HUDEP-2 integrated LV-MPRA of the human β-globin LCR

An integrated lentiviral MPRA screened overlapping 103-bp human β-globin locus control region fragments tiled every 4 bp in HUDEP-2 erythroid progenitor cells. Each query was represented by three 13-bp barcodes and a reverse-complement library; cDNA barcode abundance after four days of erythroid differentiation was normalized to plasmid DNA barcode abundance.

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:VI06
Reference genome: hg19
Design focus: Region-focused
Region of interest: chr11:5296481-5313207

Perturbation & assay details

Basal / untreated; erythroid differentiation for 4 days

A third-generation lentiviral reporter library placed 103-bp LCR query fragments upstream of a minimal human β-globin promoter driving βAS3-P2A-mCitrine, with a 13-bp barcode in the transcript 3′ UTR. The library included 4-bp-overlapping queries across the cited ~16.7-kb interval and reverse-complement query versions, was packaged in 293T cells, and was used to transduce HUDEP-2 cells at MOI 4. Cells were expanded for 7 days and differentiated on MS5 stromal cells for 4 days before gDNA and RNA barcode recovery; the paper reports 124 million plasmid, 49 million gDNA, and 117 million cDNA reads.

Quality control

The authors retained reads that perfectly matched the first 14 nt of the amplicon, located barcodes using the constant flanking sequences, normalized read counts by sequencing depth, divided cDNA barcode counts by plasmid DNA barcode counts, aggregated the three barcodes assigned to each query, and applied a 50-neighbor bootstrap with 100,000 resamples to make the enhancer map. Supplemental Figure 2 reports 762 missing barcodes and 1,011 barcodes with fewer than 10 reads, with no specific dropout pattern, plus plasmid-to-gDNA correlation r=0.854 and gDNA-to-mRNA correlation r=0.304. For this package, only complete canonical 103-bp hg19 windows at the stated 4-bp tiling interval with a non-null digitized Figure 2A score were retained; no windows failed these package-level filters.

Curation notes

The article is a genuine LV-MPRA study, but its public supplements contain primers, figures, and vector sequences rather than barcode assignments or barcode-level DNA/RNA counts. The authors state that data and code are available from the corresponding author upon reasonable request; no public GEO/SRA accession or matching MPRAbase dataset was located. The single table is therefore a researcher-usable reconstruction of the genuine published MPRA map: Figure 2A was raster-digitized and joined to 103-bp forward and reverse-complement sequences from the cited hg19 interval. The activity values are approximate at the plotted resolution (about one y-pixel and about 31 bp horizontally), orientation-specific effects cannot be separated, and the PC color band may represent a control rather than an independent tiled query. The biosample CURIE uses the requested PREFIX:ACCESSION form for Cellosaurus accession CVCL_VI06.

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HUDEP-2 integrated LV-MPRA of the human β-globin LCR

Processed data

Quality control

Curation notes

Cite OpenMPRA

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