scUTRquant SingleCellExperiment and SummarizedExperiment Objects

Overview

This dataset contains R Bioconductor objects that have 3'UTR isoform counts quantified with the scUTRquant pipeline (https://doi.org/10.5281/zenodo.8118393). These objects are part of the minimum dataset required for verifying the analysis reported in Fansler et al., bioRxiv, 2023.

Loading objects

The objects can be loaded into R 4.2 using Bioconductor 3.16. A minimal Conda environment definition is provided for creating compatible environments. For example:

conda env create -n sce_bioc_3_16 -f envs/sce_bioc_3_16.min.yaml

The .Rds objects can be loaded with (for example):

sce <- readRDS("sce/utrome_mm10_v2/bleckwehl21.txs.Rds")

Descriptions

The objects are organized as follows:

• envs - Conda environment definitions
• • sce_bioc_3_16.full.yaml - solved version for osx-64 (for record only)
  • sce_bioc_3_16.min.yaml - minimal version intended for reuse
• sce - SingleCellExperiment objects
• • gencode_vM25_pc_w500 - data quantified using truncated GENCODE vM25 protein coding transcripts
  • • dahlin18.txs.Rds - HSPCs from Dahlin et al., 2018
    • guo19.txs.Rds - mESCs from Guo et al., 2019
    • tmuris.txs.Rds - 10X Chromium 3' data from Tabula Muris
    • ximerakis19.txs.Rds - aging brain samples from Ximerakis et al., 2019
  • utrome_hg38_v1 - data quantified using the Microwell-seq-derived annotation provided in scUTRquant
  • • pbmc_10k_v3_fastq.txs.Rds - 10X v3 kit demonstration 10K PBMCs
    • pbmc_1k_v2_fastq.txs.Rds - 10X v2 kit demonstration 1K PBMCs
    • pbmc_1k_v3_fastq.txs.Rds - 10X v3 kit demonstration 1K PBMCs
    • tsapiens.txs.full_annot.Rds - 10X Chromium 3' data from Tabula Sapiens
  • utrome_mm10_v2 - data quantified using the Microwell-seq-derived annotation provided in scUTRquant
  • • bleckwehl21.txs.Rds - mESCs from Bleckwehl et al., 2021
    • guo19.txs.Rds - mESCs from Guo et al., 2019
    • heart_10k_v3_fastq.txs.Rds - 10X v3 kit demonstration 10K heart cells
    • heart_1k_v2_fastq.txs.Rds - 10X v2 kit demonstration 1K heart cells
    • heart_1k_v3_fastq.txs.Rds - 10X v3 kit demonstration 1K heart cells
    • merged.txs.full_annot.Rds - combined atlas with annotations including HSPCs from Dahlin et al., 2018; mESCs from Guo et al., 2019; 10X Chromium 3' data from Tabula Muris; brain cells from Ximerakis et al., 2019
    • neuron_10k_v3_fastq.txs.Rds - 10X v3 kit demonstration 10K neurons
    • neuron_1k_v2_fastq.txs.Rds - 10X v2 kit demonstration 1K neurons
    • neuron_1k_v3_fastq.txs.Rds - 10X v3 kit demonstration 1K neurons
• se - SummarizedExperiment objects of bulk 3'-seq or pseudobulk 10X Chromium 3' data
• • utrome_hg38_v1 - data quantified using the Microwell-seq-derived annotation provided in scUTRquant
  • • kd6_essential_bulk_expressed.Rds - K562 6-day essential Perturb-seq screen from Replogle et al., 2022
    • rd7_essential_bulk_expressed.Rds - RPE1 7-day essential Perturb-seq screen from Replogle et al., 2022
  • utrome_mm10_v2 - data quantified using the Microwell-seq-derived annotation provided in scUTRquant
  • • hspcs_bulk.txs.rds - HSCs and MPPs from Sommerkamp et al., 2020

Data Generation

UTRome Annotations

The annotations (kallisto indices) used in data quantification were generated in the pipelines:

• gencode_vM25_pc_w500 - https://github.com/Mayrlab/txcutr-db (https://doi.org/10.5281/zenodo.8118405)
• utrome_hg38_v1 - https://github.com/Mayrlab/hcl-utrome (https://doi.org/10.5281/zenodo.8118411)
• utrome_mm10_v2 - https://github.com/Mayrlab/mca-utrome (https://doi.org/10.5281/zenodo.8118416)

Sample Sheets and Configurations

Sample sheets and configuration files for how the raw data were run in scUTRquant are available in the scUTRquant-inputs repository (https://doi.org/10.5281/zenodo.10901352).

All raw data were run in scUTRquant (https://doi.org/10.5281/zenodo.8118393), with the exception of hspcs_bulk.txs.rds which used the pipeline at https://github.com/Mayrlab/sommerkamp20 (https://doi.org/10.5281/zenodo.10892210).

Post-processing Pipelines

Downstream of scUTRquant, additional annotation, filtering, merging, and summarization was performed in the following pipelines:

• merged.txs.full_annot.Rds - https://github.com/Mayrlab/atlas-mm (https://doi.org/10.5281/zenodo.10895352)
• tsapiens.txs.full_annot.Rds - https://github.com/Mayrlab/atlas-hs (https://doi.org/10.5281/zenodo.10895337)
• (kd6|rd7)_essential_bulk_expressed.Rds - https://github.com/Mayrlab/gwps-sq (https://doi.org/10.5281/zenodo.10895730)

Downstream Analyses

Additional downstream analyses which use these objects are available in https://github.com/Mayrlab/scUTRquant-figures (https://doi.org/10.5281/zenodo.8118443).