TF-associated genomic promoter-window library
CG dinucleotides enhance promoter activity independent of DNA methylationTrAC-seq measured activity for a library of mouse genomic promoter windows selected for Sp1, Sp3, GABPA, and NRF1 motif/binding analysis in wild-type TC-1 embryonic stem cells. The table retains the mm9 coordinates and CpG/GC features supplied with the GEO results.
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
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 · 19 definitions
- element_id
- Numeric construct identifier from the GEO result table.
- library
- Source expression library name.
- gc_percent
- GC content of the tested promoter window, in percent.
- cpg_percent
- CpG content of the tested promoter window, as reported by the source.
- cpg_observed_expected
- Observed-over-expected CpG density (OE) for the tested window.
- chromosome
- Mouse chromosome for the tested genomic window.
- start
- Start coordinate of the tested window in mm9.
- end
- End coordinate of the tested window in mm9.
- strand
- Strand of the tested genomic window.
- 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; 60 of 273 source rows passed this element-level filter.
Curation notes
Input: raw_data/GSE116704_HKGlib2_results.tab.gz; GEO reporter samples GSM3258681-GSM3258687. The source file contains 273 numbered windows; only 60 met the packaged 2-of-3 replicate / >=3 barcode rule. Coordinates and sequence-composition fields are source-provided; nucleotide sequences were not included in the public result table.