A modified MPRAduo library tested native, swapped, scrambled, and spacer-edited noncanonical REST half-site arrangements in K562, with positive and negative controls. The assay measured reporter activity across the deposited analysis-level result set.
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
Episomal MPRAduo tested noncanonical REST-binding-site constructs with precise half-site orientations and spacer lengths, including wild-type and spacer-scrambled/edited sequences, paired with En02. Four biological replicates were analyzed; the deposited result table reports control/experimental means, effect sizes, test statistics, and FDR-adjusted p-values.
Processed data
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Visible columns (22 of 22)
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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 · 22 definitions
element_id
Unique source construct identifier, including enhancer and noncanonical silencer/control name.
enhancer_id
Benchmark activating element paired with the motif construct.
silencer_id
Noncanonical REST motif, spacer-edit, or control construct identifier.
variant_id
Source variant identifier when available; blank for this motif-edit library.
chromosome
Source chromosome field; blank when not reported for the motif construct.
position
Source position field; blank when not reported for the motif construct.
ref_allele
Source reference allele field; blank when not applicable.
alt_allele
Source alternate allele field; blank when not applicable.
tested_allele
Source allele label; blank when not applicable.
orientation
Source strand/orientation field; blank when not reported.
variant_window
Source motif-window field; blank when not applicable.
project
Construct class, including positive_controls, negative_controls, ND, cano_WT, nonc_WT, swapped, or spacer-scrambled variants.
haplotype
Source haplotype annotation, when available.
start
Source start coordinate or interval field, when available.
stop
Source stop coordinate or interval field, when available.
control_mean
Deposited analysis-level mean expression for the control/reference condition.
experimental_mean
Deposited analysis-level mean expression for the tested condition.
log2_fold_change
Deposited log2 reporter activity estimate.
log2_fold_change_se
Standard error of the deposited log2 reporter activity estimate.
test_statistic
Deposited statistical test statistic.
p_value
Deposited nominal p-value.
adjusted_p_value
Deposited multiple-testing-adjusted p-value.
Quality control
The deposited noncanonical result file is an analysis-level output and does not expose barcode-support or plasmid-DNA count columns. This package retained the 4,509 of 4,975 rows with complete log2 fold-change, standard error, test statistic, p-value, and adjusted p-value; incomplete result rows were excluded.
Curation notes
GEO series sample GSM6528576 is the noncanonical K562 RNA sample, while the separate series-level result file is the only deposited analysis table for this library. The table retains positive/negative controls and all construct classes with complete effect statistics; count-level QC cannot be independently reproduced from the available noncanonical file.