Input files for scUTRquant-figures repository

OverviewThis dataset contains input and intermediate objects that are part of the minimum dataset required for verifying the analysis reported in Fansler et al., <i>Nat Commun., </i>2024. These objects are used in the following repositories to generate figures in the manuscript:https://github.com/Mayrlab/scUTRquant-figureshttps://github.com/Mayrlab/hcl-analysishttps://github.com/Mayrlab/mca-analysishttps://github.com/Mayrlab/gwps-sqThe repositories contain additional information on the derivation of the objects.DescriptionsThe folders contain the following data:<b>aparent2</b> - scores from analyzing human Microwell-seq cleavage sites<b>bam</b> - genomic alignments of single-cell data subsetted to the 3' cleavage site of Vamp2 in mouse<b>bed</b> - cleavage site annotations from hcl-utrome and mca-utrome; reprocessed counts from polyASite 2.0<b>celltype_score</b> - tabulation of number of cell types in which a cleavage site is detected<b>clusters</b> - APA regulator cluster information derived from Perturb-seq data<b>conservation</b> - phastCons scores for cleavage site neighborhoods<b>counts</b> - a note for where to get data from 10X Genomics<b>dge</b> - results from differential gene expression testing<b>dtu</b> - results from differential transcript usage testing (uses scUTRboot)<b>dwui</b> - results from differential WUI testing in Perturb-seq<b>gtf</b> - annotations of human and mouse UTRome<b>halflife</b> - isoform-resolved mRNA halflives from K562 SLAM-seq data<b>kallisto</b> - counts and kallisto indices for the UTRomes<b>lui</b> - longest 3'UTR isoform usage point estimates and cell counts in large survey of scRNA-seq datasets<b>seq</b> - extracted sequences used as input to APARENT2<b>tpm</b> - TPMs and counts per cell (CPC) for mouse and human summarized to cell type; also TPM tables for summarized Perturb-seq data<b>wui</b> - Weighted UTR Index quantifications for all perturbations in K562 and RPE1 essential Perturb-seq screens<br>