NucLibB MCF7 sequence-variation and tiling MPRA

A second barcoded 109-nt library was cloned into the 3' UTR of AcGFP and included transcript tiles, wild-type SIRLOIN-containing elements, and systematic sequence variants of JPX#9 and PVT1#22. MCF7 cells were transfected in two replicates and nuclear/cytoplasmic localization plus whole-cell-extract/input abundance were measured by sequencing.

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: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

AcGFP 3' UTR reporter; two biological replicates; the library combines tiling of lncRNAs and mRNAs with single-base replacements, clustered base changes, motif shuffles, motif arrays, and other synthetic sequence variants. The processed table reports replicate-level and mean log2 nuclear/cytoplasmic and whole-cell-extract/input ratios.

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 NucLibB ratio/annotation table (Supplementary Table 8) were retained; rows without a released ratio record were excluded. All retained rows have a 109-nt sequence and released localization and abundance scores.

Curation notes

Supplementary Table 7 contains 1,951 NucLibB sequence/count records, while Supplementary Table 8 releases 1,919 ratio/annotation records and is the processed table packaged here. Wild-type and variant annotations are preserved as released; an empty flag is not treated as false. MCF7 cells were reported as ATCC-derived, not authenticated, and routinely tested for mycoplasma contamination.

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NucLibB MCF7 sequence-variation and tiling MPRA

Processed data

Quality control

Curation notes

Cite OpenMPRA

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