Experiment / E69QTZCRTSingle-Cell MPRA (scMPRA / sc-lentiMPRA)

Library PoC sc-lentiMPRA in K562 cells

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

The proof-of-concept library of synthetic, endogenous, and control CREs was delivered by lentivirus to dCas9-BFP-KRAB K562 cells. The table contains enhancer-positive single-cell observations with presence-barcode and GFP quantification-barcode UMIs.

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: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:0004
Reference genome: GRCh38
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated; 20 h lentiviral infection followed by 7 d recovery

Lentiviral genomic integration with separate constitutive gRNA presence barcode and GFP 5′-UTR quantification barcode, read out with a custom 10x Genomics 5′ targeted transcriptome workflow. The PoC library contains 432 designed elements; this experiment was performed in K562-dCas9-BFP-KRAB cells.

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 cell-level QC. I retained rows with complete guide/GFP/cell fields, nonmissing GFP counts, and presence-barcode guide_count ≥3, the paper's K562 threshold. Zero GFP UMIs were retained as valid inactive observations.

Curation notes

The processed table contains 28,926 observations from 5,380 cells and 428 observed elements; all source observations met the ≥3 guide-UMI threshold. The 428 PoC design sequences were recovered by normalized design-name matching to Additional file 4/Table S3. K562 RNA feature/UMI QC fields are retained from the source object. Distinct guide/cell rows are retained because they represent separate barcode integrations.

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