N-zip MPRA in CAD cells using firefly luciferase reporter

A densely tiled library of 260-nt mouse 3′-UTR fragments and controls was inserted into the 3′ UTR of a firefly luciferase reporter and integrated into CAD cells by Cre/loxP-mediated recombination. Targeted UMI RNA-seq of cell-body and neurite fractions, with four biological replicates per compartment, quantified each oligo's localization.

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

Serum-free differentiation medium for 48 h; 1 µg/ml doxycycline induction for 48 h

The library tiled selected mouse 3′ UTRs at 260 nt with a 4-nt step and included BC1 positive controls plus soma-enriched, non-enriched, and Malat1 controls. The reporter library was introduced into LoxP CAD cells by Cre-mediated recombination; targeted RNA sequencing used an 8-nt UMI and Bowtie2 alignment to the reference oligos, and DESeq2 quantified neurite-versus-soma enrichment. The processed table reports firefly-scaffold results only; no plasmid-DNA counts were deposited for DNA normalization.

Quality control

The paper reports 100% detection of expected oligos in the synthesized library, approximately 65% of oligos without detected mutations/indels, typically 99% adapter detection and 95% alignment, UMI-based quantification, and compartment QC using β-actin and Histone H3. For this package, the 7,360 rows in published Table S2 were joined to the published sequence/annotation files and retained only when each of the four soma and four neurite UMI-count replicates contained at least 10 unique UMIs; 3,907 rows retained and 3,453 low/incomplete-coverage rows were excluded.

Curation notes

This experiment corresponds to published Table S2. The raw GEO archive has 32 UMI tables and includes 750 additional Trp53inp2 oligo IDs that are absent from the final published Table S1–S4 sequence/result set; those version-mismatched rows were not included. The three BC1 positive-control oligos are present in the final result table but have no mm10 coordinate feature in SupplementaryFile2.txt, so their coordinate fields are blank. Counts are RNA UMI counts from soma and neurite fractions rather than classic DNA-normalized enhancer scores; the authors' DESeq2 log2FC and adjusted p-value are retained as the primary localization readout.

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

N-zip MPRA in CAD cells using firefly luciferase reporter

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