dpSTR deep-perturbation MPRA in HeLa S3 RNase H1 wild-type cells
Systematic evaluation of the impact of promoter proximal short tandem repeats on expressionDeep-perturbation dpSTR library assayed in HeLa S3 cells under the RNase H1 wild-type/control condition.
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
RNase H1 wild-type / control
The same 230-nt random-barcode pGL4.23-derived minimal-promoter GFP reporter and three-replicate RNA/DNA readout were used in HeLa S3 cells; the comparator condition is the parental RNase H1 wild-type state.
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 48,001 retained variant rows across 4,901 locus/motif/orientation regression groups. Eighty-three retained rows had no exact match in the current author GitHub FASTA and therefore have a blank oligo_sequence. CVCL:0058 is the parent HeLa S3 accession; the wild-type and CRISPRi derivatives were not assigned separate Cellosaurus accessions.