Transient 3′ UTR reporter-library RNA output in HepG2
Unraveling the determinants of microRNA mediated regulation using a massively parallel reporter assayThe 14,151-element rationally designed 3′ UTR reporter library was transiently transfected into HepG2 cells and harvested 24 h later for RNA measurement. Two RNA replicates were normalized to the shared transient-plasmid DNA library sequencing run.
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 (reporter-library transfection only)
Episomal donor plasmids were transiently transfected; RNA was collected 24 h later. The public runs are SRR6456896 and SRR6456895, with SRR6456903 providing the common plasmid-DNA denominator. Reads were reduced to the 12-nt construct barcode.
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 · 13 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.
- cell_line
- Cell line assayed in this experiment: HepG2.
- dna_count
- Count for this corrected barcode in the shared transient plasmid-DNA run SRR6456903.
- rna_rep1_count
- Barcode count in transient HepG2 RNA replicate SRR6456896.
- rna_rep2_count
- Barcode count in transient HepG2 RNA replicate SRR6456895.
- rna_count_sum
- Sum of the two HepG2 RNA replicate counts.
- dna_cpm
- Plasmid-DNA count normalized to mapped-library counts per million.
- rna_rep1_cpm
- Replicate 1 RNA count normalized to mapped-library counts per million.
- rna_rep2_cpm
- Replicate 2 RNA count normalized to mapped-library counts per million.
- log2_rna_dna_cpm
- Library-size-normalized log2 RNA/DNA activity ratio, using a 0.5-count pseudocount.
- z_score_activity
- Z-score of log2_rna_dna_cpm across the QC-passing HepG2 library elements.
- qc_status
- QC outcome; all rows in the filtered table are PASS.
Quality control
Reads were retained only when the exact 18-nt forward common primer (CGAAATGGGCCGCATTGC) and a valid 12-nt barcode were present; opposite-orientation amplicon reads were excluded. One-base sequencing-error neighbors were collapsed to abundant plasmid-DNA barcode reference centers (14,349 centers with at least 30 plasmid reads). Following the paper's transient-assay criterion, elements required more than 10 combined RNA reads and at least 30 mapped plasmid-DNA reads. The final table contains 14,336 elements; replicate log1p-count Pearson correlation was 0.972.
Curation notes
This is a barcode-level reconstruction from public SRA reads. The paper's full sequence/design-to-barcode mapping and its original processed expression table were not publicly deposited, so element IDs cannot be assigned to individual miRNAs, contexts, or mutation classes. The activity score is recomputed from library-size-normalized counts and is not claimed to reproduce the authors' exact original table.