A 6,266-sequence follow-up library derived from 16 neurite-enriched tiles tested WT controls, single-base substitutions, 2/5/10-nt transition windows, scrambled controls and motif-directed mutations/deletions. The integrated lentiviral reporter was assayed in baseline PCNs and with Ago2, Hbs1l or scrambled shRNA perturbations.
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
Variant-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
Baseline; Ago2 knockdown; Hbs1l knockdown; scrambled shRNA control
The secondary library used the same synapsin-driven lentiviral GFP 3′ UTR reporter and neurite/soma fractionation as the original N-zip assay. It systematically perturbed selected localization tiles with point substitutions, A↔T/C↔G transition windows, scrambles and motif deletions; UMI-tagged reporter amplicons were sequenced and summarized as neurite/soma log2 ratios.
Processed data
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Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 26 definitions
element_id
Stable identifier generated from source gene, source tile, mutation type, position and source workbook row.
source_gene_id
Ensembl gene ID of the source gene.
source_gene_name
Source gene/tile name used by the authors.
source_tile_id
Original N-zip tile identifier from the mutagenesis design sheet.
mutation_library_row
Data-row number in Supplementary Table 2a (Excel row number).
mutation_type
Author-provided mutation class: WT, sgl, kmer2, kmer5, kmer10, scr, mut or del.
mutation_position
Author-provided mutation position or affected window, including the substituted base for point mutations.
wild_type_sequence
Unmutated sequence for the corresponding source tile reconstructed from WT rows in Supplementary Table 2a.
tested_sequence
DNA sequence of the tested mutagenized or control construct, without library adapters.
wild_type_sequence_length
Length of the reconstructed wild-type sequence in nucleotides.
tested_sequence_length
Length of the tested sequence in nucleotides.
sequence_length_delta
Tested-sequence length minus wild-type length in nucleotides.
same_length_difference_nt
Number of differing nucleotide positions when tested and wild-type sequences have equal length; blank for length-changing entries.
max_at_repeat_units_wild_type
Maximum complete alternating A/T or T/A dinucleotide repeat units in the wild-type sequence.
max_at_repeat_units_tested
Maximum complete alternating A/T or T/A dinucleotide repeat units in the tested sequence.
max_at_alternating_run_nt_wild_type
Longest alternating A/T run length in nucleotides in the wild-type sequence.
max_at_alternating_run_nt_tested
Longest alternating A/T run length in nucleotides in the tested sequence.
let7_seed_site_count_wild_type
Count of overlapping exact CTACCTC matches in the wild-type sequence.
let7_seed_site_count_tested
Count of overlapping exact CTACCTC matches in the tested sequence.
mean_log2ratio_neurite_soma_wt
Published baseline WT-PCN mean neurite/soma log2 ratio for the construct.
mean_padj_neurite_soma_wt
Benjamini–Hochberg adjusted P value for the published baseline WT-PCN result.
median_log2ratio_neurite_soma_shAgo2
Median neurite/soma log2 ratio in PCNs expressing Ago2-targeting shRNA.
median_log2ratio_neurite_soma_shHbs1l
Median neurite/soma log2 ratio in PCNs expressing Hbs1l-targeting shRNA.
median_log2ratio_neurite_soma_shScramble
Median neurite/soma log2 ratio in scrambled-shRNA control PCNs.
notes
Author-provided annotation for the mutagenesis design, when present.
qc_pass
All rows in the output passed the packaged-table QC filter.
Quality control
The paper exact-matched adapter-containing reads to library sequences, normalized mapped counts, required at least 20 reads on average and reports 5,679/6,266 mutagenized tiles with at least three samples at that threshold; replicate compartment counts were reported as highly correlated (Spearman R > 0.85), and DESeq2 Wald tests used Benjamini–Hochberg correction. Per-sample read counts are not included in the deposited workbook, so the packaged-table filter retained rows with non-missing published baseline Mean_log2ratio and Mean_padj (5,775/6,266 rows) and excluded 491 rows with missing baseline adjusted P values.
Curation notes
Supplementary Table 2b omits source_tile_id and contains seven duplicate (gene, mutation_type, mutation_position) keys for the alternative Cflar_2 source tiles. For those keys, effect rows were paired to Supplementary Table 2a sequences by within-key occurrence order; source_tile_id and sequences come from Table 2a. The table retains only constructs with a reported baseline effect and adjusted P value, while condition-specific knockdown values remain blank where the authors report NA. Secondary library output contains 5775 QC-passing constructs.