Experiment / E11RTVGF6Episomal Plasmid MPRA

455-construct FACS MPRA across mouse hepatocyte zonation bins

Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation

Variant-focused 455-library MPRA in mouse liver with GFP-positive hepatocytes sorted by ECAD/CD73-associated zonation bins. This table summarizes five released FACS cDNA groups and normalizes them against the three matched bulk mouse plasmid references.

Download processed table (CSV)Raw source data API documentation

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: CL:0000182
Reference genome: mm10
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Hydrodynamic tail-vein delivery of 20 µg MPRA plasmid; FACS assay at 48 h post-injection

pSA293-CHEQseq episomal reporter with SCP1 promoter, chimeric intron, Venus reporter, and 11-bp barcodes. Tetraploid GFP-positive hepatocytes were sorted by ECAD/CD73-associated bins; FACS cDNA barcode counts were compared to the bulk mouse plasmid reference libraries because plasmid DNA was not extracted from the sorted samples.

Processed data

50 rows per page. Click a cell to inspect its full value.

Search table valuesFilter columnOperatorValue

Visible columns (78 of 78)

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

Page 1 · 50 rows · More results available

Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.

Column dictionary · 78 definitions

element_id: Unique 455 library enhancer/variant identifier.
parent_region: Parent enhancer region or construct name.
gene: Gene associated with the parent enhancer.
mutation: Original mutation label.
mutation_edited: Normalized mutation label in the source table.
pattern: Construct pattern/category reported by the study.
window: Variant window or coordinate label.
n_mutations: Number of mutations in the construct.
sequence: Full tested reporter sequence from Supplementary Table 3.
deepliver_active_score: DeepLiver predicted activity score for the active state.
deepliver_inactive_score: DeepLiver predicted activity score for the inactive state.
deepliver_general_score: DeepLiver predicted general hepatocyte score.
deepliver_pericentral_score: DeepLiver predicted pericentral score.
deepliver_periportal_score: DeepLiver predicted periportal score.
shift_wt_deepliver_active: DeepLiver score shift from wild type for active state.
shift_wt_deepliver_inactive: DeepLiver score shift from wild type for inactive state.
shift_wt_deepliver_general: DeepLiver score shift from wild type for general state.
shift_wt_deepliver_pericentral: DeepLiver score shift from wild type for pericentral state.
shift_wt_deepliver_periportal: DeepLiver score shift from wild type for periportal state.
facs_total_count: Sum of cDNA counts across all FACS output bins, excluding assignments.
dna_reference_count_total: Sum of the three matched bulk mouse plasmid reference counts.
n_facs_samples_detected: Number of FACS cDNA samples with nonzero counts.
ecad_high_count_total: Sum of raw cDNA counts in the ecad_high FACS group.
ecad_high_n_replicates: Number of source cDNA samples in the ecad_high FACS group.
ecad_high_n_detected_replicates: Number of nonzero cDNA samples in the ecad_high FACS group.
ecad_high_replicate_log2_ratio_1: Library-size-normalized log2 RNA/DNA score for ecad_high replicate 1.
ecad_high_replicate_log2_ratio_2: Library-size-normalized log2 RNA/DNA score for ecad_high replicate 2.
ecad_high_replicate_log2_ratio_3: Library-size-normalized log2 RNA/DNA score for ecad_high replicate 3.
ecad_high_mean_log2_ratio: Mean count-derived log2 RNA/DNA score for ecad_high.
ecad_high_median_log2_ratio: Median count-derived log2 RNA/DNA score for ecad_high.
ecad_high_sd_log2_ratio: Sample standard deviation of the count-derived ecad_high scores.
ecad_low_count_total: Sum of raw cDNA counts in the ecad_low FACS group.
ecad_low_n_replicates: Number of source cDNA samples in the ecad_low FACS group.
ecad_low_n_detected_replicates: Number of nonzero cDNA samples in the ecad_low FACS group.
ecad_low_replicate_log2_ratio_1: Library-size-normalized log2 RNA/DNA score for ecad_low replicate 1.
ecad_low_replicate_log2_ratio_2: Library-size-normalized log2 RNA/DNA score for ecad_low replicate 2.
ecad_low_replicate_log2_ratio_3: Library-size-normalized log2 RNA/DNA score for ecad_low replicate 3.
ecad_low_replicate_log2_ratio_4: Library-size-normalized log2 RNA/DNA score for ecad_low replicate 4.
ecad_low_mean_log2_ratio: Mean count-derived log2 RNA/DNA score for ecad_low.
ecad_low_median_log2_ratio: Median count-derived log2 RNA/DNA score for ecad_low.
ecad_low_sd_log2_ratio: Sample standard deviation of the count-derived ecad_low scores.
