Experiment / E3VMWAPYVIntegrated lentiMPRA

HEK293 functional screen of candidate human 3′UTR RNA switches

A systematic search for RNA structural switches across the human transcriptome

A lentiviral dual eGFP–mCherry reporter library tested 3,750 candidate human 3′UTR RNA-switch fragments and matched scrambled controls in HEK293 cells. Cells were sorted into eight equal fluorescence bins in two biological replicates, and construct abundance was measured from genomic DNA and reporter RNA.

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:0045
Reference genome: hg19
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Basal / Untreated

Dual eGFP–mCherry reporter with candidate or scrambled 3′UTR inserts immediately downstream of the eGFP ORF. The lentiviral library was transduced at approximately 20% infection, puromycin-selected, sorted by eGFP:mCherry ratio into eight 12.5% bins, and quantified by paired genomic-DNA and RNA sequencing. RNA/DNA measurements provide a reporter activity and mRNA-stability-related readout.

Processed data

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

Search table valuesFilter columnOperatorValue

Visible columns (69 of 69)

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 · 69 definitions

element_id: Source RNA switch fragment identifier (Ensembl transcript fragment name).
construct_id: Unique construct identifier combining the source fragment and construct type.
construct_type: Library construct class: Original genomic 3′UTR fragment or matched Shuffled control.
transcript_id: Ensembl transcript identifier parsed from element_id.
fragment_index: Overlapping 186-nt 3′UTR fragment index parsed from element_id.
sequence: DNA sequence tested in the reporter insert.
sequence_length_bp: Length of the tested sequence in base pairs.
gc_fraction: Fraction of sequence bases that are G or C.
conformation_1_structure: SwitchFinder-predicted dot-bracket structure for conformation 1 from Supplementary Data S2.
conformation_2_structure: SwitchFinder-predicted dot-bracket structure for conformation 2 from Supplementary Data S2.
qc_pass: True for constructs retained after sequence, coverage, and matched-pair QC.
dna_r1_b1_count: Source genomic-DNA read-count value for biological replicate 1, FACS expression bin 1.
dna_r1_b2_count: Source genomic-DNA read-count value for biological replicate 1, FACS expression bin 2.
dna_r1_b3_count: Source genomic-DNA read-count value for biological replicate 1, FACS expression bin 3.
dna_r1_b4_count: Source genomic-DNA read-count value for biological replicate 1, FACS expression bin 4.
dna_r1_b5_count: Source genomic-DNA read-count value for biological replicate 1, FACS expression bin 5.
dna_r1_b6_count: Source genomic-DNA read-count value for biological replicate 1, FACS expression bin 6.
dna_r1_b7_count: Source genomic-DNA read-count value for biological replicate 1, FACS expression bin 7.
dna_r1_b8_count: Source genomic-DNA read-count value for biological replicate 1, FACS expression bin 8.
dna_r2_b1_count: Source genomic-DNA read-count value for biological replicate 2, FACS expression bin 1.
dna_r2_b2_count: Source genomic-DNA read-count value for biological replicate 2, FACS expression bin 2.
dna_r2_b3_count: Source genomic-DNA read-count value for biological replicate 2, FACS expression bin 3.
dna_r2_b4_count: Source genomic-DNA read-count value for biological replicate 2, FACS expression bin 4.
dna_r2_b5_count: Source genomic-DNA read-count value for biological replicate 2, FACS expression bin 5.
dna_r2_b6_count: Source genomic-DNA read-count value for biological replicate 2, FACS expression bin 6.
dna_r2_b7_count: Source genomic-DNA read-count value for biological replicate 2, FACS expression bin 7.
dna_r2_b8_count: Source genomic-DNA read-count value for biological replicate 2, FACS expression bin 8.
rna_r1_b1_count: Source RNA read-count value for biological replicate 1, FACS expression bin 1.
rna_r1_b2_count: Source RNA read-count value for biological replicate 1, FACS expression bin 2.
rna_r1_b3_count: Source RNA read-count value for biological replicate 1, FACS expression bin 3.
rna_r1_b4_count: Source RNA read-count value for biological replicate 1, FACS expression bin 4.
rna_r1_b5_count: Source RNA read-count value for biological replicate 1, FACS expression bin 5.
rna_r1_b6_count: Source RNA read-count value for biological replicate 1, FACS expression bin 6.
rna_r1_b7_count: Source RNA read-count value for biological replicate 1, FACS expression bin 7.
rna_r1_b8_count: Source RNA read-count value for biological replicate 1, FACS expression bin 8.
rna_r2_b1_count: Source RNA read-count value for biological replicate 2, FACS expression bin 1.
rna_r2_b2_count: Source RNA read-count value for biological replicate 2, FACS expression bin 2.
rna_r2_b3_count: Source RNA read-count value for biological replicate 2, FACS expression bin 3.
rna_r2_b4_count: Source RNA read-count value for biological replicate 2, FACS expression bin 4.
rna_r2_b5_count: Source RNA read-count value for biological replicate 2, FACS expression bin 5.
rna_r2_b6_count: Source RNA read-count value for biological replicate 2, FACS expression bin 6.
rna_r2_b7_count: Source RNA read-count value for biological replicate 2, FACS expression bin 7.
rna_r2_b8_count: Source RNA read-count value for biological replicate 2, FACS expression bin 8.
gdna_total_rep1: Sum of source genomic-DNA counts across bins 1–8 for replicate 1, on the source count scale.
rna_total_rep1: Sum of source RNA counts across bins 1–8 for replicate 1, on the source count scale.
normalized_gdna_total_rep1: Median-of-ratios normalized genomic-DNA total for replicate 1; used for activity calculation.
normalized_rna_total_rep1: Median-of-ratios normalized RNA total for replicate 1.
activity_log2_rna_dna_rep1: Log2 of normalized RNA total divided by normalized genomic-DNA total for replicate 1, using a 0.5 pseudocount.
mean_rna_expression_bin_rep1: RNA-count-weighted mean FACS bin number (1–8) for replicate 1; higher values indicate enrichment in higher-expression bins.
dna_adjusted_expression_bin_rep1: Mean FACS bin number weighted by per-bin normalized RNA/genomic-DNA enrichment for replicate 1, with 0.5 pseudocounts.
gdna_total_rep2: Sum of source genomic-DNA counts across bins 1–8 for replicate 2, on the source count scale.
rna_total_rep2: Sum of source RNA counts across bins 1–8 for replicate 2, on the source count scale.
normalized_gdna_total_rep2: Median-of-ratios normalized genomic-DNA total for replicate 2; used for activity calculation.
normalized_rna_total_rep2: Median-of-ratios normalized RNA total for replicate 2.
activity_log2_rna_dna_rep2: Log2 of normalized RNA total divided by normalized genomic-DNA total for replicate 2, using a 0.5 pseudocount.
mean_rna_expression_bin_rep2: RNA-count-weighted mean FACS bin number (1–8) for replicate 2.
dna_adjusted_expression_bin_rep2: Mean FACS bin number weighted by per-bin normalized RNA/genomic-DNA enrichment for replicate 2, with 0.5 pseudocounts.
activity_log2_rna_dna: Mean of the two replicate log2 RNA/genomic-DNA activity values.
activity_log2_rna_dna_sd: Sample standard deviation of the two replicate log2 RNA/genomic-DNA activity values.
activity_log2_rna_dna_rep2_minus_rep1: Replicate 2 minus replicate 1 log2 RNA/genomic-DNA activity.
mean_rna_expression_bin: Mean of the two RNA-weighted mean FACS-bin scores.
dna_adjusted_expression_bin: Mean of the two DNA-adjusted expression-bin scores.
expression_bin_score_rep2_minus_rep1: Replicate 2 minus replicate 1 RNA-weighted mean-bin score.
replicate_bin_profile_pearson_r: Pearson correlation between the two replicate per-bin RNA/genomic-DNA enrichment profiles.
matched_control_construct_id: Identifier of the paired construct of the opposite class (Original versus Shuffled).
matched_control_activity_log2_rna_dna: Matched construct mean log2 RNA/genomic-DNA activity.
activity_log2_rna_dna_vs_matched_control: This construct's mean log2 activity minus its matched control's mean log2 activity.
matched_control_mean_rna_expression_bin: Matched construct mean RNA-weighted FACS-bin score.
mean_rna_expression_bin_vs_matched_control: This construct's mean RNA-weighted bin score minus the matched control's score.

