MPRAduo benchmark pool, SE orientation (GM12878)
Whole-genome functional characterization of RE1 silencers using a modified massively parallel reporter assayA benchmark MPRAduo pool tested 21 activating elements and candidate silencer/control elements in GM12878, including single E/S libraries and the silencer–enhancer (SE) duo alignment. Reporter RNA was normalized to plasmid DNA across four biological replicates.
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
Episomal plasmid MPRAduo used paired enhancer (E) and silencer (S) cis-regulatory elements around a GFP open reading frame and minimal promoter. This experiment is the authors' run 1 SE orientation; 10- and 20-nucleotide barcodes identify E and S modules, respectively, and the table retains E, S, and SE library rows.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (21 of 21)
| Row | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | |||||||||||||||||||||
| 2 | |||||||||||||||||||||
| 3 | |||||||||||||||||||||
| 4 | |||||||||||||||||||||
| 5 | |||||||||||||||||||||
| 6 | |||||||||||||||||||||
| 7 | |||||||||||||||||||||
| 8 | |||||||||||||||||||||
| 9 | |||||||||||||||||||||
| 10 | |||||||||||||||||||||
| 11 | |||||||||||||||||||||
| 12 | |||||||||||||||||||||
| 13 | |||||||||||||||||||||
| 14 | |||||||||||||||||||||
| 15 | |||||||||||||||||||||
| 16 | |||||||||||||||||||||
| 17 | |||||||||||||||||||||
| 18 | |||||||||||||||||||||
| 19 | |||||||||||||||||||||
| 20 | |||||||||||||||||||||
| 21 | |||||||||||||||||||||
| 22 | |||||||||||||||||||||
| 23 | |||||||||||||||||||||
| 24 | |||||||||||||||||||||
| 25 | |||||||||||||||||||||
| 26 | |||||||||||||||||||||
| 27 | |||||||||||||||||||||
| 28 | |||||||||||||||||||||
| 29 | |||||||||||||||||||||
| 30 | |||||||||||||||||||||
| 31 | |||||||||||||||||||||
| 32 | |||||||||||||||||||||
| 33 | |||||||||||||||||||||
| 34 | |||||||||||||||||||||
| 35 | |||||||||||||||||||||
| 36 | |||||||||||||||||||||
| 37 | |||||||||||||||||||||
| 38 | |||||||||||||||||||||
| 39 | |||||||||||||||||||||
| 40 | |||||||||||||||||||||
| 41 | |||||||||||||||||||||
| 42 | |||||||||||||||||||||
| 43 | |||||||||||||||||||||
| 44 | |||||||||||||||||||||
| 45 | |||||||||||||||||||||
| 46 | |||||||||||||||||||||
| 47 | |||||||||||||||||||||
| 48 | |||||||||||||||||||||
| 49 | |||||||||||||||||||||
| 50 |
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
- Source construct identifier; duo rows are encoded as silencer^enhancer.
- library
- MPRAduo library type: E, S, or SE.
- alignment
- Duo orientation for this run, SE (silencer followed by enhancer upstream of the reporter promoter).
- enhancer_id
- Identifier of the activating E element.
- silencer_id
- Identifier of the S element or control.
- chromosome
- Source chromosome for genomic S elements, when available.
- start
- Source genomic start coordinate for the S element, when available.
- end
- Source genomic end coordinate for the S element, when available.
- project
- Source annotation/category for the tested S element.
- rna_count_1
- GFP cDNA barcode count in biological replicate 1.
- rna_count_2
- GFP cDNA barcode count in biological replicate 2.
- rna_count_3
- GFP cDNA barcode count in biological replicate 3.
- rna_count_4
- GFP cDNA barcode count in biological replicate 4.
- dna_count_1
- Plasmid DNA barcode count in biological replicate 1.
- dna_count_2
- Plasmid DNA barcode count in biological replicate 2.
- dna_count_3
- Plasmid DNA barcode count in biological replicate 3.
- dna_count_4
- Plasmid DNA barcode count in biological replicate 4.
- dna_count_mean
- Mean plasmid DNA count across the four replicates (source plmean).
- dna_barcode_count
- Observed plasmid barcode support for the oligo (source PlasmidsBCsum).
- log2_fold_change
- Source log2 RNA/DNA reporter activity estimate.
- log2_fold_change_se
- Standard error of the source log2 RNA/DNA activity estimate.
Quality control
The authors required at least 20 observed plasmid barcodes per oligo and a mean plasmid DNA count of at least 100 across four replicates, with additional cross-library consistency checks for the benchmark. This package retained rows meeting the two numeric thresholds with nonmissing log2 fold-change and standard error; 23,072 of 27,169 source rows passed.
Curation notes
GEO accession GSM5861606 supplies this run. The source count table contains single E and S libraries plus the SE duo library; it is retained losslessly in raw_data. The published analysis also performed cross-run quantile normalization for comparisons, which is not applied to this orientation-specific table.