Experiment / E8CQY5QR0Promoter / Core Promoter MPRA

POOL2 pMPRA1 HepG2 MPRA

High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity

approximately 119,000 oligo single-nucleotide deletion library spanning selected lncRNA promoters, nearby mRNA promoters, and enhancers was assayed in HepG2 cells using the minimal-promoter GFP reporter (pMPRA1). RNA barcode output was normalized to matched input DNA across 8 replicate(s).

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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:0027
Reference genome: hg19
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Transient episomal plasmid MPRA with 114-bp inserts, 11-nt barcodes, GFP RNA readout, and input-DNA normalization. POOL2 includes reference/flipped controls and single-nucleotide deletions across two overlapping tiles per selected source locus where applicable.

Processed data

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Visible columns (96 of 96)

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Column dictionary · 96 definitions

element_id: Stable processed element identifier;
unique_id: Original study design unique_id;
element_sequence: Reporter insert sequence;
sequence_role: Interpretation of the oligo type;
oligo_type: Original design category;
seq_name: seq name
tile_name: tile name
chromosome: chromosome
locus_start: locus start
locus_end: locus end
strand: strand
tile_start: tile start
tile_end: tile end
tile_number: tile number
local_start: local start
local_end: local end
snp_id: snp id
gene_id: gene id
gene_name: gene name
gene_type: gene type
biotype: biotype
tss_id: tss id
tss_description: tss description
enhancer_id: enhancer id
mean_cage_exp_all: mean cage exp all
reference_element_id: Stable identifier of the matched reference element;
variant_type: variant type
variant_id: variant id
variant_position_1based: variant position 1based
reference_sequence_base: reference sequence base
alternate_sequence_base: alternate sequence base
deleted_base: deleted base
n_barcodes_dna_ge5: n barcodes dna ge5
n_barcodes_activity_min: n barcodes activity min
n_barcodes_activity_median: n barcodes activity median
n_barcodes_activity_max: n barcodes activity max
n_replicates_with_activity: n replicates with activity
activity_log2_rep1: Per-replicate quantile-normalized log2 RNA/DNA activity recomputed from GEO barcode counts.
activity_log2_rep2: Per-replicate quantile-normalized log2 RNA/DNA activity recomputed from GEO barcode counts.
activity_log2_rep3: Per-replicate quantile-normalized log2 RNA/DNA activity recomputed from GEO barcode counts.
activity_log2_rep4: Per-replicate quantile-normalized log2 RNA/DNA activity recomputed from GEO barcode counts.
activity_log2_rep5: Per-replicate quantile-normalized log2 RNA/DNA activity recomputed from GEO barcode counts.
activity_log2_rep6: Per-replicate quantile-normalized log2 RNA/DNA activity recomputed from GEO barcode counts.
activity_log2_rep7: Per-replicate quantile-normalized log2 RNA/DNA activity recomputed from GEO barcode counts.
activity_log2_rep8: Per-replicate quantile-normalized log2 RNA/DNA activity recomputed from GEO barcode counts.
n_barcodes_activity_rep1: RNA-qualified barcode count contributing to the element median.
n_barcodes_activity_rep2: RNA-qualified barcode count contributing to the element median.
n_barcodes_activity_rep3: RNA-qualified barcode count contributing to the element median.
n_barcodes_activity_rep4: RNA-qualified barcode count contributing to the element median.
n_barcodes_activity_rep5: RNA-qualified barcode count contributing to the element median.
n_barcodes_activity_rep6: RNA-qualified barcode count contributing to the element median.
n_barcodes_activity_rep7: RNA-qualified barcode count contributing to the element median.
n_barcodes_activity_rep8: RNA-qualified barcode count contributing to the element median.
activity_log2fc_vs_random_rep1: Author-provided per-replicate log2 fold change versus RANDOM controls.
activity_log2fc_vs_random_rep2: Author-provided per-replicate log2 fold change versus RANDOM controls.
activity_log2fc_vs_random_rep3: Author-provided per-replicate log2 fold change versus RANDOM controls.
activity_log2fc_vs_random_rep4: Author-provided per-replicate log2 fold change versus RANDOM controls.
activity_log2fc_vs_random_rep5: Author-provided per-replicate log2 fold change versus RANDOM controls.
activity_log2fc_vs_random_rep6: Author-provided per-replicate log2 fold change versus RANDOM controls.
activity_log2fc_vs_random_rep7: Author-provided per-replicate log2 fold change versus RANDOM controls.
activity_log2fc_vs_random_rep8: Author-provided per-replicate log2 fold change versus RANDOM controls.
activity_padj_vs_random_rep1: Author-provided per-replicate adjusted p-value versus RANDOM controls.
activity_padj_vs_random_rep2: Author-provided per-replicate adjusted p-value versus RANDOM controls.
activity_padj_vs_random_rep3: Author-provided per-replicate adjusted p-value versus RANDOM controls.
activity_padj_vs_random_rep4: Author-provided per-replicate adjusted p-value versus RANDOM controls.
activity_padj_vs_random_rep5: Author-provided per-replicate adjusted p-value versus RANDOM controls.
activity_padj_vs_random_rep6: Author-provided per-replicate adjusted p-value versus RANDOM controls.
activity_padj_vs_random_rep7: Author-provided per-replicate adjusted p-value versus RANDOM controls.
activity_padj_vs_random_rep8: Author-provided per-replicate adjusted p-value versus RANDOM controls.
activity_log2_mean: Mean per-replicate quantile-normalized log2 RNA/DNA activity;
activity_log2_median: Median per-replicate quantile-normalized log2 RNA/DNA activity;
activity_combined_padj: Author-provided Bonferroni-adjusted combined p-value versus RANDOM controls;
activity_combined_significance: activity combined significance
activity_combined_class: Author-provided activity class versus RANDOM controls;
activity_downsampled_significance: activity downsampled significance
activity_downsampled_class: activity downsampled class
variant_effect_log2fc_rep1: Recomputed tested-element minus matched-reference log2 activity.
variant_effect_log2fc_rep2: Recomputed tested-element minus matched-reference log2 activity.
variant_effect_log2fc_rep3: Recomputed tested-element minus matched-reference log2 activity.
variant_effect_log2fc_rep4: Recomputed tested-element minus matched-reference log2 activity.
variant_effect_log2fc_rep5: Recomputed tested-element minus matched-reference log2 activity.
variant_effect_log2fc_rep6: Recomputed tested-element minus matched-reference log2 activity.
variant_effect_log2fc_rep7: Recomputed tested-element minus matched-reference log2 activity.
variant_effect_log2fc_rep8: Recomputed tested-element minus matched-reference log2 activity.
variant_effect_log2fc_mean: Mean tested-element minus reference-element activity across replicates;
variant_effect_published_log2fc: Published SNP/deletion effect size;
variant_padj: Published adjusted SNP/deletion p-value;
variant_significance: variant significance
variant_downsampled_significance: variant downsampled significance
deletion_effect_sd: deletion effect sd
deletion_effect_se: deletion effect se
reference_activity_log2fc_vs_random: reference activity log2fc vs random
reference_activity_combined_padj: reference activity combined padj
reference_activity_class: reference activity class
qc_pass: True for rows retained after documented QC;
source: Data provenance.

