Whole-genome STARR-seq enhancer activity in 2iL- and serum/LIF mouse embryonic stem cells
STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cellsAn episomal whole-genome STARR-seq library tested randomly sheared mouse genomic fragments in E14Tg2a embryonic stem cells cultured in ground-state 2i+LIF (2iL) or metastable serum+LIF (SL). The experiment used two biological replicates per condition with matched input-DNA libraries, and the table preserves the union of source-defined STARR loci plus the active-chromatin/no-STARR C3 comparison class.
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
2i+LIF (ground-state) versus serum+LIF (metastable) culture conditions; no additional treatment
Mouse genomic DNA was sonicated and size-selected at approximately 700–1200 bp (median approximately 850 bp), adapter-ligated, and cloned downstream of the minimal SCP1 promoter in the hSTARR-seq_SCP1 plasmid (Addgene 99292). Four hundred micrograms of plasmid pool were transfected into approximately 400 million E14Tg2a cells with Lipo3000; cells were harvested after 24 hours. PolyA+ reporter RNA was sequenced as four STARR output libraries and transfected plasmid DNA as four matched input libraries: 2iL biological replicates 1–2 and SL biological replicates 1–2. Libraries were paired-end sequenced, mapped to mm9 with BWA-MEM, and quantified as RNA/input enrichment.
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 · 48 definitions
- element_id
- Unique STARR-seq locus identifier from the author table.
- chromosome
- Reported mouse chromosome for the locus.
- start
- Reported locus start coordinate from the source mm9 table; coordinate convention is retained as supplied.
- end
- Reported locus end coordinate from the source mm9 table; coordinate convention is retained as supplied.
- length_bp
- Source-reported locus length in base pairs.
- summit
- Source-reported STARR-seq peak summit coordinate.
- feature
- Source genomic feature annotation, such as Intergenic or Intron.
- chromatin_class
- Author-defined locus class: C1, STARR-seq plus active chromatin; C2, STARR-seq without the active chromatin signature; C3, active chromatin without significant STARR-seq signal.
- starr_active_2iL
- Boolean derived from source enrichment_2iL >= 3 and padj_2iL1 and padj_2iL2 < 0.05.
- starr_active_SL
- Boolean derived from source enrichment_SL >= 3 and padj_SL1 and padj_SL2 < 0.05.
- starr_active_any
- Boolean indicating source-defined STARR activity in either 2iL or SL.
- rna_2iL_rep1
- Total STARR-seq reporter-RNA read count for 2iL biological replicate 1.
- rna_2iL_rep2
- Total STARR-seq reporter-RNA read count for 2iL biological replicate 2.
- rna_SL_rep1
- Total STARR-seq reporter-RNA read count for SL biological replicate 1.
- rna_SL_rep2
- Total STARR-seq reporter-RNA read count for SL biological replicate 2.
- unique_rna_2iL_rep1
- Non-duplicated STARR-seq reporter-RNA read count for 2iL replicate 1.
- unique_rna_2iL_rep2
- Non-duplicated STARR-seq reporter-RNA read count for 2iL replicate 2.
- unique_rna_SL_rep1
- Non-duplicated STARR-seq reporter-RNA read count for SL replicate 1.
- unique_rna_SL_rep2
- Non-duplicated STARR-seq reporter-RNA read count for SL replicate 2.
- input_dna_2iL_rep1
- Matched transfected-plasmid input-DNA read count for 2iL replicate 1.
- input_dna_2iL_rep2
- Matched transfected-plasmid input-DNA read count for 2iL replicate 2.
- input_dna_SL_rep1
- Matched transfected-plasmid input-DNA read count for SL replicate 1.
- input_dna_SL_rep2
- Matched transfected-plasmid input-DNA read count for SL replicate 2.
- enrichment_2iL_rep1
- Source STARR-seq-over-input enrichment for 2iL replicate 1, with source shrinkage/normalization applied.
- enrichment_2iL_rep2
- Source STARR-seq-over-input enrichment for 2iL replicate 2, with source shrinkage/normalization applied.
- enrichment_2iL_merged
- Source condition-level 2iL enrichment after merging the two biological replicates.
- enrichment_SL_rep1
- Source STARR-seq-over-input enrichment for SL replicate 1, with source shrinkage/normalization applied.
- enrichment_SL_rep2
- Source STARR-seq-over-input enrichment for SL replicate 2, with source shrinkage/normalization applied.
- enrichment_SL_merged
- Source condition-level SL enrichment after merging the two biological replicates.
