HSPC primary-cell lentiMPRA — Library H complex synthetic enhancers

Library H tested complex synthetic enhancers containing three to twelve randomly combined high-affinity motifs from the selected transcription factors, with motif identity, orientation, and spacing varied in random DNA. The library was measured across seven differentiated murine HSPC progenitor states.

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: Mouse
Taxonomy ID: NCBITaxon:10090
Biosample: CL:0000037
Reference genome: Not reported / not applicable
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated (ex vivo HSPC differentiation)

Lentiviral reporter assay using pLS-SceI (Addgene plasmid #137725), with the synthetic or genomic regulatory element cloned upstream of a minimal promoter and an EGFP reporter. Primary murine Lin−Kit+ HSPCs were infected, cultured for ex vivo differentiation, FACS-sorted into progenitor states, and assayed by DNA/RNA UMI counts from the reporter 5′ UTR. The two replicate activities are log2 library-size-normalized RNA/DNA values; random-DNA subtraction and Trp53 scaling follow the authors' published definitions.

Quality control

The authors filtered the GRE–barcode association by alignment score (290–292), dominant assignment support (assigned reads at least five times deviant-assignment reads), barcode homopolymer content (removed barcodes with more than 10 identical nucleotides), and sequencing-error correction. MPRA reads required concordant forward/reverse barcode reads and underwent UMI error correction. The supplied DATA frame is the authors' post-processing/post-QC element-by-cell-state table. Package QC additionally required complete identifiers, non-empty sequences, positive raw DNA/RNA counts, and finite normalized/activity values. No separate Library H parameter row was present in the public processing-parameter spreadsheet; the supplied DATA object is the authors' final processed screen. It retained 27,479 of 27,479 rows (0 removed); the pooled adjusted-activity replicate Pearson correlation is 0.641.

Curation notes

Library C and Library H were combined in one biological screen according to the methods; they are provided as separate child tables because the public archive exposes separate DATA objects. The source_library_label is LibB despite the object/paper identity being Library H.

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HSPC primary-cell lentiMPRA — Library H complex synthetic enhancers

Processed data

Quality control

Curation notes

Cite OpenMPRA

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