Experiment / E527LJ80M3' UTR / RNA Stability MPRA (MPRAu)

PTRE-seq of CELF6 CLIP-defined mouse 3′-UTR elements in SH-SY5Y cells

CLIP and Massively Parallel Functional Analysis of CELF6 Reveal a Role in Destabilizing Synaptic Gene mRNAs through Interaction with 3′ UTR Elements

Transient post-transcriptional reporter sequencing tested mouse 3′-UTR elements selected from in vivo CELF6 CLIP peaks, each paired with a motif-mutant sequence. Total reporter RNA and translating-ribosome-associated reporter RNA were measured under vector, CELF6, CELF3, CELF4, CELF5, and CELF3/4/5 plus CELF6 co-expression conditions.

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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:0019
Reference genome: mm10
Design focus: Synthetic / Motif-focused
Region of interest: Not reported / not applicable

Perturbation & assay details

Transient trans-factor overexpression: empty-vector control (CTL) versus His/Xpress-CELF6, CELF3, CELF4, CELF5, CELF3+CELF6, CELF4+CELF6, or CELF5+CELF6; EGFP-RPL10A was co-transfected for TRAP.

PTRE-seq used the episomal pmrPTRE-AAV tdTomato reporter. The deposited public design table contains 50-nt reference/mutant sequence fields, while the article text describes the cloned UTR elements as 120 bp; the processed package preserves the deposited 50-nt sequences and does not infer missing flanks. Six unique 9-bp barcodes were designed per element/allele; final modeling used 3–6 surviving barcodes per element. Total RNA input reports reporter abundance, EGFP-RPL10A TRAP reports ribosome-associated reporter RNA, and translation efficiency is log2 expression(TRAP) minus log2 expression(total RNA).

Processed data

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

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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 · 38 definitions

element_id: Unique mouse 3′-UTR CLIP peak identifier in gene:chromosome:strand:peak-coordinate format.
gene_name: Mouse gene symbol/name associated with the tested CLIP peak.
chromosome: Mouse mm10 chromosome containing the peak.
strand: Genomic strand of the source CLIP peak.
peak_center_mm10: Peak coordinate reported by the study on mm10.
region_annotation: Source feature annotation from the CLIP target table, typically utr3.
clip_analysis_method: CLIP enrichment analysis method used for this target in Table S2.
clip_number_of_peaks: Number of called peaks in the associated annotated region from Table S2.
clip_region_start_mm10: Start coordinate(s) of the annotated source region in mm10; semicolon-separated when the source annotation contains multiple intervals.
clip_region_end_mm10: End coordinate(s) of the annotated source region in mm10; semicolon-separated when the source annotation contains multiple intervals.
clip_region_length_bp: Length in base pairs of the annotated source region.
clip_rank_criterion: CELF6 CLIP confidence criterion: both controls or input-only.
clip_high_confidence: True when the target passed both input and WT/non-specific IP CLIP criteria.
clip_log2fc_input: CLIP edgeR log2 fold-change for YFP+ IP versus YFP input.
clip_p_input: Nominal edgeR p-value for YFP+ IP versus YFP input.
clip_log2fc_wt: CLIP edgeR log2 fold-change for YFP+ IP versus WT IP.
clip_p_wt: Nominal edgeR p-value for YFP+ IP versus WT IP.
ref_sequence_50nt: Reference sequence provided in public Table S5; all deposited sequence fields are 50 nt.
mut_sequence_50nt: Motif-mutant sequence provided in public Table S5; all deposited sequence fields are 50 nt.
hamming_distance: Number of nucleotide substitutions between the reference and mutant sequence.
motif_matches: Comma-separated RBP motif names detected in the reference design.
motif_match_starts_1based: Comma-separated 1-based starts of the motif matches.
motif_match_ends_1based: Comma-separated 1-based ends of the motif matches.
motif_match_scores: Comma-separated FIMO motif match scores.
motif_match_pvalues: Comma-separated FIMO motif match p-values.
qc_status: PASS; element is included in the paper’s final 379-element post-QC model set.
readout: Reporter readout: total input RNA abundance, TRAP ribosome-associated RNA, or translation efficiency.
condition: Trans-factor condition: CTL/vector, CELF6, CELF3, CELF4, CELF5, or CELF3/4/5 co-expressed with CELF6.
ref_minus_mut_log2fc: Mixed-model estimate of log2(reference reporter signal minus motif-mutant signal) for this condition/readout; negative values indicate lower reference signal.
effect_ci_low_95pct: Lower bound of the reported 95% confidence interval for the reference-minus-mutant effect.
effect_ci_high_95pct: Upper bound of the reported 95% confidence interval for the reference-minus-mutant effect.
model_p_sequence: Omnibus p-value for the sequence main effect in the mixed model for this readout.
model_p_condition: Omnibus p-value for the condition main effect in the mixed model for this readout.
model_p_interaction: Omnibus p-value for the condition-by-sequence interaction in the mixed model for this readout.
model_fdr_sequence: Benjamini–Hochberg FDR for the sequence main effect.
model_fdr_condition: Benjamini–Hochberg FDR for the condition main effect.
model_fdr_interaction: Benjamini–Hochberg FDR for the condition-by-sequence interaction.
model_r2: R² estimate reported by the paper for the mixed model.

Quality control

Inherited from the paper: removed elements with no DNA plasmid-pool counts; retained barcodes with at least 10 counts in at least 4 samples; required at least 3 of the original 6 barcodes for both reference and mutant; excluded one replicate batch that clustered separately; required RNA RINe > 8; replicate barcode counts had Pearson correlation > 0.9. The final analyzed set was 379 element pairs across 153 genes, including 229 high-confidence and 150 lower-stringency CLIP targets.

Curation notes

This is one multiplexed PTRE-seq reporter experiment with eight trans-factor conditions and three reported readouts, represented as 9,096 tidy rows (379 final elements × 8 conditions × 3 readouts). The public GEO series GSE118623 is primarily a 14-sample CELF6 CLIP-seq submission; its visible supplementary directory does not contain PTRE-seq barcode count matrices. Accordingly, the processed table merges the exact public Table S5 designs with the final public mixed-model outputs in Tables S6–S8 and CLIP annotations from Table S2; it does not claim an independent barcode-level reanalysis. The reporter sequences derive from mouse brain CLIP targets but were assayed in the human SH-SY5Y cell line (Cellosaurus CVCL_0019).

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