Triplicate STARR-seq RNA readouts were collected 24 hours after electroporation of the synthetic motif library into K562 cells; the shared plasmid library was sequenced in eight DNA replicates. The library tests 18 candidate motifs in controlled combinations of copy number, orientation, and order, with 113 tiled seq1305 positive-control elements.
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
hg19
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
The authors synthesized a 59,776-oligo library comprising synthetic constructs with one to three copies of nine novel motifs and nine curated TFBS, tested in forward and reverse orientations and in pair/triple permutations separated by 10 bp, plus 113 tiled 88-bp segments of the seq1305 positive-control enhancer. Inserts were cloned downstream of the core promoter in the hSTARR-seq_ORI reporter (Addgene #99296). K562 cells were transfected by Neon electroporation in triplicate and harvested after 24 hours. Ten-base UMIs were used for deduplication; DNA-library sequencing comprised eight replicates and RNA amplicon sequencing comprised three K562 replicates. CPM-normalized RNA/DNA log2 activity scores are reported, with the synthetic-background score subtracted for synthetic constructs.
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 · 67 definitions
element_id
Canonical oligo construct identifier from the GEO master count table; positive controls are numbered 1fwd-NA-NA through 113fwd-NA-NA.
cell_line
Cell line represented by this experiment; constant within this table.
reporter_oligo_sequence
Full 191-nt synthesized oligo sequence, including sequencing priming sites, partial Illumina adapters, and flanking restriction-site sequences.
assay_insert_sequence
The 88-nt assay insert between the flanking sequencing elements; this is the sequence tested by the STARR-seq reporter.
Construct class: motif_construct, synthetic_background, or positive_control.
motif_1
First motif or spacer in the oligo, in promoter-proximal order; blank for an unavailable positive-control motif field.
motif_1_orientation
Orientation of motif_1 relative to the template strand (fwd or rev).
motif_2
Second motif or spacer in the oligo; blank for an unavailable positive-control motif field.
motif_2_orientation
Orientation of motif_2 relative to the template strand (fwd or rev).
motif_3
Third motif or spacer in the oligo; blank for an unavailable positive-control motif field.
motif_3_orientation
Orientation of motif_3 relative to the template strand (fwd or rev).
num_nonspacer_motifs
Number of non-spacer motif entries in the three motif positions.
dna_library_size_rep1
Total UMI-deduplicated count used as the CPM denominator for DNA-library replicate 1.
dna_library_size_rep2
Total UMI-deduplicated count used as the CPM denominator for DNA-library replicate 2.
dna_library_size_rep3
Total UMI-deduplicated count used as the CPM denominator for DNA-library replicate 3.
dna_library_size_rep4
Total UMI-deduplicated count used as the CPM denominator for DNA-library replicate 4.
dna_library_size_rep5
Total UMI-deduplicated count used as the CPM denominator for DNA-library replicate 5.
dna_library_size_rep6
Total UMI-deduplicated count used as the CPM denominator for DNA-library replicate 6.
dna_library_size_rep7
Total UMI-deduplicated count used as the CPM denominator for DNA-library replicate 7.
dna_library_size_rep8
Total UMI-deduplicated count used as the CPM denominator for DNA-library replicate 8.
rna_library_size_rep1
Total UMI-deduplicated count used as the CPM denominator for RNA replicate 1 in this cell line.
rna_library_size_rep2
Total UMI-deduplicated count used as the CPM denominator for RNA replicate 2 in this cell line.
rna_library_size_rep3
Total UMI-deduplicated count used as the CPM denominator for RNA replicate 3 in this cell line.
dna_count_rep1
UMI-deduplicated plasmid-library DNA count for replicate 1.
dna_count_rep2
UMI-deduplicated plasmid-library DNA count for replicate 2.
dna_count_rep3
UMI-deduplicated plasmid-library DNA count for replicate 3.
dna_count_rep4
UMI-deduplicated plasmid-library DNA count for replicate 4.
dna_count_rep5
UMI-deduplicated plasmid-library DNA count for replicate 5.
dna_count_rep6
UMI-deduplicated plasmid-library DNA count for replicate 6.
dna_count_rep7
UMI-deduplicated plasmid-library DNA count for replicate 7.
dna_count_rep8
UMI-deduplicated plasmid-library DNA count for replicate 8.
dna_count_mean
Mean UMI-deduplicated DNA count across the eight DNA replicates.
dna_count_median
Median UMI-deduplicated DNA count across the eight DNA replicates.
dna_count_sd
Standard deviation of UMI-deduplicated DNA counts across the eight DNA replicates.
