NucLibA MCF7 reporter screen for RNA nuclear localization

A barcoded 109-nt tile library from human lncRNAs, mouse liver nuclear-enriched mRNA 3' UTRs, and MALAT1 homologs was cloned into the 3' or 5' UTR of AcGFP in episomal plasmids. MCF7 cells were transfected in triplicate, and whole-cell, nuclear, cytoplasmic, and input libraries were sequenced to quantify localization and expression effects.

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:0031
Reference genome: hg19
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

AcGFP UTR reporter with pAcGFP1-C1 3' UTR and pAcGFP1-N1 5' UTR constructs; unique molecular identifiers were used for insert counting. The readouts are nuclear/cytoplasmic localization ratios and whole-cell-extract/input RNA abundance ratios, reported as replicate-level log2 scores.

Quality control

The authors required the specified adapter sequence, extracted UMIs, matched inserts without indels with sequencing-quality-aware mismatches (up to 2 mismatches in the first 15-nt seed and no more than 4 overall), and discarded equal-best ambiguous matches. The paper reports retaining fragments with at least 10 reads on average in whole-cell-extract samples. For packaging, only elements present in the authors' released NucLibA ratio/annotation table (Supplementary Table 4) were retained; rows absent from that analyzed table were excluded. All retained rows have a 109-nt sequence and at least one released ratio score; blank replicate values remain blank and replicate means ignore missing values.

Curation notes

Supplementary Table 2 contains all 5,511 designed NucLibA sequences, whereas Supplementary Table 4 releases 4,884 annotated ratio records and is the processed table packaged here. The released ratio table does not cover every raw design entry, including the mouse 3' UTR subset, so omitted records were not reconstructed. The paper states that MCF7 cells were from ATCC, were not authenticated, and were routinely tested for mycoplasma contamination.

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NucLibA MCF7 reporter screen for RNA nuclear localization

Processed data

Quality control

Curation notes

Cite OpenMPRA

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