Experiment / E8506SPRXSingle-Cell MPRA (scMPRA / sc-lentiMPRA)

Library Alpha sc-lentiMPRA during murine myeloid differentiation

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

Library Alpha tested 84 synthetic enhancer designs containing motifs for seven hematopoietic TFs, selected TF pairs, and random-background controls in primary mouse HSPCs undergoing pan-myeloid differentiation. The table retains enhancer-positive barcode/cell observations and maps final cell-state labels where the integrated Seurat metadata matches.

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

Basal / Untreated; ex vivo HSPC differentiation for 6 days after lentiviral recovery with balanced CD55-positive and CD55-negative FACS enrichment

Lentiviral genomic integration with dual gRNA presence and GFP quantification barcodes plus a targeted 287-gene 5′ transcriptome panel. Cell states are the paper's final_annotation labels from the integrated Alpha/Beta Seurat object.

Processed data

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

Visible columns (36 of 36)

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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 · 36 definitions

study_id: Parent study identifier.
experiment_id: Child experiment identifier.
source_row_id: 1-based row number in the source Figshare RDS object before processing.
element_id: Stable tested construct identifier; PoC uses the source CRS, Alpha uses the design name, and Beta uses the LibGamma construct ID.
crs_id: Source construct/CRE identifier from the barcode-association data, when supplied.
design_name: Synthetic or endogenous enhancer design label.
sequence: DNA sequence of the tested enhancer construct, recovered from the source object or Additional file 4/Table S3.
guide_id: Presence-barcode/gRNA identifier.
gfp_id: Quantification-barcode/GFP identifier paired with the presence barcode.
cell_id: 10x single-cell barcode.
presence_umi: UMI count for the presence barcode; used to call construct presence.
activity_umi: UMI count for the GFP quantification barcode; direct single-cell enhancer activity measurement in the paper.
activity_log2p1: Derived log2(activity_umi + 1) convenience transform.
activity_detected: TRUE when activity_umi is greater than zero.
tf_1: Primary transcription factor motif identity, when annotated.
tf_2: Second transcription factor motif identity for paired designs, when annotated.
motif_affinity_1: Primary motif affinity/likelihood annotation from the source design.
motif_affinity_2: Second motif affinity/likelihood annotation from the source design.
motif_count: Number of motif repeats/sites in the design, when annotated.
orientation_1: Primary motif orientation.
orientation_2: Second motif orientation for paired designs.
spacer_bp: Spacer length in base pairs between motifs, when annotated.
design_replicate: Design replicate annotation from the source object.
control_for: Source control-target/paired-element annotation, when supplied.
control_class: Derived class such as synthetic, endogenous, positive_control, inert_control, or qc_failure_label.
is_endogenous: Whether the tested element is annotated as endogenous genomic sequence.
source_library: Internal source library/batch label from the deposited object.
sublibrary: Internal source sublibrary label, primarily populated for Library Beta.
task: Original task annotation from the deposited Beta object, when supplied.
n_gata: Original number of GATA motifs annotated in the deposited Beta object.
cell_state: Final cell-state annotation from the integrated Seurat object, when the cell barcode mapped exactly.
cell_cluster_sct2: Integrated Seurat cluster label at SCT_snn_res.2.
cell_nFeature_RNA: Number of detected RNA features for the cell in the supplied Seurat QC metadata.
cell_nCount_RNA: Total RNA UMI count for the cell in the supplied Seurat QC metadata.
presence_umi_threshold: Presence-barcode UMI threshold applied for this assay (3 for K562; 2 for HSPCs).
qc_pass: TRUE for every retained row; rows failing basic completeness or the paper's presence-barcode threshold were excluded.

Quality control

The deposited Seurat/count object had undergone the paper's feature/UMI cell QC and clustering. I retained complete observations with guide_count ≥2, the paper's HSPC presence threshold, and nonmissing GFP counts; zero GFP UMIs were retained. Cell-state and RNA QC fields were joined only on exact source cell keys.

Curation notes

The processed table contains 49,323 observations from 36,506 cells and all 84 Alpha design names; all source observations met the ≥2 guide-UMI threshold. Final cell-state labels were mapped for 49,030 observations using the supplied integrated Seurat object; unmatched cells remain blank rather than being inferred. Sequence fields agree with Additional file 4/Table S3/source annotations. Distinct guide/cell rows are retained as separate integrations.

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