu_WT
- Lognormal activity-distribution mu parameter for the WT genotype; blank when undefined for exact-zero activity.
- activity_sigma_WT
- Lognormal activity-distribution sigma parameter for the WT genotype; blank when undefined for exact-zero activity.
- pvalue_vs_basal_WT
- Authors Welch-test p-value comparing the WT construct with basal controls.
- qvalue_vs_basal_WT
- Authors multiple-testing-adjusted value for the basal-control comparison in the WT genotype; values above 1 were capped at 1.0.
- activity_class_WT
- Authors activity class for the WT construct (strong/weak enhancer, silencer, or inactive).
- activity_mean_R90W_het
- Mean RNA/DNA reporter activity for the R90W/+ genotype, from the authors processed S1 table.
- activity_std_R90W_het
- Standard deviation of barcode-level RNA/DNA activity for the R90W/+ genotype.
- n_observations_R90W_het
- Number of retained barcode observations contributing to the R90W/+ library-member summary.
- activity_mu_R90W_het
- Lognormal activity-distribution mu parameter for the R90W/+ genotype; blank when undefined for exact-zero activity.
- activity_sigma_R90W_het
- Lognormal activity-distribution sigma parameter for the R90W/+ genotype; blank when undefined for exact-zero activity.
- pvalue_vs_basal_R90W_het
- Authors Welch-test p-value comparing the R90W/+ construct with basal controls.
- qvalue_vs_basal_R90W_het
- Authors multiple-testing-adjusted value for the basal-control comparison in the R90W/+ genotype; values above 1 were capped at 1.0.
- activity_class_R90W_het
- Authors activity class for the R90W/+ construct (strong/weak enhancer, silencer, or inactive).
- activity_mean_E168d2_het
- Mean RNA/DNA reporter activity for the E168d2/+ genotype, from the authors processed S1 table.
- activity_std_E168d2_het
- Standard deviation of barcode-level RNA/DNA activity for the E168d2/+ genotype.
- n_observations_E168d2_het
- Number of retained barcode observations contributing to the E168d2/+ library-member summary.
- activity_mu_E168d2_het
- Lognormal activity-distribution mu parameter for the E168d2/+ genotype; blank when undefined for exact-zero activity.
- activity_sigma_E168d2_het
- Lognormal activity-distribution sigma parameter for the E168d2/+ genotype; blank when undefined for exact-zero activity.
- pvalue_vs_basal_E168d2_het
- Authors Welch-test p-value comparing the E168d2/+ construct with basal controls.
- qvalue_vs_basal_E168d2_het
- Authors multiple-testing-adjusted value for the basal-control comparison in the E168d2/+ genotype; values above 1 were capped at 1.0.
- activity_class_E168d2_het
- Authors activity class for the E168d2/+ construct (strong/weak enhancer, silencer, or inactive).
- activity_mean_R90W_hom
- Mean RNA/DNA reporter activity for the R90W/R90W genotype, from the authors processed S1 table.
- activity_std_R90W_hom
- Standard deviation of barcode-level RNA/DNA activity for the R90W/R90W genotype.
- n_observations_R90W_hom
- Number of retained barcode observations contributing to the R90W/R90W library-member summary.
- activity_mu_R90W_hom
- Lognormal activity-distribution mu parameter for the R90W/R90W genotype; blank when undefined for exact-zero activity.
- activity_sigma_R90W_hom
- Lognormal activity-distribution sigma parameter for the R90W/R90W genotype; blank when undefined for exact-zero activity.
- pvalue_vs_basal_R90W_hom
- Authors Welch-test p-value comparing the R90W/R90W construct with basal controls.
- qvalue_vs_basal_R90W_hom
- Authors multiple-testing-adjusted value for the basal-control comparison in the R90W/R90W genotype; values above 1 were capped at 1.0.
- activity_class_R90W_hom
- Authors activity class for the R90W/R90W construct (strong/weak enhancer, silencer, or inactive).
- activity_mean_E168d2_hom
- Mean RNA/DNA reporter activity for the E168d2/E168d2 genotype, from the authors processed S1 table.
