This pool systematically perturbs 25 bound genomic enhancer contexts with tiled 10-bp mutations and 20-bp sequence swaps, retaining the central PPARγ motif. The released constructs were assayed in differentiated 3T3-L1 adipocytes with matched RNA and plasmid-DNA barcode counts.
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:0123
Reference genome
mm9
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Differentiated 3T3-L1 adipocytes; no acute treatment
The Pool 4 library uses bound mouse genomic contexts centered on intact 16-bp PPARγ/RXR motifs. It includes wild-type, motif/control constructs, 10-bp block perturbations tiled every 5 bp, and 20-bp swaps between matched bound and unbound contexts, cloned into the minimal-promoter/luc2 episomal reporter. The deposited RNA and plasmid matrices contain 13 barcode-count channels per construct and were collected 16 h after transfection.
Processed data
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Visible columns (21 of 21)
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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 · 21 definitions
element_id
Original GEO construct name.
design_class
GEO construct prefix; Pool 4 entries are PPREwt.
genomic_context_id
Identifier for the bound genomic enhancer context.
chromosome
Mouse chromosome encoded in the construct name.
start_mm9
Start coordinate of the central motif as encoded in the GEO name.
end_mm9
End coordinate of the central motif as encoded in the GEO name; the source coordinate convention is retained.
strand
Strand of the source genomic motif.
pparg_motif
Central 16-bp PPARγ/RXR motif sequence encoded in the GEO name.
design_detail
Raw perturbation suffix, such as wt, mut, ctrl, comp10_<offset>, swap20_<offset>, or ctrlswap20_<offset>.
mutation_type
Leading perturbation token parsed from design_detail.
mutation_offset
Numeric tile offset parsed from two-token perturbation suffixes; blank for non-tiled controls.
barcode_count_or_channels
Number of deposited RNA/DNA barcode-count channels (13 for Pool 4).
positive_barcode_channels
Number of channels with both RNA and plasmid counts greater than zero.
rna_count
Sum of RNA-derived barcode counts across deposited channels.
plasmid_count
Sum of plasmid-DNA barcode counts across deposited channels.
rna_fraction
RNA count divided by the total RNA count across all source rows and channels.
plasmid_fraction
Plasmid count divided by the total plasmid count across all source rows and channels.
activity_log2
Median channel-level log2 RNA/DNA activity after per-channel library-size normalization.
activity_log2_from_summed_counts
Log2 RNA/DNA activity computed from the row-summed counts and aggregate library totals.
source_row
1-based line number in the downloaded source count file, including the header as line 1.
source_accession
GEO sample accessions supplying the RNA and plasmid matrices.
Quality control
GEO assigned perfect UTR-barcode matches to oligos and deposited counts for each barcode channel. Package QC retained all 2,075 of 2,075 rows: at least 3 of 13 channels had both RNA and plasmid counts greater than zero, summed plasmid count was at least 100, summed RNA count was at least 10, and the median channel-level log2 RNA/DNA activity was finite. Activity fractions use library-size totals from the deposited matrix.
Curation notes
The mutation_type and mutation_offset fields are mechanical parses of the released suffixes; the complete original suffix is retained in design_detail. The table contains RNA/DNA activity measurements, not the separate Pool 4 ChIP-seq data.