AAV parallel reporter assay of candidate rod photoreceptor CREs (Library 1)
Cis-regulatory landscapes of four cell types of the retinaThe pilot library tested 384 short candidate cis-regulatory fragments, including highly methylated negative controls, in adult mouse rod photoreceptors in vivo. Three biological replicates of FACS-isolated rods were profiled by barcode RNA sequencing and normalized to barcode abundance in the input AAV pool.
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 B2-Cre × Ai9 mice (P50–150). Candidate genomic fragments, generally shorter than 600 bp and capped at approximately 700 bp, were cloned upstream of a 31-bp minimal promoter and CpG-free eGFP followed by a randomized 15-bp barcode and polyA signal. Three weeks after injection, rods were FACS-isolated; barcode counts were library-size normalized and the RNA/AAV-input abundance ratio was summarized as the median activity across barcodes per element. Barcode-to-element assignment required a unique assignment or >90% support for one CRE.
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 · 19 definitions
- element_id
- Author-provided element 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.
- 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.
- 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_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 discarded barcode assignments linked to multiple CREs, barcode species with insufficient AAV-input coverage (2–16 reads depending on sequencing depth), and elements not covered 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 rod activity replicates; all 201 source rows passed these filters.
Curation notes
The raw GEO result is an author-processed element-level PRA summary rather than per-barcode counts; the barcode map is retained separately in raw_data. Activity columns are linear RNA/AAV-input ratios as supplied by the study; log2 means are derived here. No positive or negative control rows were removed because they remain useful as assay reference elements and pass the published coverage criteria. The rod biosample is the retinal rod cell term CL:0000604.