Pilot random 8-mer post-transcriptional 3′-UTR screen
High-throughput discovery of post-transcriptional cis-regulatory elementsA random 8-nucleotide library inserted in the human IQGAP1 3′UTR was stably integrated as single-copy reporter constructs in Flp-In T-REx 293 cells. FACS isolated low- and high-GFP populations while dsRed controlled for reporter-locus transcription, and Illumina sequencing quantified 8-mer enrichment.
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
The library was delivered by FLP/FRT recombinase-mediated site-specific integration into the single FRT locus of Flp-In T-REx 293 cells. GFP was driven by EF-1α and the variable 8-mer was placed in the human IQGAP1 3′UTR; a PGK-dsRed reporter controlled for transcriptional noise. Cells were gated for GFP+/dsRed+ status, collected from the middle 50% of dsRed intensity, and sorted into pilot low-GFP and high-GFP populations before 50-nt Illumina sequencing of the variable 8-mer region. The pilot library contained approximately 8,000 random 8-mers.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 12 definitions
- element_id
- Stable package identifier for the pilot 8-mer.
- sequence
- The tested 8-nucleotide sequence in the reporter 3′UTR.
- library_context
- Fixed human IQGAP1 3′UTR sequence context used for the variable 8-mer.
- unsorted_rpm
- Normalized reads per million for the 8-mer in the unsorted pilot library.
- high_gfp_rep1_rpm
- Normalized reads per million in high-GFP sorting replicate 1.
- high_gfp_rep2_rpm
- Normalized reads per million in high-GFP sorting replicate 2.
- low_gfp_rpm
- Normalized reads per million in the low-GFP sorting population.
- high_gfp_rep1_enrichment
- High-GFP replicate 1 enrichment relative to the unsorted pilot library.
- high_gfp_rep2_enrichment
- High-GFP replicate 2 enrichment relative to the unsorted pilot library.
- low_gfp_enrichment
- Low-GFP enrichment relative to the unsorted pilot library.
- candidate_retested
- Whether the authors selected the 8-mer for individual reporter re-testing.
- expected_effect
- Author annotation of the expected reporter effect for selected candidates; NA means not selected for re-testing.
Quality control
The authors filtered sequencing reads for a barcode, Phred quality scores greater than 20 in the barcode and variable 8-mer, and the correct CATAC and ATA flanking sequences; they counted passing 8-mers after normalization to library size. Pilot analysis required robust representation in the unsorted technical replicates before enrichment analysis. The source pilot workbook supplies 6,886 rows from this author-filtered set, and package QC retained all 6,886 rows because the sequence, RPM, enrichment, and screening-status fields are populated.
Curation notes
This is a fluorescence-bin sequencing screen rather than an allele-contrast MPRA: each row is a synthetic 8-mer, and expected_effect is a pilot selection annotation rather than a formal differential-expression call. The fixed reporter context is human IQGAP1 3′UTR; no genomic coordinates are assigned to individual 8-mers. The paper's auxiliary miRNA-seq mapping used hg19, which is why that assembly is recorded here. The exact Flp-In-T-REx-293 cell line was resolved to Cellosaurus CVCL:U427. The package also retains the complete GEO 8-mer count matrix in raw_data for users who want to reprocess the pilot replicate counts; GEO labels both unsorted pilot replicate columns as pilot_unsorted_rep_A, so their positions rather than the duplicated labels identify the two columns.