Quality control

Author workflow retained: library representation sequencing; approximately 20% low-MOI lentiviral infection; eight equal 12.5% FACS bins; two biological replicates; cutadapt trimming, UMI handling, BWA-MEM mapping, featureCounts quantification, median-of-ratios normalization, and MPRAnalyze-based RNA/DNA analysis. Additional package QC required valid A/C/G/T sequence and at least 100 source counts summed across all eight bins for both RNA and genomic DNA in each replicate, then retained only complete Original–Shuffled matched pairs. 7164/7500 construct rows (3582 pairs) passed.

Curation notes

Source: GSE266058 functional_screen.tsv.gz (the same experiment as publisher Supplementary Data S3); the complete source matrix is preserved in raw_data. The table is construct-level rather than barcode-level because the public count table contains one row per oligonucleotide and no individual barcode identifiers. Source bin counts are retained. Derived totals use median-of-ratios factors computed across the 32 source count columns; activity is log2((normalized RNA total + 0.5)/(normalized genomic-DNA total + 0.5)). Bin scores use bins 1–8, where bin 1 is the lowest and bin 8 the highest eGFP:mCherry expression. SwitchFinder structures were joined from Supplementary Data S2 by element_id. The genome build is represented as hg19 because the paper reports UCSC GENCODE Basic V28 lift37 3′UTR coordinates; the public count matrix does not include genomic coordinates.

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