HEK293T MAE-seq 25-bp enhancer screen
MAE-seq refines regulatory elements across the genomeTransient pMX-mP-mCherry plasmid libraries carrying random 25-bp genomic fragments were transfected into HEK293T cells; fluorescent cells were flow-sorted and sequenced against an input library. Three deposited output libraries (output1-output3) are represented as one HEK293T experiment.
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/transient pMX-mP-mCherry minimal-promoter reporter with random 25-bp genomic inserts. The input library was sequenced from unsorted transfected cells, and output libraries were collected from mCherry-fluorescent cells 48 hours after transfection. GEO output files report output and input normalized counts together with Poisson p-values and Benjamini-Hochberg q-values; the processed table retains the three source output libraries and derives fold enrichment and log2 fold enrichment.
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 · 31 definitions
- element_id
- Unique build-and-coordinate identifier for the tested 25-bp element.
- chromosome
- Chromosome or contig name from the GEO output file.
- start
- Reported source start coordinate; used with end to define the inclusive 25-bp span.
- end
- Reported source end coordinate; the inclusive span is end-start+1.
- length_bp
- Element length inferred from the reported coordinates; all retained rows are 25 bp.
- enhancer_class
- Known or novel classification joined from Supplementary Table S6 after the source table's one-base start-coordinate convention was normalized; blank when no matching supplementary coordinate was available.
- shared_input_observed
- 1 if the element coordinate occurs in the common GEO normalized hg19 input table, otherwise 0.
- shared_input_normalized_count
- Normalized count for the element in the common GEO input table; blank when the coordinate is absent.
- n_replicates_significant
- Number of deposited output libraries containing the element as an effective q<0.01 signal.
- replicates_significant
- Semicolon-delimited names of output libraries with an effective q<0.01 signal.
- mean_called_log2_fold_enrichment
- Mean log2(output/input) across output libraries in which the element was called.
- max_called_log2_fold_enrichment
- Maximum log2(output/input) across called output libraries.
- min_called_q_value
- Smallest source q-value across called output libraries.
- output1_output_normalized_count
- GEO output1 normalized reporter count.
- output1_input_normalized_count
- GEO output1 reported normalized input count used for the source ratio.
- output1_fold_enrichment
- output1_output_normalized_count divided by output1_input_normalized_count.
- output1_log2_fold_enrichment
- Base-2 logarithm of the output1 fold enrichment.
- output1_p_value
- Poisson p-value reported for the output1 effective signal.
- output1_q_value
- Benjamini-Hochberg q-value reported for the output1 effective signal.
- output2_output_normalized_count
- GEO output2 normalized reporter count.
- output2_input_normalized_count
- GEO output2 reported normalized input count used for the source ratio.
- output2_fold_enrichment
- output2_output_normalized_count divided by output2_input_normalized_count.
- output2_log2_fold_enrichment
- Base-2 logarithm of the output2 fold enrichment.
- output2_p_value
- Poisson p-value reported for the output2 effective signal.
- output2_q_value
- Benjamini-Hochberg q-value reported for the output2 effective signal.
- output3_output_normalized_count
- GEO output3 normalized reporter count.
- output3_input_normalized_count
- GEO output3 reported normalized input count used for the source ratio.
- output3_fold_enrichment
- output3_output_normalized_count divided by output3_input_normalized_count.
- output3_log2_fold_enrichment
- Base-2 logarithm of the output3 fold enrichment.
- output3_p_value
- Poisson p-value reported for the output3 effective signal.
- output3_q_value
- Benjamini-Hochberg q-value reported for the output3 effective signal.
Quality control
The authors aligned reads to the reference genome, retained uniquely mapped 25-bp fragments with no more than two mismatches, normalized input/output counts, and selected effective signals using a Poisson test with Benjamini-Hochberg q<0.01. For this package, rows were additionally required to have seven numeric source fields, finite positive output/input normalized counts, an inclusive 25-bp span (end-start+1=25), p/q values in [0,1], q<0.01, and unique coordinates. All 554,938 union rows in output1-output3 passed these filters. shared_input_observed and shared_input_normalized_count are informational because valid source calls can use a reported input pseudocount when the common input file lacks that coordinate; missing replicate fields are blank rather than zero.
Curation notes
The Methods text names GSE149028, but the paper Data availability section, GEO family record, and deposited files identify GSE193494; this package uses GSE193494. The paper and Supplementary Table S6 report 554,826 HEK293T enhancer loci, whereas the union of the deposited effective output1-output3 files contains 554,938 loci. Table S6 supplies 554,826 known/novel classifications; 554,536 were joined after matching chromosome, processed start+1, and processed end to the supplementary coordinate convention, leaving 402 GEO-only rows unclassified. GEO does not explicitly distinguish biological from technical replication, so output1-output3 are retained as deposited output libraries without relabeling replication type.