Polyadenylation landscape of in vivo long-term potentiation in the rat brain

This repository contains data published along our corresponding manuscript and additional data resources generated/used throughout this work. ______________________________________________________________________________

Source data accompanying the manuscript:

Supplementary Table 1. Key resource table. (A) Characteristics of analyzed material (e.g. sample identifiers, number of animals used, reads produced, accession numbers). (B) Key resources (antibodies, reagents, software).Supplementary Table 2. Summary of dentate gyri DRS data per gene. (A) Differential expression and differential adenylation data for 10 min timepoint. (B) Differential expression and differential adenylation data for 60 min timepoint. (C) GO-terms for genes with significantly elongated poly(A) tails in 10 min timepoint. (D) GO-terms for genes with significantly elongated poly(A) tails in 60 min timepoint. (E) GO-terms for upregulated genes in 10 min timepoint. (F) GO-terms for upregulated genes in 60 min timepoint. (G) GO-terms for upregulated genes with CPEB-binding motifs in 10 min timepoint. (H) GO-terms for upregulated genes with CPEB-binding motifs in 60 min timepoint.

Supplementary Table 3. Summary of dentate gyri cDNA data per gene. (A) Differential expression and differential adenylation data for 10 min timepoint. (B) Differential expression and differential adenylation data for 60 min timepoint. (C) GO-terms for genes with significantly elongated poly(A) tails in 10 min timepoint. (D) GO-terms for genes with significantly elongated poly(A) tails in 60 min timepoint. (E) GO-terms for upregulated genes in 10 min timepoint. (F) GO-terms for upregulated genes in 60 min timepoint. (G) GO-terms for upregulated genes with CPEB-binding motifs in 10 min timepoint. (H) GO-terms for upregulated genes with CPEB-binding motifs in 60 min timepoint.

Supplementary Table 4. High-confidence PASs. (A) PASs predicted for datasets obtained 10 min after LTP induction by TAPAS. (B) High confidence poly(A) clusters predicted by LAPA for datasets obtained 10 min after LTP induction. (C) PASs predicted for datasets obtained 60 min after LTP induction. (D) High confidence poly(A) clusters predicted by LAPA for datasets obtained 60 min after LTP induction.

Supplementary Table 5. Nonadenosine profiling upon LTP induction. (A) Summary of Ninetails pipeline for dentate gyrus. (B) List of genes containing semi-templated poly(A) tails with their adjacent nucleotide contexts.

Supplementary Table 6. Summary of synaptoneurosomal DRS/cDNA data per gene. (A) Differential expression and differential adenylation data for unfractionated synaptoneurosomes DRS sequencing. (B)  Summary of Ninetails pipeline for unfractionated synaptoneurosomes DRS sequencing. (C) Differential expression and differential adenylation data for monoribosome-bound mRNA synaptoneurosomes cDNA sequencing. (D) Differential expression and differential adenylation data for polyribosome-bound mRNA synaptoneurosomes cDNA sequencing. (E) Differential expression and differential adenylation data for unfractionated synaptoneurosomes cDNA sequencing.Supplementary Information - supplementary figures and captions.______________________________________________________________________________

Additional data resources:

CPEB1_motif.meme - CPE1 motif sequence represented as position-dependent letter-probability matrice required by FIMO to make predictions.CPEB2_4_motif.meme - CPE2,4 motif sequence represented as position-dependent letter-probability matrice required by FIMO to make predictions.

mRatBN7.2_TAPAS_ref_flat.txt - mRatBN7.2 reference annotation in format required by TAPASmRatBN7.2_LAPA.gtf - mRatBN7.2 reference annotation in format required by LAPA

FIMO_output.zip - compressed folder with motif predictions provided by FIMO software.LAPA_output_dentate_gyrus.zip - compressed folder with poly(A) clusters predicted by LAPA software. Each timepoint is represented by separate output. TAPAS_output_dentate_gyrus.zip - compressed folder with raw outputs produced by TAPAS software. Each timepoint is represented by separate output. Ninetails_output_dentate_gyrus.zip - compressed folder with raw outputs produced by Ninetails software for samples from dentate gyrus. Subfolders are named according to the sample identifiers provided in Supplementary Table 1. For each sequencing run, 2 tsv files are produced: read classification and nonadenosine residue classification.Ninetails_output_synaptoneurosomes.zip - compressed folder with raw outputs produced by Ninetails software for samples from synaptoneurosomes. Subfolders are named according to the sample identifiers provided in Supplementary Table 1. For each sequencing run, 2 tsv files are produced: read classification and nonadenosine residue classification.PolyA_clusters_high_confident.bed - High-confidence poly(A) clusters annotation in bed format.