cd73_s1_count_total: Sum of raw cDNA counts in the cd73_s1 FACS group.
cd73_s1_n_replicates: Number of source cDNA samples in the cd73_s1 FACS group.
cd73_s1_n_detected_replicates: Number of nonzero cDNA samples in the cd73_s1 FACS group.
cd73_s1_replicate_log2_ratio_1: Library-size-normalized log2 RNA/DNA score for cd73_s1 replicate 1.
cd73_s1_mean_log2_ratio: Mean count-derived log2 RNA/DNA score for cd73_s1.
cd73_s1_median_log2_ratio: Median count-derived log2 RNA/DNA score for cd73_s1.
cd73_s1_sd_log2_ratio: Sample standard deviation of the count-derived cd73_s1 scores.
cd73_high_count_total: Sum of raw cDNA counts in the cd73_high FACS group.
cd73_high_n_replicates: Number of source cDNA samples in the cd73_high FACS group.
cd73_high_n_detected_replicates: Number of nonzero cDNA samples in the cd73_high FACS group.
cd73_high_replicate_log2_ratio_1: Library-size-normalized log2 RNA/DNA score for cd73_high replicate 1.
cd73_high_replicate_log2_ratio_2: Library-size-normalized log2 RNA/DNA score for cd73_high replicate 2.
cd73_high_replicate_log2_ratio_3: Library-size-normalized log2 RNA/DNA score for cd73_high replicate 3.
cd73_high_mean_log2_ratio: Mean count-derived log2 RNA/DNA score for cd73_high.
cd73_high_median_log2_ratio: Median count-derived log2 RNA/DNA score for cd73_high.
cd73_high_sd_log2_ratio: Sample standard deviation of the count-derived cd73_high scores.
cd73_low_count_total: Sum of raw cDNA counts in the cd73_low FACS group.
cd73_low_n_replicates: Number of source cDNA samples in the cd73_low FACS group.
cd73_low_n_detected_replicates: Number of nonzero cDNA samples in the cd73_low FACS group.
cd73_low_replicate_log2_ratio_1: Library-size-normalized log2 RNA/DNA score for cd73_low replicate 1.
cd73_low_replicate_log2_ratio_2: Library-size-normalized log2 RNA/DNA score for cd73_low replicate 2.
cd73_low_replicate_log2_ratio_3: Library-size-normalized log2 RNA/DNA score for cd73_low replicate 3.
cd73_low_mean_log2_ratio: Mean count-derived log2 RNA/DNA score for cd73_low.
cd73_low_median_log2_ratio: Median count-derived log2 RNA/DNA score for cd73_low.
cd73_low_sd_log2_ratio: Sample standard deviation of the count-derived cd73_low scores.
author_ecad_log2_fc: Author-reported 455 MPRA ecad log2 fold-change from Supplementary Table 3.
author_ecad_padj: Author-reported BH-adjusted p-value for the 455 MPRA ecad condition.
author_ecad_high_log2_fc: Author-reported 455 MPRA ecad_high log2 fold-change from Supplementary Table 3.
author_ecad_high_padj: Author-reported BH-adjusted p-value for the 455 MPRA ecad_high condition.
author_ecad_low_log2_fc: Author-reported 455 MPRA ecad_low log2 fold-change from Supplementary Table 3.
author_ecad_low_padj: Author-reported BH-adjusted p-value for the 455 MPRA ecad_low condition.
author_cd73_log2_fc: Author-reported 455 MPRA cd73 log2 fold-change from Supplementary Table 3.
author_cd73_padj: Author-reported BH-adjusted p-value for the 455 MPRA cd73 condition.
author_cd73_high_log2_fc: Author-reported 455 MPRA cd73_high log2 fold-change from Supplementary Table 3.
author_cd73_high_padj: Author-reported BH-adjusted p-value for the 455 MPRA cd73_high condition.
author_cd73_low_log2_fc: Author-reported 455 MPRA cd73_low log2 fold-change from Supplementary Table 3.
author_cd73_low_padj: Author-reported BH-adjusted p-value for the 455 MPRA cd73_low condition.

Quality control

Author QC used Gaussian modeling of shuffled controls, BH correction, and the assigned-count quality workflow (fastp Phred >30 and DESeq2 for bulk cDNA/plasmid references). FACS has no plasmid DNA extraction, so the paper reused bulk mouse plasmid references; this package retains elements with aggregate FACS cDNA counts >=10, matched bulk-reference DNA counts >=10, and at least two nonzero FACS cDNA samples. Group scores are median reference-normalized values across the three bulk plasmids; a 0.5 pseudocount and library-size normalization were used.

Curation notes

Source: GSE218470 FACS 455 MPRA matrix plus Supplementary Table 3. The FACS matrix has 418 constructs and no plasmid columns; plasmid references come from the paired bulk mouse matrix as specified by the paper. Raw source labels are preserved as ecad_high, ecad_low, cd73_s1, cd73_high, and cd73_low. Some GEO/sample metadata labels use CD71, whereas the count columns and article methods use CD73; cd73_s1 is kept separately rather than silently relabeled. The author CD73 field is retained under author_cd73_* because its exact bin mapping is ambiguous in the released supplementary files.

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

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

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