A genome-wide FAIRE-enriched genomic-fragment library was assayed in E14 mouse embryonic stem cells after transfection and 4-hour treatment with LIF or 1 μM retinoic acid (RA). Three biological replicates were generated for each condition, and reporter RNA was quantified relative to the input plasmid library to identify active and differentially active regulatory regions.
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.
Organism
Mouse
Taxonomy ID
NCBITaxon:10090
Biosample
CVCL:C320
Reference genome
mm9
Design focus
Region-focused
Region of interest
Unbiased whole-genome assay (*)
Perturbation & assay details
LIF-maintained pluripotency versus 1 μM all-trans retinoic acid after LIF withdrawal for 4 h
Episomal pSTARR-seq_human reporter (Addgene #71509) carrying accessible mouse genomic fragments downstream of a minimal promoter so active inserts transcribe themselves. Accessible chromatin was isolated by FAIRE from RA-treated E14 cells to build the shared library; transfected cells were split into LIF and RA conditions, polyadenylated reporter RNA was reverse-transcribed with an 8-nt UMI, and input plasmid DNA was sequenced as the abundance control. The processed table combines the deposited LIF scored enhancer map and differential callsets with interval-level means from the deposited normalized log2 RNA/input BigWig tracks.
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 · 20 definitions
element_id
Stable generated identifier derived from the representative mm9 interval.
chromosome
mm9 chromosome name.
start_mm9
0-based inclusive start coordinate of the representative interval.
end_mm9
0-based exclusive end coordinate of the representative interval.
width_bp
Representative interval width in base pairs.
lif_log2_rna_over_input
Mean log2 RNA/input STARR activity under LIF; taken from the deposited scored table for LIF-map intervals and calculated as the BigWig mean0 for differential-only intervals.
ra_log2_rna_over_input
Mean log2 RNA/input STARR activity under 1 μM RA, calculated as the BigWig mean0 over the representative interval.
ra_minus_lif_log2_activity
Derived RA activity minus LIF activity difference on the log2 RNA/input scale.
lif_score_source
Provenance of the LIF activity value: official GEO scored table or a derived mean0 from the official LIF log2 BigWig.
lif_coverage_fraction
Fraction of interval bases covered by the LIF log2 BigWig.
ra_coverage_fraction
Fraction of interval bases covered by the RA log2 BigWig.
is_lif_active
TRUE when the interval is present in the deposited LIF-vs-input scored enhancer map.
is_lif_dependent
TRUE when the interval overlaps a deposited LIF-dependent differential enhancer call.
is_ra_inducible
TRUE when the interval overlaps a deposited RA-inducible differential enhancer call.
activity_call
Human-readable activity call based on the deposited differential callsets and LIF active map.
source_callsets
Semicolon-separated deposited callsets represented by the row.
mESC_peak_ids
Original peak identifier(s) from the deposited LIF active mESC BED file for the interval, if present.
lif_dependent_peak_ids
Original overlapping peak identifier(s) from the deposited LIF-dependent BED file, if present.
ra_inducible_peak_ids
Original overlapping peak identifier(s) from the deposited RA-inducible BED file, if present.
qc_pass
TRUE for intervals with finite LIF/RA activity values and complete coverage in both source BigWig tracks after source-callset filtering.
Quality control
The authors aligned 50-bp paired-end reads to mm9 with Bowtie2 (-X 800 --fr --very-sensitive), removed PCR duplicates using UMI-tools, and filtered for proper pairs, alignment quality, canonical chromosomes, and ENCODE blacklist regions with SAMtools. MACS2 used the input library as background and called each biological replicate and the merged condition; active peaks were retained when called in the merged data, in at least two of three biological replicates, and covered by at least three independent fragments. For this package, source callsets were reduced to one row per unique representative interval and rows were retained only when both deposited log2 signal tracks had finite values and complete interval coverage. The resulting table has 4,674 deposited scored intervals plus 188 differential-only intervals.
Curation notes
This is FAIRE-STARR-seq, an accessible-chromatin modification of an episomal self-transcribing STARR-seq MPRA; it is not a barcode-based allelic assay. The deposited mESC BED has 4,787 records representing 4,674 unique coordinates, and the deposited scored table has 4,674 rows. The publication reports 4,765 active enhancers, so the current GEO processed files and the publication count are not identical; this table follows the deposited files. Differential callsets are represented without losing differential-only intervals: the final table contains 4,862 rows, including 601 intervals marked LIF-dependent and 382 marked RA-inducible. E14 is resolved to ES-E14 Cellosaurus CVCL:C320.