A pooled episomal MPRA tested 1,305 human pancreatic-islet CAGE-derived 198-bp transcription-start-site fragments in four reporter configurations: human INS or synthetic SCP1 promoter, each with the insert upstream or downstream of the promoter. The library was electroporated into INS-1 832/13 rat insulinoma cells; three biological RNA replicates and one plasmid-DNA input were quantified by barcode sequencing.
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
NCBITaxon:10116
Taxonomy ID
NCBITaxon:10116
Biosample
CVCL:7226
Reference genome
hg19
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Basal / Untreated
Episomal STARR-seq-backbone plasmids carried GFP and 16-bp random barcodes. Each 198-bp forward-strand insert was tested with the human INS promoter or SCP1 promoter in upstream and downstream positions; the inserts were derived from CAGE tag clusters identified across 71 human pancreatic-islet samples. RNA barcode abundance was compared with plasmid-DNA barcode abundance using MPRAnalyze, with the assay performed 24 hours after electroporation.
Processed data
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Column dictionary · 58 definitions
element_id
GEO refname identifying the tested TSS fragment, encoded as TCs_chr_start_end.
chrom
Chromosome from the hg19 fragment coordinate.
start
0-based fragment start coordinate from GEO refname.
end
0-based half-open fragment end coordinate from GEO refname.
fragment_length_bp
Fragment length in base pairs, calculated as end minus start; expected to be 198.
reference_genome
Reference genome assembly used for the deposited coordinates (hg19).
ins_upstream_barcode_count
Number of retained barcodes for the INS-promoter upstream configuration.
ins_upstream_dna_count
Sum of plasmid-input DNA counts across retained INS-upstream barcodes.
ins_upstream_rna_rep1_count
Sum of RNA barcode counts in biological replicate 1 for INS-upstream barcodes.
ins_upstream_rna_rep2_count
Sum of RNA barcode counts in biological replicate 2 for INS-upstream barcodes.
ins_upstream_rna_rep3_count
Sum of RNA barcode counts in biological replicate 3 for INS-upstream barcodes.
ins_upstream_activity_log2_rep1
Library-size-normalized log2(RNA/DNA) activity for INS-upstream in RNA replicate 1; count pseudocount 1.
ins_upstream_activity_log2_rep2
Library-size-normalized log2(RNA/DNA) activity for INS-upstream in RNA replicate 2; count pseudocount 1.
ins_upstream_activity_log2_rep3
Library-size-normalized log2(RNA/DNA) activity for INS-upstream in RNA replicate 3; count pseudocount 1.
ins_upstream_activity_log2_mean
Mean of the three INS-upstream replicate activity scores.
ins_upstream_activity_log2_sd
Sample standard deviation of the three INS-upstream replicate activity scores.
ins_upstream_activity_log2_se
Standard error of the three INS-upstream replicate activity scores.
ins_upstream_status_summary
Semicolon-delimited counts of GEO status labels among retained INS-upstream barcodes; not used for filtering.
ins_downstream_barcode_count
Number of retained barcodes for the INS-promoter downstream configuration.
ins_downstream_dna_count
Sum of plasmid-input DNA counts across retained INS-downstream barcodes.
ins_downstream_rna_rep1_count
Sum of RNA barcode counts in biological replicate 1 for INS-downstream barcodes.
ins_downstream_rna_rep2_count
Sum of RNA barcode counts in biological replicate 2 for INS-downstream barcodes.
ins_downstream_rna_rep3_count
Sum of RNA barcode counts in biological replicate 3 for INS-downstream barcodes.
ins_downstream_activity_log2_rep1
Library-size-normalized log2(RNA/DNA) activity for INS-downstream in RNA replicate 1; count pseudocount 1.
ins_downstream_activity_log2_rep2
Library-size-normalized log2(RNA/DNA) activity for INS-downstream in RNA replicate 2; count pseudocount 1.
ins_downstream_activity_log2_rep3
Library-size-normalized log2(RNA/DNA) activity for INS-downstream in RNA replicate 3; count pseudocount 1.
ins_downstream_activity_log2_mean
Mean of the three INS-downstream replicate activity scores.
ins_downstream_activity_log2_sd
Sample standard deviation of the three INS-downstream replicate activity scores.
ins_downstream_activity_log2_se
Standard error of the three INS-downstream replicate activity scores.
ins_downstream_status_summary
Semicolon-delimited counts of GEO status labels among retained INS-downstream barcodes; not used for filtering.
scp1_upstream_barcode_count
Number of retained barcodes for the SCP1-promoter upstream configuration.
scp1_upstream_dna_count
Sum of plasmid-input DNA counts across retained SCP1-upstream barcodes.
