Experiment / E4923R6AYEpisomal Plasmid MPRA

SuRE-seq caQTL and chromatin-module enhancer fragments in GM12878

Context transcription factors establish cooperative environments and mediate enhancer communication

A 270-bp allele-aware library of caQTL lead and linked neighbor/dependent enhancer fragments was assayed for autonomous promoter activity in GM12878 using the SuRE barcoded plasmid assay. The table reports QC-filtered element/genotype groups with sequence, variant annotation, count-derived activity, and zero-RNA fractions.

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: Human
Taxonomy ID: NCBITaxon:9606
Biosample: CVCL:7526
Reference genome: GRCh37
Design focus: Variant-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

SuRE-seq (Survey of Regulatory Elements) uses 270-bp genomic fragments cloned into an episomal promoterless barcoded reporter; barcode RNA is quantified relative to plasmid DNA. It tests more/less accessible caQTL genotypes plus linked LOCAL/CM neighbor or dependent elements; forward and reverse fragment orientations were combined.

Processed data

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

Visible columns (25 of 25)

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 · 25 definitions

element_id: Canonical SuRE element label, with source _VCM suffix normalized to _CM.
sure_id: Source numeric SuRE element identifier.
triplet_id: Source linked enhancer triplet identifier.
element_type: Source element role: more, less, or dep.
enhancer_type: Source enhancer class, such as CM or LOCAL.
sequence_270bp: The tested 270-bp SuRE fragment sequence.
snp_chr: Chromosome of the annotated caQTL in the source table.
snp_pos_hg19: caQTL position on the GRCh37/hg19 assembly.
rs_id: Source dbSNP identifier when available.
genotype_call: Source genotype/construct call, including REF, SNP, or INDEL.
n_unique_barcodes_element_qc: Unique barcodes assigned to the element after mapping and coverage QC.
n_barcodes_qc: Barcode observations contributing to this element/genotype group.
sum_plasmid_dna: Combined plasmid DNA count across the two SuRE plasmid replicates.
sum_cdna_rep1: Total cDNA count for SuRE replicate 1.
sum_cdna_rep2: Total cDNA count for SuRE replicate 2.
sum_cdna_combined: Combined cDNA count across both SuRE replicates.
log2_sum_cdna_over_plasmid_rep1: Log2 of summed replicate-1 cDNA divided by summed plasmid DNA.
log2_sum_cdna_over_plasmid_rep2: Log2 of summed replicate-2 cDNA divided by summed plasmid DNA.
log2_sum_cdna_over_plasmid_combined: Log2 of combined cDNA divided by combined plasmid DNA.
mean_log2_activity_positive_cdna_rep1: Mean per-barcode log2 cDNA/plasmid ratio among replicate-1 barcodes with positive cDNA.
mean_log2_activity_positive_cdna_rep2: Mean per-barcode log2 cDNA/plasmid ratio among replicate-2 barcodes with positive cDNA.
fraction_zero_cdna_rep1: Fraction of contributing barcodes with zero replicate-1 cDNA.
fraction_zero_cdna_rep2: Fraction of contributing barcodes with zero replicate-2 cDNA.
fraction_zero_cdna_both_reps: Fraction of contributing barcodes with zero cDNA in both replicates.
qc_pass: True for rows retained after the documented SuRE filters.

Quality control

Applied the paper’s filters: retained barcode-to-element mappings with iPCR.Reads >=2; removed barcodes mapping to >1 SuRE element (including multi-element labels); required combined plasmid DNA count >0; retained elements with >=4 unique barcodes. Kept genotype calls separately. The current Zenodo record exposes raw SuRE counts but not the author’s missing processed count file, so activity columns are generated as log2(sum cDNA/sum plasmid) plus positive-cDNA mean log2 ratios and zero-cDNA fractions; zero-RNA observations are retained rather than silently discarded.

Curation notes

SuRE raw rows sometimes contain the same barcode/element with different VCF_Call values; these calls are preserved as separate output rows. 3,468 elements passed the >=4-barcode filter, yielding 10,018 element/genotype rows. rs_id is absent for linked dependent fragments where the source annotation is blank.

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