Genome-wide integrated promoterless LUC TRIP MPRA in Arabidopsis T87 cells
Plant genome response to incoming coding sequences: stochastic transcriptional activation independent of integration lociThree independent Agrobacterium-transformed Arabidopsis T87 cell pools carried thousands of random, uniquely barcoded promoterless firefly LUC inserts. Inverse-PCR junction mapping linked inserts to TAIR10 contexts and paired cellular-DNA/cDNA barcode sequencing quantified relative reporter transcription; this package contains the explicitly reported aggregate MPRA results because no per-insert source table was deposited.
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
This is an integrated random T-DNA promoter-trap/TRIP MPRA rather than an episomal or transposon MPRA. Three independently transformed pools were combined for the genome scan, and the paper also shows three biological expression profiles. Illumina MiSeq was used for 301-bp paired-end junction mapping and 76-bp paired-end DNA/cDNA barcode amplicon libraries. Relative transcription was normalized cDNA/DNA x 10,000.
Agrobacterium-mediated delivery of a modified pGreenII T-DNA into Arabidopsis T87 cells; each reporter carries a 12-bp random barcode, a promoterless firefly luciferase coding sequence and a nos terminator, with a separate NptII/kanamycin-selection cassette. Random T-DNA integration is mapped by inverse-PCR junction sequencing; expression is read from barcode abundance in cellular DNA versus oligo-dT cDNA.
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 · 15 definitions
- record_id
- Unique identifier for a reported aggregate MPRA result row.
- source_figure
- Figure or figure panel in the target paper from which the row was transcribed.
- record_type
- Standardized class of aggregate result, such as insertion class, transcription state, chromatin context, or neighbor-pair fate.
- analysis_scope
- Population or subset to which the row's values apply.
- category
- Reported biological category or transcriptional fate.
- category_n
- Reported or explicitly count-derived number of observations in the category; null when only a percentage is printed.
- denominator_n
- Number of observations used as the denominator for the reported value.
- reported_value
- Reported percentage, count, or measured pair count, depending on reported_unit.
- reported_unit
- Unit/interpretation of reported_value.
- observed_count
- Observed neighbor-pair count for neighbor-pair rows; null otherwise.
- expected_count_30pct_rule
- Expected neighbor-pair count under the paper's 30% stochastic activation rule; null otherwise.
- fisher_exact_pvalue
- Fisher's exact-test P value reported for the corresponding neighbor-pair comparison; null otherwise.
- neighbor_distance_threshold_bp
- Maximum base-pair distance defining the neighboring LUC-pair analysis; null for non-neighbor rows.
- value_provenance
- Whether the value is explicit in prose/figure, figure-labeled, or calculated from explicit counts.
- notes
- Provenance and interpretation notes, including limitations of the reported aggregate value.
Quality control
Study pipeline: trim mapping reads at Q30; extract LUC + 12-bp barcode + 25–50-bp genomic flank; require unique Bowtie TAIR10 mapping (-m 1 -v 3); retain locus–barcode pairs with at least 3 reads and at least 90% of reads at each mapped locus supporting one barcode; omit DNA barcodes with <=5 reads; set cDNA barcodes with <=5 reads to zero; normalize each library to total reads; calculate relative transcription as normalized cDNA/normalized DNA x 10,000. The processed table contains only already-reported aggregate summaries that passed the paper’s pipeline.
Curation notes
The target paper is a genuine integrated TRIP/promoter-trap MPRA, but the OA release has no machine-readable per-insert barcode/count table or original sequencing-read accession. The single table therefore preserves explicit figure/text-level MPRA summaries only; it excludes unlabeled graph heights and does not invent barcode IDs, genomic coordinates, DNA/RNA counts, or per-insert activity scores. T87 is represented by Cellosaurus CVCL:D5GW.