Experiment / E2E737C60Episomal Plasmid MPRA

Pool 5: motif-mutated genomic enhancers

Systematic dissection of genomic features determining transcription factor binding and enhancer function

This pool tests mutations disrupting occurrences of TF motifs correlated with activity across bound mouse genomic enhancer backgrounds. The GEO release provides oligo-level RNA and plasmid counts summed across assigned barcodes, which are packaged here with the motif and position tokens encoded in each name.

Download processed table (CSV)Raw source data API documentation

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 manuscript describes disruption of 38 significantly correlated TF motifs across 375 PPARγ-bound genomic sequences. The GEO Pool 5 file contains oligo-level rows with tags, counts.rna, and counts.plasmid; the latter two are sums across barcode assignments, and tags is the number of assigned barcodes. RNA and plasmid barcodes were measured after transfection into differentiated 3T3-L1 adipocytes and a 16-h expression period.

Processed data

50 rows per page. Click a cell to inspect its full value.

Visible columns (22 of 22)

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Page 1 · 50 rows · More results available

Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.

Column dictionary · 22 definitions

element_id: Original GEO oligo name; unmapped NA_all rows were excluded.
design_class: GEO construct prefix; Pool 5 entries are PPREwt.
genomic_context_id: Identifier for the bound genomic enhancer background.
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 motif perturbation suffix, for example motif_position, motif_ctrl, or wt.
motif_name: TF motif token parsed from the design suffix; blank for wild-type rows.
motif_position: Numeric motif-position token parsed from motif_position suffixes.
control_type: wild_type, control, or motif_mutation based on the raw suffix form.
barcode_count_or_channels: GEO tags value: number of barcode-to-oligo assignments contributing to the aggregate counts.
positive_barcode_channels: Blank because the deposited Pool 5 counts are already summed across barcodes.
rna_count: GEO counts.rna value, summed across assigned barcodes.
plasmid_count: GEO counts.plasmid value, summed across assigned barcodes.
rna_fraction: RNA count divided by the total RNA count across parseable source rows.
plasmid_fraction: Plasmid count divided by the total plasmid count across parseable source rows.
activity_log2: Library-size-normalized log2 RNA/plasmid activity from aggregate counts.
activity_log2_from_summed_counts: Same aggregate-count activity score as activity_log2 for Pool 5.
source_row: 1-based line number in the downloaded source count file, including the header as line 1.
source_accession: GEO series accession supplying the aggregate Pool 5 matrix.

Quality control

GEO barcode reconstruction retained proper paired alignments with mapping score at least 25 and edit distance at most 5, and removed singleton or multiply matched barcodes. Package QC removed the 101 unmapped NA_all rows and retained 2,970 of 3,075 source rows with tags at least 3, plasmid count at least 100, and RNA count at least 10. Activity is a library-size-normalized log2 RNA/plasmid ratio from the deposited aggregate counts; four named low-coverage rows were excluded.

Curation notes

The barcode assignment table is retained in raw_data for provenance, while the processed table uses the GEO aggregate Pool 5 count file. The source includes 101 NA_all rows without a parseable genomic construct name; these were intentionally excluded rather than treated as a biological element.

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