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Experiment / E5NUQEFTDIntegrated lentiMPRA

HSPC primary-cell lentiMPRA — Library A single-factor motifs

Design principles of cell-state-specific enhancers in hematopoiesis

Library A tested one to six motifs for each of 38 transcription factors, varying motif number, affinity, orientation, arrangement, and spacing in random DNA. The lentiviral library was measured across seven FACS-defined progenitor states generated from differentiating primary murine HSPCs.

Download processed table (CSV)Raw source dataAPI documentation

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.

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 · 28 definitions
element_id
Unique identifier for the tested gene-regulatory element (source CRS).
source_data_object
Name of the main DATA object in the public Figshare R archive.
cell_state_id
Source cell-state cluster identifier; aggregate_HSPC denotes the supplied across-cell-state aggregate view.
cell_state
Cell-state label mapped from the archived cellstate.map vector; K562 denotes State_9K.
library
Paper/library identity assigned from the public DATA-object name and the article (A–H).
source_library_label
Verbatim Library field in the R archive, retained for provenance; it is inconsistent with the object/paper identity for some libraries.
sequence
Reporter insert DNA sequence; in synthetic libraries uppercase letters encode placed motifs and lowercase letters encode background DNA as supplied.
rna_count_rep1
Raw UMI-derived reporter RNA molecule count for replicate 1.
dna_count_rep1
Raw UMI-derived plasmid DNA molecule count for replicate 1.
rna_count_rep2
Raw UMI-derived reporter RNA molecule count for replicate 2.
dna_count_rep2
Raw UMI-derived plasmid DNA molecule count for replicate 2.
rna_normalized_rep1
Library-size-normalized reporter RNA count for replicate 1.
dna_normalized_rep1
Library-size-normalized plasmid DNA count for replicate 1.
rna_normalized_rep2
Library-size-normalized reporter RNA count for replicate 2.
dna_normalized_rep2
Library-size-normalized plasmid DNA count for replicate 2.
activity_log2_raw_rep1
Raw log2 RNA/DNA activity for replicate 1 after library-size normalization.
activity_log2_raw_rep2
Raw log2 RNA/DNA activity for replicate 2 after library-size normalization.
activity_log2_adjusted_rep1
Replicate-1 activity after subtracting the median random-DNA baseline.
activity_log2_adjusted_rep2
Replicate-2 activity after subtracting the median random-DNA baseline.
activity_log2_raw_mean
Mean raw log2 RNA/DNA activity across the two replicates.
activity_log2_adjusted_mean
Mean baseline-adjusted log2 RNA/DNA activity across the two replicates; preferred quantitative activity score.
activity_scaled_mean
Source visualization scale with random-DNA activity at 0 and the Trp53 reference at 1; not the preferred score for modeling or statistical testing.
tf
Single transcription factor whose motif was placed in the sequence (Library A).
motif_count
Number of repeated instances of the single TF motif (source nrepeats).
motif_affinity_quantile
Designed motif affinity quantile from 0–1/percentage-like source scale (source affinitynum).
motif_orientation
Designed motif orientation: forward, reverse, or tandem/alternating (source orientation).
motif_spacing_bp
Spacing between placed motif sites in base pairs (source spacer).
motif_biophysical_affinity_sum
Sum of biophysical motif affinities across the sequence (source sum.biophys.affinity).

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. The public DATA object retained 43,673 of 43,673 rows (0 removed); the pooled adjusted-activity replicate Pearson correlation is 0.874.

Curation notes

The DATA object is HSPC.libA and contains 8,492 unique construct IDs across the seven states. The biosample annotation denotes the starting Lin−Kit+ HSPC population; each table row is measured after differentiation in one of seven sorted states.

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