mESC 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 E14 mouse embryonic stem cells; fluorescent cells were flow-sorted and sequenced against an input library. Four deposited output libraries (outputA-outputD) are represented as one mESC 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 four 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 · 37 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 S5; blank when no matching supplementary coordinate was available.
- shared_input_observed
- 1 if the element coordinate occurs in the common GEO normalized mm9 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.
- outputA_output_normalized_count
- GEO outputA normalized reporter count.
- outputA_input_normalized_count
- GEO outputA reported normalized input count used for the source ratio.
- outputA_fold_enrichment
- outputA_output_normalized_count divided by outputA_input_normalized_count.
- outputA_log2_fold_enrichment
- Base-2 logarithm of the outputA fold enrichment.
- outputA_p_value
- Poisson p-value reported for the outputA effective signal.
- outputA_q_value
- Benjamini-Hochberg q-value reported for the outputA effective signal.
- outputB_output_normalized_count
- GEO outputB normalized reporter count.
- outputB_input_normalized_count
- GEO outputB reported normalized input count used for the source ratio.
- outputB_fold_enrichment
- outputB_output_normalized_count divided by outputB_input_normalized_count.
- outputB_log2_fold_enrichment
- Base-2 logarithm of the outputB fold enrichment.
- outputB_p_value
- Poisson p-value reported for the outputB effective signal.
- outputB_q_value
- Benjamini-Hochberg q-value reported for the outputB effective signal.
- outputC_output_normalized_count
- GEO outputC normalized reporter count.
- outputC_input_normalized_count
- GEO outputC reported normalized input count used for the source ratio.
- outputC_fold_enrichment
- outputC_output_normalized_count divided by outputC_input_normalized_count.
- outputC_log2_fold_enrichment
- Base-2 logarithm of the outputC fold enrichment.
- outputC_p_value
- Poisson p-value reported for the outputC effective signal.
- outputC_q_value
- Benjamini-Hochberg q-value reported for the outputC effective signal.
- outputD_output_normalized_count
- GEO outputD normalized reporter count.
- outputD_input_normalized_count
- GEO outputD reported normalized input count used for the source ratio.
- outputD_fold_enrichment
- outputD_output_normalized_count divided by outputD_input_normalized_count.
- outputD_log2_fold_enrichment
- Base-2 logarithm of the outputD fold enrichment.
- outputD_p_value
- Poisson p-value reported for the outputD effective signal.
- outputD_q_value
- Benjamini-Hochberg q-value reported for the outputD 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 628,186 union rows in outputA-outputD 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 reports 626,879 mESC enhancers, while the union of the deposited effective outputA-outputD files contains 628,186 loci. Supplementary Table S5 contains 626,879 classifications; 626,043 were joined to the GEO union by chromosome and coordinates, leaving 2,143 unclassified GEO-only rows. E14 is labeled only at subline level in GEO; CVCL:9108 is used based on the authors' statement that the ATCC E14TG2a line was used. GEO does not explicitly distinguish biological from technical replication, so outputA-outputD are retained as deposited output libraries without relabeling replication type.