Experiment / E5N6RLJ0BSort-Seq / Flow-Seq MPRA

AAVS1-integrated 3′ UTR reporter library sorted into fluorescence bins in K562

Unraveling the determinants of microRNA mediated regulation using a massively parallel reporter assay

The reporter library was integrated as approximately single-copy constructs at the AAVS1 locus with ZFN-mediated targeting, and K562 cells were sorted into 16 mNeonGreen/mCherry expression bins. The public pooled sequencing run preserves 48 bin-primer barcodes (three per bin) and construct barcodes; this package provides the corrected construct-by-bin count matrix.

Download processed table (CSV)Raw source data API documentation

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: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:0004
Reference genome: Not reported / not applicable
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated (AAVS1-integrated reporter; no exogenous miRNA perturbation)

A single-copy reporter construct was targeted to AAVS1 with a zinc-finger nuclease system. mCherry-positive cells were sorted into 16 bins by the mNeonGreen/mCherry ratio, with three unique 8-nt PCR bin barcodes per bin. The table retains bin-barcode counts because the public SRA metadata do not identify which barcode corresponds to each ascending FACS-bin rank.

Processed data

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Visible columns (55 of 55)

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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 · 55 definitions

element_id: Corrected construct-barcode identifier in the form barcode_<12-nt barcode>.
barcode_sequence: The 12-nt construct barcode; the public SRA package does not provide its mapping to the full 162-nt variable sequence.
total_mapped_bin_reads: Total reads assigned to the construct across all retained bin barcodes after error correction.
n_bins_detected: Number of retained bin-barcode columns with a nonzero count for the construct.
dominant_bin_barcode: Retained 8-nt bin barcode with the largest count for the construct; it is not an ascending-expression-bin label.
dominant_bin_fraction: Fraction of total_mapped_bin_reads in dominant_bin_barcode.
bin_TTGAAGAT_count: Count assigned to bin-primer barcode TTGAAGAT.
bin_GTCGATCC_count: Count assigned to bin-primer barcode GTCGATCC.
bin_CCTTATCT_count: Count assigned to bin-primer barcode CCTTATCT.
bin_CGATGCGC_count: Count assigned to bin-primer barcode CGATGCGC.
bin_AGATCACC_count: Count assigned to bin-primer barcode AGATCACC.
bin_GAGGTTCG_count: Count assigned to bin-primer barcode GAGGTTCG.
bin_AGTATCTG_count: Count assigned to bin-primer barcode AGTATCTG.
bin_AATGAGAA_count: Count assigned to bin-primer barcode AATGAGAA.
bin_GATGAATC_count: Count assigned to bin-primer barcode GATGAATC.
bin_ATCCGCGT_count: Count assigned to bin-primer barcode ATCCGCGT.
bin_ACTATGAC_count: Count assigned to bin-primer barcode ACTATGAC.
bin_GCTTCTTC_count: Count assigned to bin-primer barcode GCTTCTTC.
bin_CGCCGGTC_count: Count assigned to bin-primer barcode CGCCGGTC.
bin_CGTAGCCT_count: Count assigned to bin-primer barcode CGTAGCCT.
bin_TTAGTTCA_count: Count assigned to bin-primer barcode TTAGTTCA.
bin_CGGCGTGA_count: Count assigned to bin-primer barcode CGGCGTGA.
bin_CCAGTATG_count: Count assigned to bin-primer barcode CCAGTATG.
bin_TATACACC_count: Count assigned to bin-primer barcode TATACACC.
bin_CTCTCTCG_count: Count assigned to bin-primer barcode CTCTCTCG.
bin_GGCTCCTG_count: Count assigned to bin-primer barcode GGCTCCTG.
bin_AGTTAAGA_count: Count assigned to bin-primer barcode AGTTAAGA.
bin_ACATGGAG_count: Count assigned to bin-primer barcode ACATGGAG.
bin_GGCTTGGT_count: Count assigned to bin-primer barcode GGCTTGGT.
bin_AGGCCAAG_count: Count assigned to bin-primer barcode AGGCCAAG.
bin_CCGAACTT_count: Count assigned to bin-primer barcode CCGAACTT.
bin_GCAGTCGA_count: Count assigned to bin-primer barcode GCAGTCGA.
bin_AGGTATTG_count: Count assigned to bin-primer barcode AGGTATTG.
bin_GACAGAAG_count: Count assigned to bin-primer barcode GACAGAAG.
bin_GTATTCAC_count: Count assigned to bin-primer barcode GTATTCAC.
bin_TCCAAGGC_count: Count assigned to bin-primer barcode TCCAAGGC.
bin_TCATCGGA_count: Count assigned to bin-primer barcode TCATCGGA.
bin_TGACCATT_count: Count assigned to bin-primer barcode TGACCATT.
bin_AATTTCAT_count: Count assigned to bin-primer barcode AATTTCAT.
bin_GTGAGTAC_count: Count assigned to bin-primer barcode GTGAGTAC.
bin_GACGCGTA_count: Count assigned to bin-primer barcode GACGCGTA.
bin_TTGCGCTC_count: Count assigned to bin-primer barcode TTGCGCTC.
bin_TCACATCC_count: Count assigned to bin-primer barcode TCACATCC.
bin_CTGTGAAG_count: Count assigned to bin-primer barcode CTGTGAAG.
bin_CTTCCACT_count: Count assigned to bin-primer barcode CTTCCACT.
bin_AACTTGTC_count: Count assigned to bin-primer barcode AACTTGTC.
bin_CCTCTGGA_count: Count assigned to bin-primer barcode CCTCTGGA.
bin_GTCCTACA_count: Count assigned to bin-primer barcode GTCCTACA.
bin_TATCGGAT_count: Count assigned to bin-primer barcode TATCGGAT.
bin_AGTGCTGC_count: Count assigned to bin-primer barcode AGTGCTGC.
bin_ATATCCTT_count: Count assigned to bin-primer barcode ATATCCTT.
bin_TGAGGTGG_count: Count assigned to bin-primer barcode TGAGGTGG.
bin_TCGTTATA_count: Count assigned to bin-primer barcode TCGTTATA.
bin_ATTCACCC_count: Count assigned to bin-primer barcode ATTCACCC.
qc_status: QC outcome; all rows in the filtered table are PASS.

Quality control

The 61,665,679-spot Lib1Bins run was parsed for the 13-nt bin-primer prefix plus the common 18-nt forward primer and valid 12-nt construct barcode. The 48 highest-abundance 8-nt bin barcodes were retained; one-base sequencing-error neighbors were collapsed to those bin centers and to 14,349 plasmid-DNA construct-barcode reference centers. Rows with fewer than 100 mapped bin reads were removed, following the paper's first row-level filter. The final table contains 13,709 constructs and 48 bin-count columns. No protein-repression score was invented because the public files do not provide the FACS rank-to-bin-barcode mapping.

Curation notes

This table is a public-read reconstruction of the protein-output arm at the barcode-count level. The article's original FACS bin centers, sequence/design-to-barcode mapping, and processed protein-repression table were not publicly deposited. Because the SRA run only exposes pooled primer barcodes, bin columns are intentionally labeled by their 8-nt barcode and no log2 protein-repression value is reported.

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