Episomal 12K library testing accessible-region enhancer activity in mouse AML12 hepatocyte-like cells. This table summarizes two paired 5-prime AML12 cDNA/plasmid samples from the later GSE236121 submission.
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:0140
Reference genome
mm10
Design focus
Region-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Lipofectamine 3000 plasmid transfection; cDNA/plasmid harvested 48 h post-transfection
pSA293-CHEQseq episomal plasmid reporter with SCP1 promoter, chimeric intron, Venus reporter, and 12-bp barcodes; cDNA/plasmid barcode counts were assigned with the study's CHEQ-seq workflow and summarized as normalized RNA/DNA scores.
Processed data
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Visible columns (33 of 33)
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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 · 33 definitions
element_id
Unique 12K library enhancer identifier.
chromosome
Chromosome parsed from the cloned enhancer coordinate.
start
Start coordinate as reported in the source coordinate string.
end
End coordinate as reported in the source coordinate string.
enhancer_barcode
12-bp barcode associated with the cloned enhancer.
reference_genome
Assembly reported for the source sequence, usually mm10.
mlv_enhancer_region
Broader MLV/accessible region associated with the cloned enhancer.
enhancer_type
Source annotation for the enhancer.
hepatocyte_shared_class
Hepatocyte shared chromatin class.
hepatocyte_topic_class
Hepatocyte topic class.
hepatocyte_refined_class
Refined hepatocyte class.
hepatocyte_consensus_class
Consensus hepatocyte class.
annotation
Genomic annotation such as promoter, intron, or intergenic.
distance_to_tss
Reported distance to the nearest transcription start site.
nearest_gene
Nearest or associated gene symbol.
linked_genes
Linked gene symbols reported by the study.
regulon
Regulon annotation reported by the study.
rna_count_total
Sum of RNA/cDNA counts across retained condition replicates.
dna_count_total
Sum of plasmid DNA counts across retained condition replicates.
n_replicates
Number of biological cDNA/plasmid paired samples used.
replicate_log2_ratio_1
Library-size-normalized log2 RNA/DNA score for condition replicate 1.
replicate_log2_ratio_2
Library-size-normalized log2 RNA/DNA score for condition replicate 2.
replicate_log2_ratio_3
Library-size-normalized log2 RNA/DNA score for condition replicate 3.
replicate_log2_ratio_4
Library-size-normalized log2 RNA/DNA score for condition replicate 4.
replicate_log2_ratio_5
Library-size-normalized log2 RNA/DNA score for condition replicate 5.
replicate_log2_ratio_6
Library-size-normalized log2 RNA/DNA score for condition replicate 6.
replicate_log2_ratio_7
Library-size-normalized log2 RNA/DNA score for condition replicate 7.
count_based_mean_log2_ratio
Mean of the count-derived replicate log2 RNA/DNA scores.
count_based_median_log2_ratio
Median of the count-derived replicate log2 RNA/DNA scores.
count_based_sd_log2_ratio
Sample standard deviation of the count-derived replicate scores.
author_condition_log2_fc
Author-reported condition log2 fold-change from Supplementary Table 2.
author_condition_padj
Author-reported BH-adjusted p-value from Supplementary Table 2.
main_12k_activity_pattern
Author 12K activity call: Both, HepG2, Invivo, or None.
Quality control
The study's assigned-count workflow used fastp (Phred >30) and DESeq2 for cDNA versus plasmid comparisons. The later AML12 GEO series does not provide a separate per-element author DESeq2 summary, so this package additionally requires a matching 12K metadata row, aggregate cDNA counts >=10, and aggregate plasmid counts >=10; assignment columns are absent from this table. Count-derived scores use a 0.5 pseudocount and library-size normalization.
Curation notes
Source: GSE236121 AML12 count matrix, joined to the 12K element annotations in Supplementary Table 2. The AML12 submission is part of the study's GEO superseries but has no separate AML12 author effect/p-value columns; main_12k_activity_pattern is therefore a reference annotation, not an AML12 call.