CAD 3′UTR RNA-stability MPRA with Actinomycin D

Wild-type 150-nt native 3′UTR tiles from the reporter library were transfected into differentiated CAD cells in six-well plates. Transcription was inhibited with 20 ng/ml Actinomycin D and reporter RNA was measured at 0, 4, and 24 hours in duplicate samples; the table contains the published relative RNA-abundance effects.

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:0199
Reference genome: mm10
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

20 ng/ml Actinomycin D; reporter RNA collected at 0, 4, and 24 h after transcriptional inhibition

The same CMV-eGFP-12-nt-barcode-150-nt-3′UTR episomal reporter design was used, but only the 13,753 wild-type native-tile sequences were assayed for stability. edgeR log2 fold-changes compare reporter RNA abundance at 4 or 24 h with the 0-h sample; positive values indicate higher relative stability than the library population rather than an absolute half-life.

Quality control

The eligible library was restricted to the paper’s ‘wt scanning 50’ subset of 13,753 native 3′UTR tiles. Because per-timepoint Actinomycin-D sample-level counts were not deposited in the GEO series, rows were retained only when both the published 4 h/0 h and 24 h/0 h edgeR log2 fold-changes and p-values were present and finite, yielding 13,508 rows. Stability calls use p<0.05 and the sign of each published log2 fold-change; all retained rows are marked qc_pass=true.

Curation notes

The paper reports duplicate samples at each Actinomycin-D time point, but the public GEO series exposes the 12 soma/neurite localization libraries rather than separate stability count columns. Therefore this table uses the published S2 edgeR stability summaries and a complete-result filter; the CAD localization columns are contextual and were not used as the stability QC criterion. The reference genome is recorded as mm10 because the Supplementary Table S1 mouse coordinates match the mm10/GRCm38 assembly, although the article does not print an assembly label.

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

CAD 3′UTR RNA-stability MPRA with Actinomycin D

Processed data

Quality control

Curation notes

Cite OpenMPRA

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