AAV parallel reporter assay of TF-motif mutants in rod photoreceptors (Library 4)
Cis-regulatory landscapes of four cell types of the retinaThe motif-mutant library tested wild-type and randomized transcription-factor motif versions of two active photoreceptor CREs, Faim-Intra (e107) and Intergenic3 (e483), in adult mouse rods. Four rod biological replicates were measured by barcode RNA sequencing relative to AAV-input barcode abundance, enabling direct mutant-versus-wild-type activity comparisons.
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
Synthetic motif mutants were cloned into the same AAV reporter configuration used for the other libraries and assayed in rod-labeled B2-Cre × Ai9 mice. Motif matches were identified by known transcription-factor position weight matrices at score >9, and all instances for a factor within a fragment were randomized together. The library contains wild-type and MEIS1, ID4, Sp1, Nr1h3, CRX, En2, or NRL motif-mutant constructs across two endogenous photoreceptor enhancers; four rod replicate activity ratios are provided. The package derives mean activities and mutant/wild-type ratios within each enhancer; these derived comparisons are not fitted statistical tests from the paper.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (16 of 16)
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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 · 16 definitions
- enhancer_id
- Source enhancer identifier, e107 or e483.
- enhancer_name
- Enhancer name mapped from the paper's figure and sequence annotations: Faim-Intra for e107 or Intergenic3 for e483.
- mutation_id
- Source construct label, such as wt, MEIS1mut, or NRLmut.
- motif_target
- Transcription-factor motif targeted by the construct; blank for wild type.
- construct_type
- wild_type for the unmodified construct or motif_mutant for a motif-randomized 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_activity_rep4_ratio
- Published rod barcode RNA abundance divided by AAV-input abundance for biological replicate 4.
- rod_mean_activity_ratio
- Arithmetic mean of the four published rod activity ratios.
- rod_log2_mean_activity_ratio
- Base-2 logarithm of rod_mean_activity_ratio, derived for convenient effect-size interpretation.
- mutant_vs_wt_activity_ratio
- For a motif mutant, its rod_mean_activity_ratio divided by the wild-type mean for the same enhancer; blank for wild type.
- mutant_vs_wt_log2_activity
- Base-2 logarithm of mutant_vs_wt_activity_ratio; positive values indicate higher mutant activity than wild type.
- n_barcodes
- Number of barcodes assigned to the construct and retained by the authors.
- 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 applied the same barcode-assignment, AAV-input coverage, and element-level barcode coverage criteria as for the other PRA libraries. The packaged table additionally required n_barcodes ≥3 and at least two numeric rod activity replicates; all 9 source rows passed these filters.
Curation notes
The source table contains 9 constructs: wild type and four motif mutants for e107/Faim-Intra, and wild type and four motif mutants for e483/Intergenic3. The activity columns are linear RNA/AAV-input ratios as supplied by the study; log2 means and mutant-versus-wild-type effects are derived here. No p-values were imputed because the deposited Lib4 result table does not provide fitted significance statistics. The rod biosample is the retinal rod cell term CL:0000604.