AAV parallel reporter assay of photoreceptor CREs in cones and rods (Library 2)
Cis-regulatory landscapes of four cell types of the retinaThe cone/rod library tested candidate regulatory fragments selected from differential methylation patterns in adult mouse cones and rods. The same library was assayed in three cone and three rod biological replicates, and the table retains the published activity ratios and element-level specificity calls for both cell types.
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
Basal / Untreated
AAV serotype 8 libraries were delivered by subretinal injection to adult cone-labeled D4-Cre × Ai9 mice and rod-labeled B2-Cre × Ai9 mice (P50–150). Library 2 contained fragments selected for cone/rod differential methylation, similarly methylated controls, unmethylated controls, and validated reference elements; constructs used a 31-bp minimal promoter, CpG-free eGFP, randomized 15-bp barcode, and polyA signal. Three weeks after injection, FACS-isolated cones or rods were profiled by barcode RNA sequencing and normalized to AAV-input barcode abundance.
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 · 27 definitions
- element_id
- Author-provided element/orientation identifier, with a coordinate-derived identifier used only if the source ID is missing.
- source_element_id
- Element identifier exactly as supplied in the GEO/supplemental result table.
- chromosome
- Mouse mm9 chromosome with the chr prefix.
- start_mm9
- Source interval start coordinate on mm9; retained in the source coordinate convention.
- end_mm9
- Source interval end coordinate on mm9; retained in the source coordinate convention.
- fragment_length_bp
- Interval length calculated as end_mm9 minus start_mm9.
- strand
- Orientation of the tested fragment in the reporter construct.
- cone_activity_rep1_ratio
- Published cone barcode RNA abundance divided by AAV-input abundance for biological replicate 1.
- cone_activity_rep2_ratio
- Published cone barcode RNA abundance divided by AAV-input abundance for biological replicate 2.
- cone_activity_rep3_ratio
- Published cone barcode RNA abundance divided by AAV-input abundance for biological replicate 3.
- cone_mean_activity_ratio
- Arithmetic mean of the available published cone activity ratios.
- cone_log2_mean_activity_ratio
- Base-2 logarithm of cone_mean_activity_ratio, derived for convenient effect-size interpretation.
- rod_activity_rep1_ratio
- Published rod barcode RNA abundance divided by AAV-input abundance for biological replicate 1.
- rod_activity_rep2_ratio
- Published rod barcode RNA abundance divided by AAV-input abundance for biological replicate 2.
- rod_activity_rep3_ratio
- Published rod barcode RNA abundance divided by AAV-input abundance for biological replicate 3.
- rod_mean_activity_ratio
- Arithmetic mean of the available published rod activity ratios.
- rod_log2_mean_activity_ratio
- Base-2 logarithm of rod_mean_activity_ratio, derived for convenient effect-size interpretation.
- active
- Published TRUE/FALSE indicator for whether the element was called active in the authors' analysis.
- expression_assay_specificity
- Published element-level specificity class, such as coneSpec, rodSpec, shared, or inactive.
- n_barcodes
- Number of barcodes assigned to the element and retained by the authors.
- methylation_rods
- Mean endogenous DNA methylation fraction for the source region in rods, from the supplemental annotation table.
- methylation_cones
- Mean endogenous DNA methylation fraction for the source region in cones, from the supplemental annotation table.
- methylation_hc
- Mean endogenous DNA methylation fraction for the source region in horizontal cells, from the supplemental annotation table.
- methylation_sbac
- Mean endogenous DNA methylation fraction for the source region in starburst amacrine cells, from the supplemental annotation table.
- n_cone_activity_replicates
- Number of numeric cone activity replicate values available for the row.
- n_rod_activity_replicates
- Number of numeric rod activity replicate values available for the row.
- qc_pass
- TRUE for rows retained after the package QC filter.
Quality control
The authors required unambiguous barcode-to-CRE assignment, sufficient AAV-input barcode coverage, and element coverage by at least three barcodes in at least two of three biological replicates. The packaged GEO result table was additionally required to have n_barcodes ≥3 and at least two numeric activity replicates in both the cone and rod readouts; all 129 source rows passed these filters.
Curation notes
The source table combines two labeled biosamples, so biosample_id is null rather than assigning a misleading single term. Component Cell Ontology identifiers are CL:0000573 for retinal cone cell and CL:0000604 for retinal rod cell. Activity columns are linear RNA/AAV-input ratios as supplied by the study; log2 means are derived here. Rows represent the source fragment orientation (for example, 627+ and 627−) and are not collapsed across strand.