Experiment / E8O9A7U6MIntegrated lentiMPRA

Library Alpha bulk lentiMPRA of CD55-negative HSPCs

Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity

Bulk validation lentiMPRA was performed on two biological replicates of FACS-sorted CD55-negative primary mouse HSPCs using the Alpha synthetic enhancer library. The table reports replicate RNA/DNA counts, normalized counts, and mean log2 RNA/DNA activity.

Download processed table (CSV)Raw source data API 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: mm10
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

FACS-sorted CD55-negative HSPC fraction; Basal / Untreated

Lentiviral genomic integration with barcode-based reporter RNA/DNA normalization. Two biological replicates were measured for the CD55-sorted HSPC condition; log2_ratio_mean is the source mean.norm activity score.

Processed data

50 rows per page. Click a cell to inspect its full value.

Visible columns (31 of 31)

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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 · 31 definitions

study_id: Parent study identifier.
experiment_id: Child experiment identifier.
condition: FACS-sorted bulk MPRA condition.
source_row_id: 1-based row number in the source Figshare RDS object before QC filtering.
element_id: Source bulk construct identifier.
crs_id: Source bulk construct identifier (CRS).
design_name: Enhancer design label joined through bulk_meta_libAlpha.rds.
sequence: DNA sequence joined to the Alpha design from Additional file 4/Table S3.
tf_1: Primary transcription factor motif identity, when annotated.
tf_2: Second transcription factor motif identity, when annotated.
motif_affinity_1: Primary motif affinity/likelihood annotation.
motif_affinity_2: Second motif affinity/likelihood annotation.
motif_count: Number of motif repeats/sites in the design.
orientation_1: Primary motif orientation.
orientation_2: Second motif orientation.
spacer_bp: Spacer length in base pairs.
design_replicate: Design replicate annotation.
control_class: Derived class such as synthetic, positive_control, inert_control, or qc_failure_label.
is_endogenous: Whether the tested element is annotated as endogenous genomic sequence; FALSE for the Alpha synthetic library.
rna_count_rep1: Raw reporter RNA count in bulk replicate 1.
dna_count_rep1: Raw DNA/barcode count in bulk replicate 1.
rna_norm_rep1: Library-size-normalized reporter RNA count in replicate 1.
dna_norm_rep1: Library-size-normalized DNA/barcode count in replicate 1.
log2_ratio_rep1: Source log2 RNA/DNA activity score for replicate 1.
rna_count_rep2: Raw reporter RNA count in bulk replicate 2.
dna_count_rep2: Raw DNA/barcode count in bulk replicate 2.
rna_norm_rep2: Library-size-normalized reporter RNA count in replicate 2.
dna_norm_rep2: Library-size-normalized DNA/barcode count in replicate 2.
log2_ratio_rep2: Source log2 RNA/DNA activity score for replicate 2.
log2_ratio_mean: Mean of the two source replicate log2 RNA/DNA activity scores (`mean.norm`).
qc_pass: TRUE for every retained element; source `pass` QC flag and additional DNA/nonmissing-score checks passed.

Quality control

The source bulk object supplies a pass flag generated by the study's bulk lentiMPRA workflow. I retained only pass == TRUE rows with nonzero DNA counts in both replicates and a nonmissing mean.norm score; zero RNA counts were not removed because they are valid low-activity measurements.

Curation notes

The processed table retains 74 of 84 elements. Ten elements failed the deposited source pass flag. Bulk IDs were joined through bulk_meta_libAlpha.rds and annotated with Alpha design sequences and motif metadata. These bulk data are supplied as the study's validation screen.

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