Targeted human islet CAGE-element enhancer activity in INS-1 832/13 cells
A Transcription Start Site Map in Human Pancreatic Islets Reveals Functional Regulatory SignaturesA targeted episomal STARR-seq/MPRA library tested 7,188 human pancreatic-islet CAGE elements, each 198 bp with 16-bp anchors and random 16-bp reporter barcodes, in rat INS-1 832/13 insulinoma cells in three biological replicates. The packaged table contains the 3,378 final element-level results supported by the deposited filtered barcode counts and the authors’ MPRAnalyze model output.
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
Modified targeted UMI-STARR-seq/MPRA in an episomal plasmid. Human hg19 CAGE elements were cloned into a STARR-seq backbone, linked to random 16-bp barcodes, and transfected into INS-1 832/13 cells; input plasmid DNA and three reporter cDNA libraries were sequenced. The authors used Starcode for barcode error handling, UMI-based PCR-duplicate removal, upper-quartile library-depth normalization, and MPRAnalyze 1.3.1 negative-binomial generalized linear models with barcode information in the DNA model and replicate information in the RNA model.
Processed data
50 rows per page. Click a cell to inspect its full value.
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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 · 18 definitions
- element_id
- Original CAGE element identifier in chr_start_end format.
- chromosome
- Chromosome name parsed from element_id.
- start_hg19
- 0-based start coordinate on hg19/GRCh37, parsed from the original element identifier.
- end_hg19
- End coordinate on hg19/GRCh37; end minus start is 198 bp.
- length_bp
- Length of the tested CAGE insert in base pairs.
- barcode_count
- Number of retained element-linked reporter barcodes in the filtered GEO count file.
- dna_count_total
- Sum of filtered input-plasmid DNA barcode counts across the element’s retained barcodes.
- rna_count_rep1_total
- Sum of filtered reporter RNA/cDNA barcode counts for biological replicate 1.
- rna_count_rep2_total
- Sum of filtered reporter RNA/cDNA barcode counts for biological replicate 2.
- rna_count_rep3_total
- Sum of filtered reporter RNA/cDNA barcode counts for biological replicate 3.
- glm_activity_statistic
- Enhancer activity/transcription-rate statistic from the authors’ MPRAnalyze generalized linear model; it is not a simple RNA/DNA ratio.
- activity_zscore
- MPRAnalyze enhancer activity z score relative to the inferred null distribution.
- activity_mad_score
- MPRAnalyze enhancer activity median-absolute-deviation score relative to the inferred null distribution.
- p_value_mad
- Nominal p-value for the MAD-based activity score supplied in Supplementary Table 8.
- p_value_zscore
- Nominal p-value for the z-score-based activity test supplied in Supplementary Table 8.
- fdr_mad_bh
- Benjamini–Hochberg adjusted p_value_mad across all 3,378 retained elements, computed during packaging.
- fdr_zscore_bh
- Benjamini–Hochberg adjusted p_value_zscore across all 3,378 retained elements, computed during packaging.
- active_5pct_fdr
- TRUE when fdr_zscore_bh is <0.05; this reproduces the paper’s 2,279 significant elements at 5% FDR.
Quality control
The source count table is already filtered by the authors’ stated QC: barcode DNA counts ≥10 and at least two qualifying barcodes per CAGE element, after barcode error clustering and UMI-based PCR-duplicate removal. All 35,153 barcode rows and 3,378 elements in the filtered GEO file were retained after confirming every barcode has DNA count ≥10, every element has ≥2 barcodes, and the element set exactly matches Supplementary Table 8. Benjamini–Hochberg FDRs were computed across the 3,378 supplied p-values; pval.zscore yields 2,279 elements with FDR <0.05, matching the publication’s reported activity count.
Curation notes
This is one region-focused experiment, not an allele/variant-contrast MPRA; the library contains scattered human islet CAGE elements and no rsIDs. The reporter context is rat INS-1 832/13 (Cellosaurus CVCL:7226), while the tested element coordinates are human hg19, so target_organism describes the assayed cell context. The article and supplementary methods describe a modified MPRA/STARR-seq assay; GEO labels the same assay STARR-seq. The main article and supplementary methods state 50 µg library input, whereas the GEO Series design text says 10 µg. The article’s methods mention 3,446 initially quantifiable elements, while the final Supplementary Table 8 and filtered GEO count file contain 3,378; this package follows the final 3,378-element result set.