Experiment / E80NDMWPMAAV-MPRA / in vivo MPRA

AAV parallel reporter assay of interneuron CREs in SBACs and horizontal cells (Library 3)

Cis-regulatory landscapes of four cell types of the retina

The third library combined five photoreceptor reference fragments with 365 candidate elements selected for hypomethylation in horizontal cells and/or starburst amacrine cells. The library was measured in three biological replicates each of FACS-isolated SBACs and horizontal cells, with three whole-retina RNA readouts retained as a comparator.

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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.

Organism: Mouse
Taxonomy ID: NCBITaxon:10090
Biosample: Not reported / not applicable
Reference genome: mm9
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

AAV serotype 8 libraries were delivered by subretinal injection to adult ChAT-Cre × Ai9 mice for starburst amacrine cells and Gja10-Cre × Ai9 mice for horizontal cells (P50–150). Constructs used a 31-bp minimal promoter, CpG-free eGFP, randomized 15-bp barcode, and polyA signal. Three weeks after injection, sorted SBAC or horizontal-cell RNA and whole-retina RNA were quantified relative to AAV-input barcode abundance; the deposited table contains SBAC1–3, HC1–3, and whole1–3 activity summaries.

Processed data

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Visible columns (32 of 32)

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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 · 32 definitions

element_id: Author-provided element/orientation identifier, with a coordinate-derived identifier used only if the source ID is missing; duplicated source identifiers receive a __<occurrence> suffix to keep packaged rows uniquely addressable.
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.
sbac_activity_rep1_ratio: Published SBAC barcode RNA abundance divided by AAV-input abundance for biological replicate 1.
sbac_activity_rep2_ratio: Published SBAC barcode RNA abundance divided by AAV-input abundance for biological replicate 2.
sbac_activity_rep3_ratio: Published SBAC barcode RNA abundance divided by AAV-input abundance for biological replicate 3.
sbac_mean_activity_ratio: Arithmetic mean of the available published SBAC activity ratios.
sbac_log2_mean_activity_ratio: Base-2 logarithm of sbac_mean_activity_ratio, derived for convenient effect-size interpretation.
hc_activity_rep1_ratio: Published horizontal-cell barcode RNA abundance divided by AAV-input abundance for biological replicate 1; blank if the source reports NA.
hc_activity_rep2_ratio: Published horizontal-cell barcode RNA abundance divided by AAV-input abundance for biological replicate 2; blank if the source reports NA.
hc_activity_rep3_ratio: Published horizontal-cell barcode RNA abundance divided by AAV-input abundance for biological replicate 3; blank if the source reports NA.
hc_mean_activity_ratio: Arithmetic mean of the available published horizontal-cell activity ratios.
hc_log2_mean_activity_ratio: Base-2 logarithm of hc_mean_activity_ratio, derived for convenient effect-size interpretation.
whole_retina_activity_rep1_ratio: Published whole-retina barcode RNA abundance divided by AAV-input abundance for biological replicate 1.
whole_retina_activity_rep2_ratio: Published whole-retina barcode RNA abundance divided by AAV-input abundance for biological replicate 2.
whole_retina_activity_rep3_ratio: Published whole-retina barcode RNA abundance divided by AAV-input abundance for biological replicate 3.
whole_retina_mean_activity_ratio: Arithmetic mean of the available published whole-retina activity ratios.
whole_retina_log2_mean_activity_ratio: Base-2 logarithm of whole_retina_mean_activity_ratio, derived for convenient effect-size interpretation.
expression_assay_specificity: Published element-level specificity class, such as HCSpec 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_sbac_activity_replicates: Number of numeric SBAC activity replicate values available for the row.
n_hc_activity_replicates: Number of numeric horizontal-cell activity replicate values available for the row.
n_whole_retina_activity_replicates: Number of numeric whole-retina 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 table was additionally required to have n_barcodes ≥3 and at least two numeric activity replicates for each of SBAC, horizontal-cell, and whole-retina readouts; all 198 source rows passed these filters.

Curation notes

The source table combines SBAC, horizontal-cell, and whole-retina readouts, so biosample_id is null. Component Cell Ontology identifiers are CL:0004232 for starburst amacrine cell and CL:0000745 for retina horizontal cell; whole retina is a tissue-level comparator rather than a cell biosample. Activity columns are linear RNA/AAV-input ratios as supplied by the study; log2 means are derived here. One source row has ID=NA; its packaged element_id is coordinate-derived and source_element_id preserves the original NA. Four source identifiers occur twice in the deposited result table; those rows are retained and disambiguated in element_id with __1/__2 suffixes while source_element_id remains unchanged.

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