TN05 RFX motif mutagenesis AAV MPRA in primary mouse cortical neurons
High-throughput functional comparison of promoter and enhancer activitiesMouse genomic tiles carrying targeted RFX/CREB motif mutations and matched control designs were tested in enhancer and promoter MPRA reporters. The library was assayed in unstimulated and KCl-depolarized neurons with and without an RFX dominant-negative perturbation, using three biological replicates per condition.
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
Unstimulated or 55 mM KCl depolarization for 12 h, with or without RFX dominant-negative (DN)
Ex vivo primary E16 CD-1 mouse cortical neurons were transduced with AAV1/AAV2 reporter libraries. Targeted motif substitutions were made in mouse genomic tiles, and enhancer/promoter reporter activity was read from DNA-normalized cDNA barcode counts under basal, KCl, RFX-DN basal, and RFX-DN KCl conditions.
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 · 100 definitions
- element_id
- Stable identifier generated from the deposited construct or tile label.
- source_label
- Original sequence/construct label from the GEO tally supplement.
- source_class
- Library-defined class parsed from the original label.
- is_negative_control
- Whether the element was used as the negative-control class for activity normalization.
- barcode_count
- Number of unique deposited barcode records retained for this element after mapping cleanup.
- qc_min_read_count
- Minimum summed DNA or RNA read count across all samples represented in this table; all output rows meet the >=20-read QC threshold.
- sequence
- Representative mapped sequence from the deposited key/tally; for TN03/TN05 it is the highest-support observed tile sequence.
- sequence_length
- Length in nucleotides of the representative mapped sequence.
- species
- Species encoded by the deposited label (mouse or human ortholog).
- reference_assembly
- Reference genome assembly associated with the mapped sequence.
- chromosome
- Chromosome parsed from the deposited genomic label.
- position
- Genomic coordinate parsed from the deposited label; this is the labeled tile/locus coordinate, not a complete interval.
- locus_id
- Study-defined numeric locus or construct coordinate identifier parsed from the label.
- variant_design
- RFX/CREB motif-mutagenesis annotation encoded after the $ delimiter in the TN05 label.
- motif_annotations
- Motif calls or motif mutation annotations encoded in the original label.
- source_data
- GEO series and library tally source for the row.
- dna_enhancer_count
- Summed DNA/plasmid barcode count for the enhancer reporter library.
- dna_promoter_count
- Summed DNA/plasmid barcode count for the promoter reporter library.
- enhancer_unstimulated_rep1_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- enhancer_unstimulated_rep2_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- enhancer_unstimulated_rep3_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- promoter_unstimulated_rep1_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- promoter_unstimulated_rep2_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- promoter_unstimulated_rep3_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- enhancer_kcl_rep1_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- enhancer_kcl_rep2_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- enhancer_kcl_rep3_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- promoter_kcl_rep1_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- promoter_kcl_rep2_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- promoter_kcl_rep3_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- enhancer_unstimulated_dn_rep1_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- enhancer_unstimulated_dn_rep2_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- enhancer_unstimulated_dn_rep3_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- promoter_unstimulated_dn_rep1_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- promoter_unstimulated_dn_rep2_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- promoter_unstimulated_dn_rep3_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- enhancer_kcl_dn_rep1_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- enhancer_kcl_dn_rep2_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- enhancer_kcl_dn_rep3_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- promoter_kcl_dn_rep1_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- promoter_kcl_dn_rep2_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- promoter_kcl_dn_rep3_rna_count
- Raw cDNA/RNA barcode count for the indicated reporter assay, condition, and biological replicate.
- enhancer_unstimulated_activity_fold
- Mean per-replicate RNA/DNA ratio divided by the mean ratio of the library negative controls; activity fold relative to negative controls.
- enhancer_unstimulated_log2_activity
- Log2-transformed normalized MPRA activity fold relative to negative controls.
- enhancer_unstimulated_log2_sd
- Sample standard deviation across replicate-level log2 normalized activity values.
- enhancer_unstimulated_replicate_n
- Number of biological replicates contributing to the normalized activity value.
- enhancer_unstimulated_pvalue
- Empirical p-value: fraction of QC-passing negative-control elements with normalized activity at least as high as this element.