rna_count_rep1
UMI-deduplicated K562 RNA count for replicate 1.
rna_count_rep2
UMI-deduplicated K562 RNA count for replicate 2.
rna_count_rep3
UMI-deduplicated K562 RNA count for replicate 3.
rna_count_mean_nonzero
Mean K562 RNA count across nonzero RNA replicates.
rna_count_median_nonzero
Median K562 RNA count across nonzero RNA replicates.
rna_count_sd_nonzero
Standard deviation of K562 RNA counts across nonzero RNA replicates.
dna_cpm_rep1
CPM-normalized DNA count for DNA-library replicate 1.
dna_cpm_rep2
CPM-normalized DNA count for DNA-library replicate 2.
dna_cpm_rep3
CPM-normalized DNA count for DNA-library replicate 3.
dna_cpm_rep4
CPM-normalized DNA count for DNA-library replicate 4.
dna_cpm_rep5
CPM-normalized DNA count for DNA-library replicate 5.
dna_cpm_rep6
CPM-normalized DNA count for DNA-library replicate 6.
dna_cpm_rep7
CPM-normalized DNA count for DNA-library replicate 7.
dna_cpm_rep8
CPM-normalized DNA count for DNA-library replicate 8.
dna_cpm_mean
Mean DNA CPM across the eight replicates, used as the collapsed DNA denominator for activity scores.
dna_cpm_median
Median DNA CPM across the eight DNA replicates.
dna_cpm_sd
Standard deviation of DNA CPM across the eight DNA replicates.
rna_cpm_rep1
CPM-normalized K562 RNA count for replicate 1.
rna_cpm_rep2
CPM-normalized K562 RNA count for replicate 2.
rna_cpm_rep3
CPM-normalized K562 RNA count for replicate 3.
rna_cpm_mean_nonzero
Mean K562 RNA CPM across nonzero RNA replicates.
rna_cpm_median_nonzero
Median K562 RNA CPM across nonzero RNA replicates.
rna_cpm_sd_nonzero
Standard deviation of K562 RNA CPM across nonzero RNA replicates.
activity_log2_rna_dna_rep1
Unadjusted log2(RNA CPM / collapsed DNA CPM) activity score for K562 RNA replicate 1.
activity_log2_rna_dna_rep2
Unadjusted log2(RNA CPM / collapsed DNA CPM) activity score for K562 RNA replicate 2.
activity_log2_rna_dna_rep3
Unadjusted log2(RNA CPM / collapsed DNA CPM) activity score for K562 RNA replicate 3.
background_adjusted_activity_log2_rna_dna_rep1
Activity score for K562 RNA replicate 1 after subtracting the empty synthetic-background score; blank where the source did not calculate an adjusted score.
background_adjusted_activity_log2_rna_dna_rep2
Activity score for K562 RNA replicate 2 after subtracting the empty synthetic-background score; blank where the source did not calculate an adjusted score.
background_adjusted_activity_log2_rna_dna_rep3
Activity score for K562 RNA replicate 3 after subtracting the empty synthetic-background score; blank where the source did not calculate an adjusted score.
activity_log2_rna_dna_mean_nonzero
Mean unadjusted activity score across available nonzero RNA replicates.
background_adjusted_activity_mean_nonzero
Mean background-adjusted activity score across available nonzero adjusted replicates; blank for positive controls and the empty background control.
rna_positive_replicates
Number of the three K562 RNA replicates with a positive UMI-deduplicated count.
Quality control
The deposited source pipeline extracted 10-bp UMIs (UMI-tools v1.1.4), removed adapters with cutadapt v4.7 (quality cutoff 10; minimum length 80), mapped reads with Bowtie2 v2.5.3, and retained primary, properly paired alignments with perfect matches (NM:0). Counts were UMI-deduplicated. For this package, rows were retained only when all eight DNA UMI counts were at least 10 and at least two of the three K562 RNA UMI counts were greater than zero, following the article's explicit activity-score filter. The resulting table contains 50,733 rows; rows failing either criterion were excluded.
Curation notes
The deposited GEO master file contains 50,764 rows per cell line, while the article narrative reports 50,634 and 50,650 activity-score oligos; this package uses the deposited file and the explicit count filters, yielding 50,733 K562 rows. DNA-library measurements are shared across both cell-line tables. The source background-adjusted activity fields are populated for synthetic motif constructs; positive-control rows retain unadjusted activity scores and have blank adjusted fields because no synthetic-background subtraction was defined for them. K562 RNA replicate correlation was high in the paper, while the Jurkat replicate correlation was lower.