Original N-zip 3′ UTR tiling library in primary cortical neurons

A 4,813-element library of 75–110-nt tiles spanning selected mouse 3′ UTRs was cloned downstream of GFP in a pooled lentiviral reporter and assayed after neurite/soma fractionation. The packaged table contains the published baseline WT localization scores and the reported shElavl234/shScramble and depolarization comparisons.

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:0010012
Reference genome: mm10 (GRCm38.p6; Ensembl release 91)
Design focus: Region-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Baseline; 3-hour 55 mM KCl depolarization; shElavl2/3/4 versus scrambled shRNA

A neuron-specific synapsin promoter drove a lentiviral GFP reporter carrying each tiled 3′ UTR fragment. RNA from soma and neurites was reverse-transcribed using an adapter primer, UMI-tagged, PCR-amplified and sequenced; the primary readout is neurite/soma log2 enrichment rather than conventional whole-cell transcriptional activity.

Quality control

The paper retained reads containing the 3′ adapter, extracted the preceding UMI, exact-matched reads to library sequences, normalized counts to total mapped reads, and required at least 20 reads on average; it reports 4,745 tiles with at least three samples at that threshold (98.5%) and Spearman R > 0.85 across compartment replicates. DESeq2 Wald tests with Benjamini–Hochberg correction were used for tile significance. Because per-sample read counts were not included in the deposited supplementary workbook, the reproducible packaged-table filter retained rows with non-missing published WT DESeq2 log2ratio and adjusted P value (4,775/4,813 rows) and excluded the 38 rows with missing primary QC/statistical values.

Curation notes

The table is a clean sequence-to-localization-effect view of Supplementary Tables 1a/1b. It does not contain per-sample DNA/RNA counts because those are not provided in the supplementary workbook; the authors’ raw reads are deposited under E-MTAB-10902/ERP133202 and were not downloaded. The paper’s reported read-threshold total (4,745) cannot be reproduced row-by-row from the supplement, so rows with missing WT DESeq2 effect or adjusted P value were removed as the available QC proxy. Original library output contains 4775 QC-passing tiles.

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

Original N-zip 3′ UTR tiling library in primary cortical neurons

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