- enhancer_unstimulated_fdr
- Benjamini–Hochberg FDR-adjusted empirical p-value across QC-passing elements for this assay and condition.
- promoter_unstimulated_activity_fold
- Mean per-replicate RNA/DNA ratio divided by the mean ratio of the library negative controls; activity fold relative to negative controls.
- promoter_unstimulated_log2_activity
- Log2-transformed normalized MPRA activity fold relative to negative controls.
- promoter_unstimulated_log2_sd
- Sample standard deviation across replicate-level log2 normalized activity values.
- promoter_unstimulated_replicate_n
- Number of biological replicates contributing to the normalized activity value.
- promoter_unstimulated_pvalue
- Empirical p-value: fraction of QC-passing negative-control elements with normalized activity at least as high as this element.
- promoter_unstimulated_fdr
- Benjamini–Hochberg FDR-adjusted empirical p-value across QC-passing elements for this assay and condition.
- enhancer_kcl_activity_fold
- Mean per-replicate RNA/DNA ratio divided by the mean ratio of the library negative controls; activity fold relative to negative controls.
- enhancer_kcl_log2_activity
- Log2-transformed normalized MPRA activity fold relative to negative controls.
- enhancer_kcl_log2_sd
- Sample standard deviation across replicate-level log2 normalized activity values.
- enhancer_kcl_replicate_n
- Number of biological replicates contributing to the normalized activity value.
- enhancer_kcl_pvalue
- Empirical p-value: fraction of QC-passing negative-control elements with normalized activity at least as high as this element.
- enhancer_kcl_fdr
- Benjamini–Hochberg FDR-adjusted empirical p-value across QC-passing elements for this assay and condition.
- promoter_kcl_activity_fold
- Mean per-replicate RNA/DNA ratio divided by the mean ratio of the library negative controls; activity fold relative to negative controls.
- promoter_kcl_log2_activity
- Log2-transformed normalized MPRA activity fold relative to negative controls.
- promoter_kcl_log2_sd
- Sample standard deviation across replicate-level log2 normalized activity values.
- promoter_kcl_replicate_n
- Number of biological replicates contributing to the normalized activity value.
- promoter_kcl_pvalue
- Empirical p-value: fraction of QC-passing negative-control elements with normalized activity at least as high as this element.
- promoter_kcl_fdr
- Benjamini–Hochberg FDR-adjusted empirical p-value across QC-passing elements for this assay and condition.
- enhancer_unstimulated_dn_activity_fold
- Mean per-replicate RNA/DNA ratio divided by the mean ratio of the library negative controls; activity fold relative to negative controls.
- enhancer_unstimulated_dn_log2_activity
- Log2-transformed normalized MPRA activity fold relative to negative controls.
- enhancer_unstimulated_dn_log2_sd
- Sample standard deviation across replicate-level log2 normalized activity values.
- enhancer_unstimulated_dn_replicate_n
- Number of biological replicates contributing to the normalized activity value.
- enhancer_unstimulated_dn_pvalue
- Empirical p-value: fraction of QC-passing negative-control elements with normalized activity at least as high as this element.
- enhancer_unstimulated_dn_fdr
- Benjamini–Hochberg FDR-adjusted empirical p-value across QC-passing elements for this assay and condition.
- promoter_unstimulated_dn_activity_fold
- Mean per-replicate RNA/DNA ratio divided by the mean ratio of the library negative controls; activity fold relative to negative controls.
- promoter_unstimulated_dn_log2_activity
- Log2-transformed normalized MPRA activity fold relative to negative controls.
- promoter_unstimulated_dn_log2_sd
- Sample standard deviation across replicate-level log2 normalized activity values.
- promoter_unstimulated_dn_replicate_n
- Number of biological replicates contributing to the normalized activity value.
- promoter_unstimulated_dn_pvalue
- Empirical p-value: fraction of QC-passing negative-control elements with normalized activity at least as high as this element.
- promoter_unstimulated_dn_fdr
- Benjamini–Hochberg FDR-adjusted empirical p-value across QC-passing elements for this assay and condition.
- enhancer_kcl_dn_activity_fold
- Mean per-replicate RNA/DNA ratio divided by the mean ratio of the library negative controls; activity fold relative to negative controls.
