Data for Transplanting rejuvenated blood stem cells extends lifespan of aged immunocompromised mice

Dataset

DOI

This dataset contains the raw data of the experiments described in the paper "Transplanting rejuvenated blood stem cells extends lifespan of aged immunocompromised mice" by Montserrat-Vazquez, Noelle, Matteini et al., as well as the code used to analyse the single-cell RNA sequencing (scRNA-seq) data, the raw count matrices and all the output obtained from running the code. scRNA-seq was applied on sorted Lin- Sca1+ cKit+ (LSK) cells from the bone marrow of young, aged and aged CASIN-treated C57Bl6 mice and the raw FASTQ files can be found under the GEO accession number GSE197070. The code is in an easily reproducible format, as Rmarkdown and jupyter notebooks that contain comments that describe all the steps in the analysis. To start reproducing it, download all the files, open the .Rproj file in an Rstudio session and start following the instructions in the file "LSK_scRNAseq_data_analysis.Rmd".

R, 4.0.2

Bioconductor, 3.11

Seurat, 4.0.2

python, 3.8.10

scanpy, 1.8.1

sccoda, 0.1.2.post1

R, 4.1.0

Bioconductor, 3.13

BASiCS, 2.4.0

python, 3.7.9

scanpy, 1.8.0

tradeSeq, 1.6.0

Identifier
DOI	https://doi.org/10.34810/data163
Metadata Access	https://dataverse.csuc.cat/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=doi:10.34810/data163

Provenance
Creator	Montserrat-Vazquez, Sara ; Ali, Noelle J.; Matteini, Francesca ; Lozano, Javier ; Tu, Zhaowei; Mejia-Ramirez, Eva ; Marka, Gina; Vollmer, Angelika; Soller, Karin; Sacma, Mehmet; Sakk, Vadim; Mularoni, Loris ; Mallm, Jan Philipp; Plass, Mireya ; Zheng, Yi; Geiger, Hartmut; Florian, Maria Carolina
Publisher	CORA.Repositori de Dades de Recerca
Contributor	Montserrat Vazquez, Sara; Stem Cell Aging Lab
Publication Year	2022
Funding Reference	Spanish Ministry of Science, Innovation and University RYC2018-025979-I ; Spanish Ministry of Science, Innovation and University RYC2018-024564-I ; LaCaixa Foundation LCF/PR/HR20/52400014 ; European Research Council (ERC) 101002453 ; Deutsche Forschungsgemeinschaft INST 40/662, INST 40/667, SFB1506 (HG)
Rights	CC BY 4.0; info:eu-repo/semantics/openAccess; http://creativecommons.org/licenses/by/4.0
OpenAccess	true
Contact	Montserrat Vazquez, Sara (Institut d'Investigació Biomèdica de Bellvitge)

Representation
Resource Type	Experimental data; Dataset
Format	text/tab-separated-values; image/png; application/vnd.oasis.opendocument.spreadsheet; application/gzip; text/x-r-source; text/x-r-markdown; application/x-ipynb+json; application/x-r-project; application/x-yaml; text/plain
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Version	2.0
Discipline	Life Sciences; Medicine
Spatial Coverage	Institute of Molecular Medicine, University of Ulm, Ulm, Germany; Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany; Bellvitge Institute for Biomedical Research (IDIBELL), L’Hospitalet de Llobregat, Spain