An episomal synSTARR-seq library varied eight consecutive nucleotides within a glucocorticoid receptor binding sequence half-site, nominally representing 65,536 synthetic variants. U2OS-GR cells were treated with 1 µM dexamethasone or 0.1% ethanol vehicle for 4 h in three biological replicates per condition; the released DESeq2 table contains the 33,689 variants passing the paper’s mean-count >100 filter.
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:0042
Reference genome
Not reported / not applicable
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
1 µM dexamethasone for 4 h versus 0.1% ethanol vehicle control
Synthetic STARR-seq (synSTARR-seq) used synthetic oligos cloned into an episomal human STARR-seq reporter downstream of a minimal promoter, so active inserts were quantified through self-transcribing reporter RNA. Five million U2OS-GR cells were nucleofected with 5 µg library DNA, treated the next day with 1 µM dexamethasone or 0.1% ethanol for 4 h, and sequenced using Illumina 50 bp paired-end reads. Reads were retained only when they exactly matched the expected synthetic insert length and nucleotide composition; duplicate reads were intentionally retained for quantitative sequence-level counting. DESeq2 compared dexamethasone and vehicle counts across three biological replicates per condition.
Processed data
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Visible columns (12 of 12)
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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 · 12 definitions
element_id
Unique package identifier for the synthetic half-site sequence.
library
Synthetic library label; GBS_half_site denotes the GR binding sequence half-site library.
sequence
Full 15 bp synthetic sequence analyzed by the released DESeq2 table.
variable_sequence
The eight randomized nucleotides in the half-site library (the source table’s kmer field).
fixed_context
The fixed 7 bp sequence immediately 5′ of the randomized segment.
base_mean
DESeq2 baseMean, the mean normalized read abundance across the analyzed samples.
log2_fold_change
DESeq2 log2 fold change for dexamethasone-treated versus ethanol-vehicle reporter RNA counts.
log2_fold_change_se
DESeq2 standard error for the log2 fold change.
test_statistic
DESeq2 Wald test statistic for the treatment contrast.
Package-derived call: significant_activation when adjusted_p_value < 0.01 and log2_fold_change > 0, significant_negative_effect when adjusted_p_value < 0.01 and log2_fold_change < 0, otherwise not_significant.
Quality control
The authors filtered reads to exact insert matches, retained duplicate reads, required a DESeq2 adjusted p-value cutoff of 0.01 for significance, and removed half-site variants with mean read count below 100 across all dexamethasone and vehicle experiments. Package QC additionally required a 15 bp A/C/G/T-only sequence with an 8 bp variable segment, unique sequence identifiers, finite baseMean/log2FoldChange/lfcSE/stat/pvalue/padj values, positive baseMean, p-value and adjusted p-value in [0,1], and nonnegative lfcSE. All 33,689 of 33,689 released rows passed these checks and were retained.
Curation notes
The ArrayExpress source file All_GBS_4h_DESeq2_with-pval_baseMean100.tab omits the leading sequence name from its header; conversion treated the first token of each data row as sequence and preserved the remaining seven source fields. CVCL:0042 is the parental human U2OS osteosarcoma line; the assayed U2OS-GR derivative stably expresses rat GRα and has no separate Cellosaurus accession identified. The table is synthetic rather than genome-coordinate based, so reference_genome and region_of_interest are null. The paper reports 1,696 significantly activated variants; apparent negative effects were not reproduced consistently in individual reporter validation and should be interpreted cautiously.