- activity_std_E168d2_hom
- Standard deviation of barcode-level RNA/DNA activity for the E168d2/E168d2 genotype.
- n_observations_E168d2_hom
- Number of retained barcode observations contributing to the E168d2/E168d2 library-member summary.
- activity_mu_E168d2_hom
- Lognormal activity-distribution mu parameter for the E168d2/E168d2 genotype; blank when undefined for exact-zero activity.
- activity_sigma_E168d2_hom
- Lognormal activity-distribution sigma parameter for the E168d2/E168d2 genotype; blank when undefined for exact-zero activity.
- pvalue_vs_basal_E168d2_hom
- Authors Welch-test p-value comparing the E168d2/E168d2 construct with basal controls.
- qvalue_vs_basal_E168d2_hom
- Authors multiple-testing-adjusted value for the basal-control comparison in the E168d2/E168d2 genotype; values above 1 were capped at 1.0.
- activity_class_E168d2_hom
- Authors activity class for the E168d2/E168d2 construct (strong/weak enhancer, silencer, or inactive).
- activity_mean_CrxKO
- Mean RNA/DNA reporter activity for the Crx-/- genotype, from the authors processed S1 table.
- activity_std_CrxKO
- Standard deviation of barcode-level RNA/DNA activity for the Crx-/- genotype.
- n_observations_CrxKO
- Number of retained barcode observations contributing to the Crx-/- library-member summary.
- activity_mu_CrxKO
- Lognormal activity-distribution mu parameter for the Crx-/- genotype; blank when undefined for exact-zero activity.
- activity_sigma_CrxKO
- Lognormal activity-distribution sigma parameter for the Crx-/- genotype; blank when undefined for exact-zero activity.
- pvalue_vs_basal_CrxKO
- Authors Welch-test p-value comparing the Crx-/- construct with basal controls.
- qvalue_vs_basal_CrxKO
- Authors multiple-testing-adjusted value for the basal-control comparison in the Crx-/- genotype; values above 1 were capped at 1.0.
- activity_class_CrxKO
- Authors activity class for the Crx-/- construct (strong/weak enhancer, silencer, or inactive).
- log2_activity_change_R90W_het_vs_WT
- Log2 change in mean RNA/DNA activity versus WT, using a 1e-3 pseudocount (R90W_het versus WT).
- log2_activity_change_E168d2_het_vs_WT
- Log2 change in mean RNA/DNA activity versus WT, using a 1e-3 pseudocount (E168d2_het versus WT).
- log2_activity_change_R90W_hom_vs_WT
- Log2 change in mean RNA/DNA activity versus WT, using a 1e-3 pseudocount (R90W_hom versus WT).
- log2_activity_change_E168d2_hom_vs_WT
- Log2 change in mean RNA/DNA activity versus WT, using a 1e-3 pseudocount (E168d2_hom versus WT).
- log2_activity_change_CrxKO_vs_WT
- Log2 change in mean RNA/DNA activity versus WT, using a 1e-3 pseudocount (CrxKO versus WT).
Quality control
Used the authors processed Supplemental Table S1 summaries after their barcode-level count aggregation, RPM normalization, plasmid-DNA normalization, barcode-map join, and Welch tests against basal controls. Package QC retained a member only when all six genotype summaries had finite nonnegative activity mean and standard deviation, integer n_observations >= 3, finite nonnegative p-value/q-value, and a nonempty activity class; 3747 of 3747 library members passed, yielding 22482 of 22482 member-by-genotype summaries. Source activity_mu/activity_sigma values that were non-finite for exact-zero activity were emitted as blank; q-values above 1.0 were capped at 1.0.
Curation notes
This is the Hsp68 promoter arm of the study; the parallel Hsp68/Rho arm is stored as a separate experiment and both are represented in Supplemental Table S1 and GEO GSE230090. Coordinates and source peak annotations are mm9; nearby-gene columns are the authors GRCm39/mm39 TSS annotations and are explicitly suffixed. The library includes CRX motif mutants and controls rather than natural human allelic variants, so it is classified as Region-focused. Activity statistics and classes are preserved from the authors table, with only the documented finite-value/Q-value serialization cleanup applied.