HSPC primary-cell lentiMPRA — Library G genomic regulatory elements

Library G tested 1,667 genomic elements selected from differentially accessible regions and enhancer/promoter annotations in the primary murine HSPC culture system. The genomic library was measured across six available differentiated 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: mm10
Design focus: Region-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 G parameter row was present in the public processing-parameter spreadsheet; the supplied DATA object is the authors' final processed screen. It retained 8,768 of 8,768 rows (0 removed); the pooled adjusted-activity replicate Pearson correlation is 0.864.

Curation notes

Library F and Library G 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. Genomic coordinates are retained as supplied in mm10 and the source_library_label is LibV.

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HSPC primary-cell lentiMPRA — Library G genomic regulatory elements

Processed data

Quality control

Curation notes

Cite OpenMPRA

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