dpSTR deep-perturbation MPRA in HEK293T
Systematic evaluation of the impact of promoter proximal short tandem repeats on expressionDeep-perturbation library testing repeat copy number, alternate repeat-unit sequence, random controls, and orientation across 300 candidate promoter-proximal STR loci in HEK293T cells.
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.
Perturbation & assay details
Basal / Untreated
The dpSTR library used 230-nt randomly barcoded oligos in the same pGL4.23-derived minimal-promoter GFP reporter and three biological replicates, with systematic repeat-unit and copy-number perturbations including random and GC-matched controls.
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 · 52 definitions
- variant_id
- Deposited STR variant/allele identifier used in the GEO ratio file.
- locus_id
- Numeric Human_STR identifier for the underlying promoter-proximal STR locus.
- regression_group
- Locus-level regression group from the deposited regression table; hSTR is locus|motif and dpSTR is the source locus string including original/current motif and orientation code.
- original_repeat_unit
- Reference/original repeat unit represented in the source design; for dpSTR this is the source orientation used in the regression group.
- tested_repeat_unit
- Repeat unit or sequence category tested in the reporter variant.
- variant_category
- hSTR allele label (m5, ref, p3, or p5) or dpSTR current perturbation category (for example original, ref, a repeat motif, random, or randomMatchedGC).
- perturbation_type
- Interpretation of the dpSTR category: hSTR internal control, perfect repeat unit, alternate repeat unit, random sequence, or GC-matched random sequence; blank for hSTR.
- orientation_code
- Source dpSTR orientation code (0 or 1); both orientations were designed, and the code is retained without imposing a genomic-strand interpretation. Blank for hSTR.
- copy_number_delta
- hSTR requested copy-number change relative to the hg38 reference encoded by the allele label; blank for dpSTR.
- repeat_copy_number
- dpSTR designed repeat copy number encoded by the pN suffix; blank for hSTR because its m/p labels are relative and the smallest allele can be censored at zero.
- reference_repeat_copies
- hSTR reference repeat count nrep_ref from the author design table; blank for dpSTR.
- reference_repeat_unit_bed
- Reference motif from the dpSTR BED annotation; it may be the reverse complement of the sequence-normalized original_repeat_unit. Blank for hSTR.
- str_chrom
- Chromosome of the STR locus from the author annotation.
- str_start_source
- STR interval start as reported by the retained author annotation (BED-like source coordinate for dpSTR).
- str_end_source
- STR interval end as reported by the retained author annotation.
- tss_chrom
- Chromosome of the associated transcription start site from the hSTR TSS/STR annotation; blank for dpSTR.
- tss_start_source
- TSS start as reported by the hSTR TSS/STR annotation; blank for dpSTR.
- tss_end_source
- TSS end as reported by the hSTR TSS/STR annotation; blank for dpSTR.
- gene_id
- Associated Ensembl gene identifier(s) from the hSTR TSS/STR annotation, semicolon-separated when multiple; blank for dpSTR.
- gene_strand
- Associated gene strand from the hSTR TSS/STR annotation; blank for dpSTR.
- n_barcodes_raw
- Number of source barcode rows observed for the variant across all three replicates before dpSTR outlier trimming.
- n_barcodes_qc
- Number of unique barcode observations retained after the experiment-specific QC trimming.
- cdna_reads_qc
- Total retained cDNA/RNA barcode reads across replicates.
- gdna_reads_qc
- Total retained plasmid-DNA barcode reads across replicates.
- rna_dna_ratio_pooled
- Pooled activity score calculated as total retained cDNA reads divided by total retained gDNA reads.
- log2_rna_dna_ratio_pooled
- Base-2 logarithm of the pooled RNA/DNA activity score.
- mean_replicate_ratio
- Arithmetic mean of the three replicate-level RNA/DNA ratios available for the variant.
- sd_replicate_ratio
- Sample standard deviation of the available replicate-level RNA/DNA ratios.
- n_replicates
- Number of replicates with retained data for the variant.
- n_barcodes_raw_rep1
- Source barcode-row count for replicate 1 before dpSTR outlier trimming.
- n_barcodes_qc_rep1
- Unique barcode count retained for replicate 1.
- cdna_reads_qc_rep1
- Retained cDNA/RNA reads for replicate 1.
- gdna_reads_qc_rep1
- Retained plasmid-DNA reads for replicate 1.
- rna_dna_ratio_rep1
- Retained cDNA/gDNA ratio for replicate 1, calculated from summed reads.
- n_barcodes_raw_rep2
- Source barcode-row count for replicate 2 before dpSTR outlier trimming.
- n_barcodes_qc_rep2
- Unique barcode count retained for replicate 2.
- cdna_reads_qc_rep2
- Retained cDNA/RNA reads for replicate 2.
- gdna_reads_qc_rep2
- Retained plasmid-DNA reads for replicate 2.
- rna_dna_ratio_rep2
- Retained cDNA/gDNA ratio for replicate 2, calculated from summed reads.
- n_barcodes_raw_rep3
- Source barcode-row count for replicate 3 before dpSTR outlier trimming.
- n_barcodes_qc_rep3
- Unique barcode count retained for replicate 3.
- cdna_reads_qc_rep3
- Retained cDNA/RNA reads for replicate 3.
- gdna_reads_qc_rep3
- Retained plasmid-DNA reads for replicate 3.
- rna_dna_ratio_rep3
- Retained cDNA/gDNA ratio for replicate 3, calculated from summed reads.
- regression_r
- Pearson correlation coefficient from the author-supplied locus-level regression output.
- regression_beta_0
- Intercept (beta_0) from the author-supplied RNA/DNA ratio regression.
- regression_beta_1
- Copy-number slope (beta_1) from the author-supplied regression; it is repeated on each variant row in the same regression group.
- regression_p_value
- Author-supplied p_value_1 for the copy-number slope.
- regression_padj
- Author-supplied multiple-testing-adjusted p-value when deposited (hSTR); blank because the dpSTR regression files do not provide this field.
- computed_bh_p_value
- Benjamini–Hochberg adjustment computed during ingestion over the supplied regression p_value_1 values for this experiment; included separately from the author-supplied field.
- qc_pass
- Always true in this filtered table; indicates that the row passed the documented barcode/read and regression-group minimums.
- oligo_sequence
- Full synthesized oligo sequence from the retained author design reference when an exact design record could be matched; blank for a small number of dpSTR variants absent from the current GitHub FASTA.
Quality control
Quality-control details were not reported in the metadata.
Curation notes
The processed table contains 49,457 retained variant rows across 4,843 locus/motif/orientation regression groups. Seventy-six retained rows had no exact match in the current author GitHub FASTA and therefore have a blank oligo_sequence; their deposited expression measurements are retained.