An episomal GFP reporter MPRA tested 2,225 synthesized oligos tiling the mouse Linc-p21 locus and 500 bp of its promoter. The library contained 90-bp genomic inserts starting every 50 bp, with five unique barcodes per tile, and was assayed in C2C12 myoblasts using three RNA-library and three vector-library replicates.
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
CVCL:0188
Reference genome
mm10
Design focus
Region-focused
Region of interest
chr17:29057511-29079626
Perturbation & assay details
Basal / Untreated
The plasmid library used a GFP reporter and was transfected with Lipofectamine 3000; cells were harvested after 24 hours. The source analysis counted reads containing GFP and a perfect match to a designed 10-nt barcode, normalized each RNA or vector library to its total tag count, and calculated RNA/vector activity. GEO samples are exp_1–3 (GSM2214665–GSM2214667) and vec_1–3 (GSM2214668–GSM2214670).
Processed data
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Visible columns (27 of 27)
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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 · 27 definitions
element_id
Stable package identifier derived from source LocalOrder; one row per 90-bp tiled genomic element.
source_local_order
Source LocalOrder identifying the tile in the authors' library annotation.
sequence_90bp
The 90-bp genomic insert tested by the reporter, in the source library orientation.
chromosome
Chromosome containing the tested tile.
start_mm10
1-based inclusive mm10 start coordinate of the 90-bp tile.
end_mm10
1-based inclusive mm10 end coordinate of the 90-bp tile.
start_mm9
Source mm9 start coordinate retained for cross-assembly traceability.
end_mm9
Source mm9 end coordinate retained for cross-assembly traceability.
strand
Strand of the tiled Linc-p21 locus in the source annotation.
local_coordinates_mm10
Source mm10 interval for the tested tile.
n_barcodes_total
Number of designed barcodes represented for the tile in the deposited table.
n_barcodes_qc
Number of tile barcodes passing vector-coverage QC (vecMed > 0).
n_barcodes_expression_signal
Number of QC-passing barcodes with expMed > 0.
rna_fraction_rep1_median
Median normalized RNA tag fraction across QC-passing barcodes for RNA replicate exp_1.
rna_fraction_rep2_median
Median normalized RNA tag fraction across QC-passing barcodes for RNA replicate exp_2.
rna_fraction_rep3_median
Median normalized RNA tag fraction across QC-passing barcodes for RNA replicate exp_3.
dna_fraction_rep1_median
Median normalized vector-library tag fraction across QC-passing barcodes for vector replicate vec_1.
dna_fraction_rep2_median
Median normalized vector-library tag fraction across QC-passing barcodes for vector replicate vec_2.
dna_fraction_rep3_median
Median normalized vector-library tag fraction across QC-passing barcodes for vector replicate vec_3.
rna_fraction_median
Median of barcode-level expMed values, where expMed is the median normalized RNA fraction across the three RNA replicates.
dna_fraction_median
Median of barcode-level vecMed values, where vecMed is the median normalized vector fraction across the three vector replicates.
activity_ratio
RNA/vector activity ratio calculated as rna_fraction_median divided by dna_fraction_median.
log2_activity_ratio
Base-2 logarithm of activity_ratio; NA when the activity ratio is zero.
barcode_activity_ratio_median
Median of barcode-level RNA/vector ratios among QC-passing barcodes.
barcode_activity_ratio_iqr
Interquartile range of barcode-level RNA/vector ratios among QC-passing barcodes.
source_barcodes
Semicolon-separated designed barcodes contributing to the tile after QC.
source_oligo_ids
Semicolon-separated source OligoID values corresponding to the retained barcodes.
Quality control
The study's analysis set tag counts below 40 to zero before library-depth normalization and required perfect barcode matches from GFP-containing reads. For this package, a tile passed additional coverage QC when at least 3 of its 5 designed barcodes had vecMed > 0, where vecMed is the median normalized vector-library fraction across the three vector replicates. This retained 348 of 445 tiles and 1,475 of 2,225 barcode observations. Tiles with insufficient vector support were excluded; tiles with RNA activity equal to zero were retained when DNA coverage passed QC, and log2_activity_ratio is NA for those zero-activity tiles.
Curation notes
The published methods specify 145-nt synthesis oligos, and all deposited finaloligo sequences are 145 nt; each contains a 90-bp genomic insert. The GEO series also contains unrelated E14.5 tissue RNA-seq samples, which are not part of this MPRA experiment package. The processed CSV is an element-level re-aggregation of the deposited normalized barcode table, not a reanalysis of raw sequence reads. C2C12 is the immortalized mouse myoblast line C2C12 (ATCC CRL-1772; Cellosaurus CVCL_0188).