scp1_upstream_rna_rep1_count
Sum of RNA barcode counts in biological replicate 1 for SCP1-upstream barcodes.
scp1_upstream_rna_rep2_count
Sum of RNA barcode counts in biological replicate 2 for SCP1-upstream barcodes.
scp1_upstream_rna_rep3_count
Sum of RNA barcode counts in biological replicate 3 for SCP1-upstream barcodes.
scp1_upstream_activity_log2_rep1
Library-size-normalized log2(RNA/DNA) activity for SCP1-upstream in RNA replicate 1; count pseudocount 1.
scp1_upstream_activity_log2_rep2
Library-size-normalized log2(RNA/DNA) activity for SCP1-upstream in RNA replicate 2; count pseudocount 1.
scp1_upstream_activity_log2_rep3
Library-size-normalized log2(RNA/DNA) activity for SCP1-upstream in RNA replicate 3; count pseudocount 1.
scp1_upstream_activity_log2_mean
Mean of the three SCP1-upstream replicate activity scores.
scp1_upstream_activity_log2_sd
Sample standard deviation of the three SCP1-upstream replicate activity scores.
scp1_upstream_activity_log2_se
Standard error of the three SCP1-upstream replicate activity scores.
scp1_upstream_status_summary
Semicolon-delimited counts of GEO status labels among retained SCP1-upstream barcodes; not used for filtering.
scp1_downstream_barcode_count
Number of retained barcodes for the SCP1-promoter downstream configuration.
scp1_downstream_dna_count
Sum of plasmid-input DNA counts across retained SCP1-downstream barcodes.
scp1_downstream_rna_rep1_count
Sum of RNA barcode counts in biological replicate 1 for SCP1-downstream barcodes.
scp1_downstream_rna_rep2_count
Sum of RNA barcode counts in biological replicate 2 for SCP1-downstream barcodes.
scp1_downstream_rna_rep3_count
Sum of RNA barcode counts in biological replicate 3 for SCP1-downstream barcodes.
scp1_downstream_activity_log2_rep1
Library-size-normalized log2(RNA/DNA) activity for SCP1-downstream in RNA replicate 1; count pseudocount 1.
scp1_downstream_activity_log2_rep2
Library-size-normalized log2(RNA/DNA) activity for SCP1-downstream in RNA replicate 2; count pseudocount 1.
scp1_downstream_activity_log2_rep3
Library-size-normalized log2(RNA/DNA) activity for SCP1-downstream in RNA replicate 3; count pseudocount 1.
scp1_downstream_activity_log2_mean
Mean of the three SCP1-downstream replicate activity scores.
scp1_downstream_activity_log2_sd
Sample standard deviation of the three SCP1-downstream replicate activity scores.
scp1_downstream_activity_log2_se
Standard error of the three SCP1-downstream replicate activity scores.
scp1_downstream_status_summary
Semicolon-delimited counts of GEO status labels among retained SCP1-downstream barcodes; not used for filtering.
ins_position_effect_log2_up_minus_down
INS promoter position contrast: INS-upstream mean activity minus INS-downstream mean activity.
scp1_position_effect_log2_up_minus_down
SCP1 promoter position contrast: SCP1-upstream mean activity minus SCP1-downstream mean activity.
upstream_promoter_effect_log2_scp1_minus_ins
Upstream promoter contrast: SCP1-upstream mean activity minus INS-upstream mean activity.
downstream_promoter_effect_log2_scp1_minus_ins
Downstream promoter contrast: SCP1-downstream mean activity minus INS-downstream mean activity.
Quality control
Used the GEO-provided library_counts.tsv file. Retained rows with passes=TRUE and DNA count at least the row-level minDNA threshold (10); all 57,972 deposited barcode rows met both criteria. Aggregated retained barcodes by fragment and configuration; all 5,220 fragment-configuration groups had at least two barcodes. No status-label filter was applied because the GEO status values (pass, no_variants_input, apparently_wt_no_passing_vars) are retained library annotations rather than a documented assay-QC flag. Replicate activity is library-size-normalized log2(RNA/DNA) from aggregate counts with a count pseudocount of 1; all retained count fields were numeric and nonnegative.
Curation notes
The manuscript's Data Availability section names GSE279057, but GEO GSE279057 is a distinct larger Kyono metabolic-variant library. GEO GSE322788 has the exact paper title, exactly 1,305 unique refnames, all four expected configurations, and the library_counts file used here, so it was selected as the matching data source. The deposited count-file labels INS1_promoter and SCP1_promoter were mapped to INS and SCP1; dwn was mapped to downstream and UP to upstream. The processed table contains no insert sequences, CAGE-strand labels, ChromHMM states, or ATAC-seq overlaps because these were not included in GSE322788's deposited count file.