Wild-type housekeeping promoter and CMV control library
CG dinucleotides enhance promoter activity independent of DNA methylationTrAC-seq measured transcriptional activity for 10 pooled promoter constructs comprising mouse housekeeping-gene promoters and a CMV control in wild-type TC-1 mouse embryonic stem cells. Constructs were integrated into the same beta-globin RMCE locus and quantified by RNA/DNA barcode enrichment.
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 · 12 definitions
- element_id
- Unique promoter or control construct identifier from the GEO result table.
- library
- Source expression library name.
- 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; all 10 of 10 source rows passed.
Curation notes
Input: raw_data/GSE116704_HKGlib1_results.tab.gz; GEO reporter samples GSM3258674-GSM3258680. The source table is element-level summarized activity, not raw sequencing reads; no promoter nucleotide sequences were supplied in the public result table. Cellosaurus CVCL:M350 is the TC1 [Mouse ESC] line (TC-1 synonym).