High-CpG E. coli fragment library with housekeeping controls
CG dinucleotides enhance promoter activity independent of DNA methylationTrAC-seq measured wild-type activity for E. coli genomic fragments selected for high CpG density, mixed with mouse housekeeping-promoter controls, in TC-1 mouse embryonic stem cells. The assay tests whether CpG density alone is sufficient to drive transcription in chromatin.
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; wild-type TC-1 mouse embryonic stem cells
TrAC-seq used pooled promoter-barcode cassettes inserted by recombinase-mediated cassette exchange into the beta-globin locus. RNA/cDNA and genomic-DNA barcodes were sequenced separately; per-barcode RNA/DNA enrichment used the study pseudocount alpha=0.05 and was summarized across barcodes and three biological replicates. The library contained a CpG-free eGFP spacer and a unique barcode.
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 · 15 definitions
- element_id
- Identifier for an E. coli genomic fragment (source interval/orientation label) or a mixed-library housekeeping-promoter control.
- library
- Source expression library name.
- gc_percent
- GC content of the tested fragment, in percent.
- cpg_percent
- CpG content of the tested fragment, as reported by the source.
- cpg_observed_expected
- Observed-over-expected CpG density (OE) for the tested fragment.
- activity_rep1
- RNA/DNA barcode enrichment for biological replicate 1; source activity includes the study pseudocount.
- dna_barcodes_rep1
- Number of DNA-supported barcodes contributing to replicate 1 activity.
- activity_rep2
- RNA/DNA barcode enrichment for biological replicate 2; source activity includes the study pseudocount.
- dna_barcodes_rep2
- Number of DNA-supported barcodes contributing to replicate 2 activity.
- activity_rep3
- RNA/DNA barcode enrichment for biological replicate 3; source activity includes the study pseudocount.
- dna_barcodes_rep3
- Number of DNA-supported barcodes contributing to replicate 3 activity.
- activity_geomean
- Geometric mean of the non-missing per-replicate activity enrichments.
- log2_activity
- Mean log2-transformed activity enrichment across non-missing replicates.
- mean_dna_barcodes
- Arithmetic mean of numeric DNA-supported barcode counts across replicates.
- qc_replicates
- Number of replicates with activity and at least 3 DNA-supported barcodes; retained rows have at least 2.
Quality control
The paper retained uniquely assigned promoter barcodes (or assignments with second-most abundant sequence / most abundant sequence <0.3), required >20 normalized genomic-DNA reads per barcode, assigned absent RNA observations zero counts, and used alpha=0.05. For this packaged element table, rows were retained only when activity and at least 3 DNA-supported barcodes were available in at least 2 of 3 biological replicates; 17 of 83 source rows passed this element-level filter.
Curation notes
Input: raw_data/GSE116704_CpGDensitylib1_results.tab.gz; GEO reporter samples GSM3258747-GSM3258753. The library mixes non-mouse E. coli genomic fragments with mouse housekeeping controls, so mm9 is recorded for the mouse assay context and E. coli entries have no mouse coordinates. The source file contains 83 rows; 17 passed the packaged QC.