- padj_2iL_rep1
- Benjamini–Hochberg-adjusted binomial p-value for the 2iL replicate 1 locus test.
- padj_2iL_rep2
- Benjamini–Hochberg-adjusted binomial p-value for the 2iL replicate 2 locus test.
- padj_SL_rep1
- Benjamini–Hochberg-adjusted binomial p-value for the SL replicate 1 locus test.
- padj_SL_rep2
- Benjamini–Hochberg-adjusted binomial p-value for the SL replicate 2 locus test.
- log2fc_SL_vs_2iL
- Author-reported DESeq2 log2 fold change for SL versus 2iL STARR-seq activity; blank for C3 loci without a differential STARR signal.
- pval_SL_vs_2iL
- GEO-supplied DESeq2 p-value for differential STARR-seq activity between SL and 2iL; blank for C3 loci.
- padj_SL_vs_2iL
- GEO-supplied Benjamini–Hochberg-adjusted DESeq2 p-value for SL versus 2iL; blank for C3 loci.
- atac_signal_2iL
- Author-provided ATAC-seq signal associated with the locus in 2iL cells.
- atac_signal_SL
- Author-provided ATAC-seq signal associated with the locus in SL cells.
- p300_signal_union
- Author-provided P300 overlap/call in the union chromatin annotation.
- med1_signal_2iL
- Author-provided MED1 ChIP-seq signal associated with the locus in 2iL cells.
- med1_signal_SL
- Author-provided MED1 ChIP-seq signal associated with the locus in SL cells.
- p300_signal_2iL
- Author-provided P300 ChIP-seq signal associated with the locus in 2iL cells.
- p300_signal_SL
- Author-provided P300 ChIP-seq signal associated with the locus in SL cells.
- gc_fraction_center_500bp
- GC fraction calculated by the authors in the central 500 bp of the locus.
- cpg_count_center_500bp
- Number of CpGs calculated by the authors in the central 500 bp of the locus.
- epicseg_state_2iL
- Numeric EpiCSeg five-state chromatin segmentation code for 2iL; state labels/intervals are supplied in raw_data/author_Epistates.tsv.
- epicseg_state_SL
- Numeric EpiCSeg five-state chromatin segmentation code for SL; state labels/intervals are supplied in raw_data/author_Epistates.tsv.
- package_qc_pass
- TRUE for rows retained after package-level ID, interval, cross-source, and finite-value integrity checks.
Quality control
The paper discarded mapped reads with MAPQ < 10 and non-proper pairing, and assessed library complexity, GC bias, insert size, PCR duplication, and genome coverage with PICARD and bedtools. Initial loci were called with MACS2 against matched input DNA, read counts were obtained with featureCounts, per-library significance used a right-tailed binomial model with Benjamini–Hochberg correction, and enrichment was stabilized with beta-binomial Bayesian shrinkage. One million GC- and size-matched random regions supported the empirical enrichment threshold. Final STARR loci were defined by condition-level enrichment >= 3 and adjusted binomial p < 0.05 in both biological replicates. Differential activity used DESeq2 custom normalization for RNA/input depth and local input coverage; absolute fold change >= 2.5 and p < 0.05 defined differential loci. Package QC required unique locus IDs, agreement between the author and GEO tables for chromosome/interval/class, finite numeric values, nonnegative starts, end > start, and summit within the reported interval. One source row (starr_15915) was excluded because its reported summit (52967375) falls outside chr6:52967360-52967369. The processed table retains 27565 of 27566 source rows; C3 rows are intentionally retained as the authors' active-chromatin/no-STARR dormant comparison class rather than treated as failed sequencing rows.
Curation notes
The study's MPRA is a whole-genome episomal STARR-seq assay, represented by one experiment folder because the eight sequencing libraries are four RNA/input pairs spanning two culture conditions analyzed as one comparison. The source union has 18544 C1, 7072 C2, and 1950 C3 loci; the processed table retains 18543 C1, 7072 C2, and 1950 C3 rows after removing the single anomalous-summit row. Source-defined active counts are 18116 loci in 2iL and 18543 in SL; the packaged table has 18116 and 18542 respectively because the excluded row was SL-active. C3 is retained to preserve the paper's dormant/negative chromatin comparison, and its differential fields are null because it was not part of the STARR-positive set. E14Tg2a is resolved to Cellosaurus CVCL:9108 (ES-E14TG2a; 129P2/Ola mouse embryonic stem cell). Raw FASTQ/BW archives are not packaged; the raw-read GEO archive remains linked in the parent metadata.