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>

数据集概览
本数据集包含用于验证Fansler等人2024年发表于《自然·通讯》的分析结果所需的最小数据集的输入文件与中间对象。这些对象将用于以下仓库中生成论文插图：
https://github.com/Mayrlab/scUTRquant-figures
https://github.com/Mayrlab/hcl-analysis
https://github.com/Mayrlab/mca-analysis
https://github.com/Mayrlab/gwps-sq
上述仓库中包含了关于这些对象衍生过程的额外信息。

数据说明：
各文件夹包含如下数据：
<b>aparent2</b> - 针对人类Microwell-seq剪切位点的分析得分
<b>bam</b> - 小鼠单细胞数据的基因组比对结果，该结果已子集化至Vamp2基因的3'剪切位点
<b>bed</b> - 来自hcl-utrome与mca-utrome的剪切位点注释文件，以及经重新处理的polyASite 2.0计数数据
<b>celltype_score</b> - 剪切位点被检测到的细胞类型数量统计表
<b>clusters</b> - 源自Perturb-seq数据的可变多聚腺苷酸化（Alternative Polyadenylation, APA）调控因子聚类信息
<b>conservation</b> - 剪切位点周边区域的phastCons进化保守性得分
<b>counts</b> - 关于从10X Genomics获取原始数据的说明文件
<b>dge</b> - 差异基因表达（Differential Gene Expression, DGE）分析结果
<b>dtu</b> - 差异转录本使用量（Differential Transcript Usage, DTU）分析结果，分析过程使用了scUTRboot工具
<b>dwui</b> - Perturb-seq实验中的差异加权UTR指数（Weighted UTR Index, WUI）分析结果
<b>gtf</b> - 人类与小鼠UTRome的基因组注释文件
<b>halflife</b> - 基于K562细胞SLAM-seq数据得到的转录本分辨率的mRNA半衰期数据
<b>kallisto</b> - UTRome的计数数据与kallisto索引文件
<b>lui</b> - 大规模单细胞RNA测序（single-cell RNA-seq, scRNA-seq）数据集调查中，最长3'UTR转录本使用量的点估计值与细胞计数数据
<b>seq</b> - 用作APARENT2模型输入的提取序列数据
<b>tpm</b> - 已按细胞类型汇总的人类与小鼠的每细胞TPM（Transcripts Per Million, TPM）值与细胞计数（Counts Per Cell, CPC）；同时包含经汇总的Perturb-seq数据的TPM表格
<b>wui</b> - 针对K562与RPE1细胞系的必需基因Perturb-seq筛选中所有扰动实验的加权UTR指数（Weighted UTR Index, WUI）定量结果