Experiment / E3D5UKUNPIntegrated lentiMPRA

K562 integrated lenti-TSS-MPRA, short insert library

Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation

200-nt construct containing a 153-bp genomic insert library was assayed in K562 cells under basal conditions using integrated lentimpra. The table summarizes element-level reporter activity, barcode-supported RNA/DNA ratios, nucleotide-resolution TSS profiles, and WIP comparison to the paired endogenous csRNA-seq profile.

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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: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated K562 cells

Lentiviral TSS-MPRA in K562 cells using the pLenti-TSS-MPRA reporter backbone. The short library contains 153-bp human genomic inserts with four barcode replicates; pooled lentivirus was transduced and integrated before RNA/DNA collection. RNA 5-prime ends report nucleotide-resolution initiation and barcode DNA counts provide input normalization.

Processed data

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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 · 47 definitions

element_id: Unique tested sequence identifier from the GEO library annotation workbook, with barcode suffix removed.
design_category: Sequence design class inferred from the library identifier: random regulatory element, motif mutation/control, GWAS/SNP allele construct, or splice-donor construct.
variant_id: dbSNP rs identifier parsed from the element identifier or annotation; blank for constructs without an rs identifier.
chromosome: Chromosome reported in the GEO library annotation workbook.
start_grch38: Genomic start coordinate reported in the GEO hg38 annotation workbook; source coordinate convention is preserved.
end_grch38: Genomic end coordinate reported in the GEO hg38 annotation workbook; source coordinate convention is preserved.
strand: Genomic strand reported for the tested sequence.
tss_genomic_position: Main endogenous TSS coordinate parsed from the annotation description.
tss_offset_in_insert_0based: Zero-based position of the annotated main TSS within the genomic insert, parsed from tssOffset.
sequence: Genomic sequence cloned into the reporter, excluding the barcode and cloning arms.
sequence_length: Length in nucleotides of the genomic sequence column.
full_construct_length: Length in nucleotides of the complete synthesized insert construct, including barcode and cloning/primer arms.
annotation_desc: Original compact annotation string containing annotated TSS, motif, mutation, and interval information.
barcode_ids: JSON array of barcode replicate labels retained after DNA-support and barcode-outlier filtering.
n_barcodes_used_rep1: Number of retained barcode replicates with positive DNA abundance in biological replicate 1.
n_barcodes_used_rep2: Number of retained barcode replicates with positive DNA abundance in biological replicate 2.
n_positive_rna_barcodes_rep1: Number of retained barcode replicates with positive RNA abundance in biological replicate 1.
n_positive_rna_barcodes_rep2: Number of retained barcode replicates with positive RNA abundance in biological replicate 2.
n_barcode_outliers_rep1: Number of barcode replicates excluded in biological replicate 1 by the paper-inspired three-global-SD activity outlier rule.
n_barcode_outliers_rep2: Number of barcode replicates excluded in biological replicate 2 by the paper-inspired three-global-SD activity outlier rule.
rna_count_sum_rep1: Sum of released RNA barcode abundances for retained barcodes in biological replicate 1.
dna_count_sum_rep1: Sum of released DNA barcode abundances for retained barcodes in biological replicate 1.
rna_count_sum_rep2: Sum of released RNA barcode abundances for retained barcodes in biological replicate 2.
dna_count_sum_rep2: Sum of released DNA barcode abundances for retained barcodes in biological replicate 2.
rna_cpm_sum_rep1: Retained RNA abundance in counts per million using the complete released RNA block total for biological replicate 1.
dna_cpm_sum_rep1: Retained DNA abundance in counts per million using the complete released DNA block total for biological replicate 1.
rna_cpm_sum_rep2: Retained RNA abundance in counts per million using the complete released RNA block total for biological replicate 2.
dna_cpm_sum_rep2: Retained DNA abundance in counts per million using the complete released DNA block total for biological replicate 2.
activity_log2_rna_dna_rep1: Log2 of CPM-normalized RNA/DNA activity for biological replicate 1.
activity_log2_rna_dna_rep2: Log2 of CPM-normalized RNA/DNA activity for biological replicate 2.
activity_log2_rna_dna_mean: Mean of the two biological-replicate log2 RNA/DNA activity scores.
activity_log2_rna_dna_rep2_minus_rep1: Biological replicate 2 minus replicate 1 log2 RNA/DNA activity score.
activity_rna_dna_ratio_geometric_mean: Geometric mean of the two biological-replicate CPM-normalized RNA/DNA activity ratios.
tss_dominant_position: One-based position within the full synthesized construct with the highest mean MPRA initiation frequency.
tss_dominant_offset_bp: Dominant MPRA initiation position relative to the annotated endogenous TSS; negative values are upstream.
tss_dominant_fraction: Mean MPRA initiation frequency at the dominant position.
tss_profile_entropy_bits: Shannon entropy in bits of the mean normalized MPRA TSS profile; larger values indicate a broader profile.
tss_profile_replicate_pearson: Pearson correlation between the two biological-replicate mean MPRA TSS profiles.
wip_to_csrna_rep1: Wishbone WIP dissimilarity score between MPRA biological replicate 1 and the paired endogenous csRNA-seq profile; lower values indicate greater similarity.
wip_to_csrna_rep2: Wishbone WIP dissimilarity score between MPRA biological replicate 2 and the paired endogenous csRNA-seq profile; lower values indicate greater similarity.
wip_to_csrna_mean: Mean of the two MPRA-to-endogenous csRNA-seq WIP dissimilarity scores.
tss_profile_rep1: JSON array of the biological-replicate-1 mean normalized MPRA TSS frequencies for full-construct positions 1..N.
tss_profile_rep2: JSON array of the biological-replicate-2 mean normalized MPRA TSS frequencies for full-construct positions 1..N.
tss_profile_mean: JSON array of the mean normalized MPRA TSS frequencies for full-construct positions 1..N.
csrna_profile_rep1: JSON array of the paired endogenous csRNA-seq normalized TSS frequencies for positions 1..N, included as the paper's ground-truth reference profile.
csrna_profile_rep2: JSON array of the second paired endogenous csRNA-seq normalized TSS frequencies for positions 1..N.
qc_pass: True for every exported row; only element groups passing the documented barcode and DNA-support QC are present.

Quality control

The authors' released GEO quantification contains per-barcode TPM-transformed, sum-to-one TSS profiles and RNA/DNA barcode abundances; the paper reports high RNA/DNA replicate reproducibility and describes a three-standard-deviation barcode-replicate outlier rule. For this package, barcode rows with non-positive DNA abundance were excluded, barcode activity outliers at or beyond three global residual standard deviations from their element median were excluded, and an element was exported only when at least two retained barcodes had positive DNA in each biological replicate and at least one retained barcode had positive RNA in each replicate. 495 of 499 element groups passed these filters.

Curation notes

The corresponding GEO norm.quant file stores four equal blocks: MPRA RNA/DNA replicate 1, MPRA RNA/DNA replicate 2, endogenous csRNA-seq replicate 1, and endogenous csRNA-seq replicate 2. Only the first two blocks are treated as reporter measurements here; the last two are retained as paired endogenous reference profiles for WIP scoring. Element activity is recomputed from released barcode counts as log2(CPM RNA / CPM DNA), while TSS profiles use the released position-normalized values. The study also tested a small set of 450-, 700-, and 950-bp constructs, but no separate element-level quantification table for those targeted constructs was released in the GEO series; they are therefore not represented as standalone child experiments.

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