Quality control

Retained input-DNA barcodes with >=5 reads and RNA observations with >5 reads, following the released author implementation. The element inclusion set was based on HepG2 DNA coverage for POOL2; each condition table additionally requires at least one condition-specific DNA-qualified barcode and one RNA-qualified barcode. Non-control elements were required to have >=3 DNA-qualified barcodes in that library-level inclusion set, while available RANDOM/SCRAMBLED controls were retained. Added pseudocount 1, CPM-normalized DNA/RNA, calculated RNA/DNA log2 activity, median-centered and quantile-normalized replicates, then collapsed barcode activities by element median. Author significance fields use Mann–Whitney tests versus RANDOM controls, Stouffer combination, and Bonferroni correction. The article prose says five or more RNA reads, but the released implementation uses a strict >5 comparison.

Curation notes

GEO count files: GSM3304520_POOL2_pMPRA1_HepG2_rep1_COUNTS.txt.gz, GSM3304521_POOL2_pMPRA1_HepG2_rep2_COUNTS.txt.gz, GSM3304522_POOL2_pMPRA1_HepG2_rep3_COUNTS.txt.gz, GSM3304523_POOL2_pMPRA1_HepG2_rep4_COUNTS.txt.gz, GSM3304524_POOL2_pMPRA1_HepG2_rep5_COUNTS.txt.gz, GSM3304525_POOL2_pMPRA1_HepG2_rep6_COUNTS.txt.gz, GSM3304526_POOL2_pMPRA1_HepG2_rep7_COUNTS.txt.gz, GSM3304527_POOL2_pMPRA1_HepG2_rep8_COUNTS.txt.gz. Raw GEO replicate order is used in activity_log2_rep columns; the authors’ HepG2 tables label corresponding replicates rna_3 onward because rna_1/rna_2 were pilot samples. Rows retained: 8149; DNA-qualified barcode rows: 110967. Coordinates use hg19/FANTOM5/Gencode-era indexes; no FASTQs are included.

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