- enhancer_kcl_dn_log2_activity
- Log2-transformed normalized MPRA activity fold relative to negative controls.
- enhancer_kcl_dn_log2_sd
- Sample standard deviation across replicate-level log2 normalized activity values.
- enhancer_kcl_dn_replicate_n
- Number of biological replicates contributing to the normalized activity value.
- enhancer_kcl_dn_pvalue
- Empirical p-value: fraction of QC-passing negative-control elements with normalized activity at least as high as this element.
- enhancer_kcl_dn_fdr
- Benjamini–Hochberg FDR-adjusted empirical p-value across QC-passing elements for this assay and condition.
- promoter_kcl_dn_activity_fold
- Mean per-replicate RNA/DNA ratio divided by the mean ratio of the library negative controls; activity fold relative to negative controls.
- promoter_kcl_dn_log2_activity
- Log2-transformed normalized MPRA activity fold relative to negative controls.
- promoter_kcl_dn_log2_sd
- Sample standard deviation across replicate-level log2 normalized activity values.
- promoter_kcl_dn_replicate_n
- Number of biological replicates contributing to the normalized activity value.
- promoter_kcl_dn_pvalue
- Empirical p-value: fraction of QC-passing negative-control elements with normalized activity at least as high as this element.
- promoter_kcl_dn_fdr
- Benjamini–Hochberg FDR-adjusted empirical p-value across QC-passing elements for this assay and condition.
- enhancer_kcl_vs_unstimulated_log2
- Change in enhancer log2 activity after KCl depolarization versus unstimulated neurons.
- promoter_kcl_vs_unstimulated_log2
- Change in promoter log2 activity after KCl depolarization versus unstimulated neurons.
- max_enhancer_noDN_condition
- Condition (unstimulated or KCl) with the highest enhancer activity, excluding TN05 DN conditions.
- max_enhancer_noDN_log2_activity
- Maximum enhancer log2 activity across unstimulated and KCl conditions, excluding TN05 DN conditions.
- max_promoter_noDN_condition
- Condition (unstimulated or KCl) with the highest promoter activity, excluding TN05 DN conditions.
- max_promoter_noDN_log2_activity
- Maximum promoter log2 activity across unstimulated and KCl conditions, excluding TN05 DN conditions.
- enhancer_unstimulated_dn_vs_unstimulated_log2
- TN05 change in enhancer log2 activity with RFX dominant-negative perturbation under unstimulated conditions.
- promoter_unstimulated_dn_vs_unstimulated_log2
- TN05 change in promoter log2 activity with RFX dominant-negative perturbation under unstimulated conditions.
- enhancer_kcl_dn_vs_kcl_log2
- TN05 change in enhancer log2 activity with RFX dominant-negative perturbation under KCl conditions.
- promoter_kcl_dn_vs_kcl_log2
- TN05 change in promoter log2 activity with RFX dominant-negative perturbation under KCl conditions.
Quality control
Applied the paper supplemental-methods QC: remove sequence tiles with fewer than 20 reads in any DNA/cDNA sample. Counts were aggregated at the labeled element after barcode mapping cleanup; normalized activity is the mean replicate RNA/DNA ratio divided by the mean ratio of QC-passing negative controls, reported as fold and log2 activity. Empirical p-values are the fraction of negative controls at or above each element, with Benjamini–Hochberg FDR correction. TN05 negative-control normalization used the QC-passing inactive class supplied in the tally.
Curation notes
The deposited TN05 tally is a legacy 65,535-row .xls supplement, so this package uses the deposited tally subset rather than reconstructing unprovided rows from the larger key workbook. Duplicate/ambiguous barcode assignments were handled before aggregation, and 38 QC-passing inactive elements were used as negative controls. Region_of_interest is null because the tested genomic loci are scattered across the mouse genome. GEO TN03 and TN05 tally supplements are legacy .xls files with a 65,535-row spreadsheet limit, while their deposited key files contain more barcode assignments; processed tables aggregate the deposited tally rows only. Duplicate (barcode, label) records were collapsed, barcodes assigned to multiple labels were excluded, and the >=20-read filter was applied after element-level aggregation. Raw SRA read files were not packaged because GEO lists approximately 47.9 GB of runs. Processed output contains 1256 QC-passing elements and 38 QC-passing negative-control elements.