Pooled yeast 3′-end sequence library expression screen

A low-copy plasmid library of 13,000 designed yeast 3′-end sequences was measured in the Y8205 strain, with native 3′ UTRs, scanning mutants, synthetic processing motifs, and RNA-binding-protein motif constructs represented by 14,955 oligo/barcode records. Cells were sorted into 16 YFP/mCherry expression bins and barcode abundance across bins was used to infer a mean expression score for each library oligo.

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: Budding yeast
Taxonomy ID: NCBITaxon:4932
Biosample: UNMAPPED:Y8205
Reference genome: Not reported / not applicable
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Galactose-induced GAL1/10 promoter (SC-URA; mid-exponential growth)

Low-copy episomal plasmid with YFP driven by GAL1/10 and mCherry driven by TEF2; the designed 3′-end insert was placed downstream of YFP in a constant reporter context containing a mutated CYC1 3′ UTR. FACSAria sorting used the YFP/mCherry ratio to assign cells to 16 expression bins; Illumina HiSeq 2000 sequencing of barcode-containing reporter amplicons and gamma-distribution fitting yielded the per-oligo expression score.

Quality control

The paper reports a median technical relative standard deviation of 13.2% across 87 groups of at least 10 identical 3′-end sequences differing only in their 11-bp barcodes, and R² = 0.77 for paired random mutations at the same position. For this package, a row was retained only when Expression was finite and numeric, Design ID and Lib ID were numeric, the oligo was a valid 150-bp A/C/G/T sequence, and the 11-bp barcode was valid and matched the barcode extracted from the oligo. The 783 S3 records with missing Expression were excluded; no additional value-based outlier filter was applied because per-bin counts are not supplied in the supplemental table.

Curation notes

The source S3 table contains 14,955 barcode/oligo rows and 13,000 unique Lib IDs; 783 rows have blank Expression and are absent from the processed table, leaving 14,172 rows and 12,249 Lib IDs with at least one score. Barcode-level rows are preserved, while library_barcode_count, library_mean_expression, and library_sd_expression summarize repeated Lib IDs. The paper's Expression field is the gamma-fit mean expression score inferred from FACS-bin distributions, not a standard MPRA RNA/DNA log ratio. Multiple element annotations are joined with semicolons, and controls without an annotated Element have blank element columns. S4 arrayed validation, qPCR, and 3′ RACE measurements are retained as raw supplemental context but are not mixed into this pooled MPRA table.

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Pooled yeast 3′-end sequence library expression screen

Processed data

Quality control

Curation notes

Cite OpenMPRA

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