A pooled plasmid MPRA tested 90-bp elements tiled every 50 bp across six mouse lincRNA loci and their nearest protein-coding neighbors, with five redundant 10-nt barcodes per element plus promoter controls. Five C2C12 RNA libraries were compared with five VEC plasmid-DNA input libraries to quantify enhancer activity.
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.
The construct contains a 90-nt genomic or control element, restriction-enzyme sites, a unique 10-nt barcode, universal primer sequences, and a minimal-promoter GFP reporter. The five C2C12 RNA samples are C2C12_A_1, C2C12_A_2, C2C12_B_1, C2C12_B_2, and C2C12_B_3; the five DNA input controls are VEC_A_1, VEC_A_2, VEC_A_3, VEC_B_1, and VEC_B_2. The paper describes RNA biological replicates from two passages and DNA libraries generated on two separate days.
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 · 44 definitions
element_id
Stable package identifier formed from the source annotation name and local element order.
annotation_name
Exact element-group name from the MPRA oligo annotation.
locus
Leading locus/control name parsed from annotation_name.
element_sequence
The 90-nt genomic or control sequence represented by the element, in the supplied oligo orientation.
strand
Reported genomic strand; blank for non-genomic controls.
annotation_coordinates
Exact localCoordinates values supplied in the annotation; pipe-separated when redundant control rows have multiple labels.
coordinate_chromosome
Parsed mm10 chromosome for genomic elements; blank for controls.
coordinate_start
Parsed interval start from localCoordinates.
coordinate_end
Parsed interval end from localCoordinates.
local_order
Element order within the source locus/construct.
element_type
Whether the row is a genomic_locus, positive_control, or negative_control.
region_type
promoter for an element within 1,000 bp of a matched TSS, gene_body otherwise, or control for synthetic controls.
tss_name
Matched GENCODE TSS name used for the promoter/gene-body annotation.
tss_distance_bp
Signed strand-aware distance in bp from the element start to the selected TSS; blank when no TSS applies.
n_barcodes_total
Number of annotated barcode replicates mapped to the element before QC.
n_barcodes_pass_qc
Number of mapped barcode replicates passing the all-five-VEC-DNA count threshold.
barcode_qc_fraction
n_barcodes_pass_qc divided by n_barcodes_total.
barcodes_pass_qc
Pipe-separated barcode sequences retained for the row.
C2C12_A_1_rna_count
Median raw barcode count across passing barcodes in C2C12_A_1 RNA.
C2C12_A_2_rna_count
Median raw barcode count across passing barcodes in C2C12_A_2 RNA.
C2C12_B_1_rna_count
Median raw barcode count across passing barcodes in C2C12_B_1 RNA.
C2C12_B_2_rna_count
Median raw barcode count across passing barcodes in C2C12_B_2 RNA.
C2C12_B_3_rna_count
Median raw barcode count across passing barcodes in C2C12_B_3 RNA.
VEC_A_1_dna_count
Median raw barcode count across passing barcodes in VEC_A_1 DNA input.
VEC_A_2_dna_count
Median raw barcode count across passing barcodes in VEC_A_2 DNA input.
VEC_A_3_dna_count
Median raw barcode count across passing barcodes in VEC_A_3 DNA input.
VEC_B_1_dna_count
Median raw barcode count across passing barcodes in VEC_B_1 DNA input.
VEC_B_2_dna_count
Median raw barcode count across passing barcodes in VEC_B_2 DNA input.
C2C12_A_1_rna_norm
Median depth-normalized and sample-median-centered RNA barcode count across passing barcodes in C2C12_A_1.
C2C12_A_2_rna_norm
Median depth-normalized and sample-median-centered RNA barcode count across passing barcodes in C2C12_A_2.
C2C12_B_1_rna_norm
Median depth-normalized and sample-median-centered RNA barcode count across passing barcodes in C2C12_B_1.
C2C12_B_2_rna_norm
Median depth-normalized and sample-median-centered RNA barcode count across passing barcodes in C2C12_B_2.
C2C12_B_3_rna_norm
Median depth-normalized and sample-median-centered RNA barcode count across passing barcodes in C2C12_B_3.
VEC_A_1_dna_norm
Median depth-normalized and sample-median-centered DNA barcode count across passing barcodes in VEC_A_1.
VEC_A_2_dna_norm
Median depth-normalized and sample-median-centered DNA barcode count across passing barcodes in VEC_A_2.
VEC_A_3_dna_norm
Median depth-normalized and sample-median-centered DNA barcode count across passing barcodes in VEC_A_3.
VEC_B_1_dna_norm
Median depth-normalized and sample-median-centered DNA barcode count across passing barcodes in VEC_B_1.
VEC_B_2_dna_norm
Median depth-normalized and sample-median-centered DNA barcode count across passing barcodes in VEC_B_2.
activity_ratio
Median RNA/DNA activity ratio across passing barcode ratios.
log2_activity
Base-2 logarithm of activity_ratio; positive values indicate higher reporter RNA relative to DNA input.
activity_ratio_sd
Sample standard deviation of passing barcode activity ratios for the element.
activity_ratio_iqr
Interquartile range of passing barcode activity ratios for the element.
n_barcode_activity_values
Number of passing barcode activity ratios contributing to the element summary.
qc_status
QC status; all packaged rows pass the all-five-VEC-DNA-libraries threshold.
Quality control
The source analysis reported normalized replicate correlations of R2 > 0.99 and an RNA-versus-DNA input correlation of approximately 0.8544. Counts below 10 were treated as missing during library-depth and median normalization; barcode rows were retained only when all five VEC DNA input libraries had at least 10 counts. In the full GEO count matrix, 15,988 rows meet this threshold; after joining to the oligo annotation, 14,948 annotated barcode rows were retained. The 1,285 GEO count rows lacking oligo annotation were omitted from the packaged table. This yielded 4,182 element rows; elements with no passing annotated barcode were excluded, while the number of passing barcodes is retained per row. Element activity is the median of passing barcode activity ratios. For deterministic processing, all 100 possible combinations of two RNA replicates and three DNA replicates were used for each barcode, which follows the paper's median-of-resampled-ratios procedure while avoiding dependence on a random draw sequence; the paper used 1,000 random draws. The paper's 500-bp sliding-window significance analysis with 1% Benjamini-Hochberg FDR is not represented as a per-element p-value in this table.
Curation notes
This is one pooled region-focused MPRA experiment, not a Peril-only assay: the library covers Crnde/Irx5, Fendrr/Foxf1, LincEnc1/Enc1, Lincp21/Cdkn1a, Peril/Sox2, and Tug1/Morc2a, with CMV, EF1a, TK, and scrambled controls. The table is element-level and therefore intentionally aggregates redundant barcodes; the raw GEO barcode count matrix and full oligo annotation remain in raw_data. Blank coordinate/TSS fields identify non-genomic controls. This assay measures tiled regulatory activity rather than allelic variant effects. The paper's prose describes selecting one RNA and one DNA replicate for each resample, while the supplied R Markdown implements two RNA and three VEC selections; this package follows the supplied code and uses all 100 possible two-RNA/three-DNA combinations deterministically.