Chick OLIG2 LS-MPRA, E5 retina
Massively parallel reporter assay for mapping gene-specific regulatory regions at single-nucleotide resolutionA BAC-derived chick OLIG2 locus library was electroporated into embryonic day 5 chick retinal explants and cultured ex vivo for 24 hours before barcode RNA readout. Four biological replicates were released.
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
BAC-based episomal locus-specific MPRA (LS-MPRA). Randomly fragmented BAC inserts were cloned upstream of a minimal TATAA promoter driving an intron-containing EGFP reporter, with a 24-bp barcode in the 3-prime UTR. Reporter RNA barcode abundance was normalized to the electroporated library input and released as a deepTools bamCompare ratio BigWig.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 13 definitions
- chrom
- Reference-genome chromosome or contig for the released LS-MPRA track.
- start_0based
- 0-based inclusive interval start.
- end_0based
- 0-based exclusive interval end.
- interval_length_bp
- Length of the interval in base pairs.
- activity_ratio_rep1
- Published replicate 1 BigWig ratio value, representing normalized reporter RNA barcode abundance relative to the library input.
- activity_ratio_rep2
- Published replicate 2 BigWig ratio value, representing normalized reporter RNA barcode abundance relative to the library input.
- activity_ratio_rep3
- Published replicate 3 BigWig ratio value, representing normalized reporter RNA barcode abundance relative to the library input.
- activity_ratio_rep4
- Published replicate 4 BigWig ratio value, representing normalized reporter RNA barcode abundance relative to the library input; present for four-replicate chick experiments.
- activity_ratio_mean
- Arithmetic mean of the released replicate activity ratios over the interval.
- activity_ratio_sd
- Sample standard deviation of the released replicate activity ratios over the interval.
- activity_log2_ratio_mean
- log2-transformed mean activity ratio; blank if the mean is not positive.
- n_replicates
- Number of released biological replicate tracks contributing to the mean and standard deviation.
- qc_pass
- True for rows retained after finite-value and ROI/background filtering.
Quality control
The released tracks are the authors' barcode-fragment-associated and library-normalized LS-MPRA bamCompare ratio BigWigs. The authors describe adapter trimming, barcode extraction, library-specific filtering, whitelist/Hamming-error correction, and replicate/library-complexity QC; Source data 1 documents sequencing depth, unique fragments and barcodes, saturation, barcode collisions, and replicate profiling. For this package, genome-wide default 1.0 background intervals outside the BAC-derived non-background interval were excluded, while within-ROI intervals were retained at the released bedGraph resolution. Rows were retained only when every replicate had a finite value; no additional activity threshold was imposed, so weak and negative regulatory intervals remain available.
Curation notes
E5 chick retina explants; 24-hour ex vivo culture; four biological replicates; chick OLIG2 BAC clone CH261-60J3. Source tracks, in replicate order, are: OLIG2_bc101-ratio.bw, OLIG2_bc202-ratio.bw, OLIG2_bc303-ratio.bw, OLIG2_bc404-ratio.bw. The table contains the released normalized activity ratio and derived replicate summary, not allele-specific variant effects; raw per-replicate BigWigs remain under raw_data/ls_mpra_tracks. The article also reports Olig2 d-MPRA experiments, but the public repository exposes their raw FASTQ inputs and processing scripts rather than a compact processed numeric mutation-effect table; d-MPRA input FASTA, scripts, motif results, and source-data QC are preserved in raw_data.